1
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Prall TM, Karl JA, Varghese JM, Baker DA, Minor NR, Raveendran M, Harris RA, Rogers J, Wiseman RW, O'Connor DH. Complete Genomic Assembly of Mauritian Cynomolgus Macaque Killer Ig-like Receptor and Natural Killer Group 2 Haplotypes. J Immunol 2024:ji2300856. [PMID: 38639635 DOI: 10.4049/jimmunol.2300856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/24/2024] [Indexed: 04/20/2024]
Abstract
Mauritian-origin cynomolgus macaques (MCMs) serve as a powerful nonhuman primate model in biomedical research due to their unique genetic homogeneity, which simplifies experimental designs. Despite their extensive use, a comprehensive understanding of crucial immune-regulating gene families, particularly killer Ig-like receptors (KIR) and NK group 2 (NKG2), has been hindered by the lack of detailed genomic reference assemblies. In this study, we employ advanced long-read sequencing techniques to completely assemble eight KIR and seven NKG2 genomic haplotypes, providing an extensive insight into the structural and allelic diversity of these immunoregulatory gene clusters. Leveraging these genomic resources, we prototype a strategy for genotyping KIR and NKG2 using short-read, whole-exome capture data, illustrating the potential for cost-effective multilocus genotyping at colony scale. These results mark a significant enhancement for biomedical research in MCMs and underscore the feasibility of broad-scale genetic investigations.
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Affiliation(s)
- Trent M Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Joshua M Varghese
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Nicholas R Minor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jeffery Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI
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2
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Wang Q, Clark KM, Tiwari R, Raju N, Tharp GK, Rogers J, Harris RA, Raveendran M, Bosinger SE, Burdo TH, Silvestri G, Shan L. The CARD8 inflammasome dictates HIV/SIV pathogenesis and disease progression. Cell 2024; 187:1223-1237.e16. [PMID: 38428396 PMCID: PMC10919936 DOI: 10.1016/j.cell.2024.01.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/16/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
While CD4+ T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this depletion remain incompletely understood, with most cell death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause CD4+ depletion and AIDS despite high-level viremia. Here, we report that the CARD8 inflammasome is activated immediately after HIV entry by the viral protease encapsulated in incoming virions. Sensing of HIV protease activity by CARD8 leads to rapid pyroptosis of quiescent cells without productive infection, while T cell activation abolishes CARD8 function and increases permissiveness to infection. In humanized mice reconstituted with CARD8-deficient cells, CD4+ depletion is delayed despite high viremia. Finally, we discovered loss-of-function mutations in CARD8 from "natural hosts," which may explain the peculiarly non-pathogenic nature of these infections. Our study suggests that CARD8 drives CD4+ T cell depletion during pathogenic HIV/SIV infections.
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Affiliation(s)
- Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kolin M Clark
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ritudhwaj Tiwari
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nagarajan Raju
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven E Bosinger
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Tricia H Burdo
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Guido Silvestri
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
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3
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Patel H, Harris RA, Qian JH, Oezguen N, Watson A, Szigeti RG, Cho S, Ruan W, Britto S, Opekun A, Preidis G, Kellermayer R. Genetic Variation Between Small Bowel and Colon-Predominant Crohn Disease. Cell Mol Gastroenterol Hepatol 2024:S2352-345X(24)00038-9. [PMID: 38369131 DOI: 10.1016/j.jcmgh.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Affiliation(s)
- Halee Patel
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - R Alan Harris
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justin H Qian
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Ashleigh Watson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Reka G Szigeti
- Clinical Pathology and Genomic Medicine, Methodist Hospital, Weill Cornell Medical College, Houston, Texas
| | - Stanley Cho
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Wenly Ruan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Savini Britto
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Antone Opekun
- Department of Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Geoffrey Preidis
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Richard Kellermayer
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas; USDA Children's Nutrition and Research Center, Houston, Texas.
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4
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Tan L, Cao Y, Yan J, Mao K, Liu L, Wang X, Ye W, Harris RA, Zhang H. TiO 2 nanorod arrays@PDA/Ag with biomimetic polydopamine as binary mediators for duplex SERS detection of illegal food dyes. Anal Chim Acta 2024; 1287:342047. [PMID: 38182363 DOI: 10.1016/j.aca.2023.342047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/11/2023] [Accepted: 11/18/2023] [Indexed: 01/07/2024]
Abstract
Based on TiO2 nanorod arrays@PDA/Ag (TNRs@PDA/Ag), a better surface-enhanced Raman scattering (SERS) sensor with effective enrichment and enhancement was investigated for duplex SERS detection of illicit food dyes. Biomimetic PDA functions as binary mediators by utilizing the structural characteristics of polydopamine (PDA), which include the conjugated structure and abundant hydrophilic groups. One PDA functioned as an electron transfer mediator to enhance the efficiency of electron transfer, and the other as an enrichment mediator to effectively enrich rhodamine B (RhB) and crystal violet (CV) through hydrogen bonding, π-π stacking, and electrostatic interactions. Individual and duplex detection of illicit food dyes (RhB and CV) was performed using TNRs@PDA/Ag to estimate SERS applications. Their linear equations and limits of detection of 1 nM for RhB and 5 nM for CV were derived. Individual and duplex food colour detection was successfully accomplished even in genuine chili meal with good results. The bifunctional TNRs@PDA/Ag-based highly sensitive and duplex SERS dye detection will have enormous potential for food safety monitoring.
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Affiliation(s)
- Lin Tan
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Special Functional Materials and Structural Design (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Yanqiang Cao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Special Functional Materials and Structural Design (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Juanjuan Yan
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Special Functional Materials and Structural Design (Ministry of Education), Lanzhou University, Lanzhou 730000, China
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Li Liu
- Center for Inspection of Gansu Drug Administration (Center for Vaccine Inspection of Gansu), Lanzhou 730030, China
| | - Xiaolong Wang
- State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Weichun Ye
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Special Functional Materials and Structural Design (Ministry of Education), Lanzhou University, Lanzhou 730000, China.
| | - R A Harris
- Department of Physics, University of the Free State, Bloemfontein 9301, South Africa.
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China.
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5
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Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Karakikes I, Wang KC, Umapathy G, Roos C, Boubli JP, Siepel A, Kundaje A, Paten B, Lindblad-Toh K, Rogers J, Marques Bonet T, Farh KKH. Identification of constrained sequence elements across 239 primate genomes. Nature 2024; 625:735-742. [PMID: 38030727 PMCID: PMC10808062 DOI: 10.1038/s41586-023-06798-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
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Affiliation(s)
- Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Jacob C Ulirsch
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Sabrina Rashid
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Mohamed Ameen
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Anthony J Cox
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Arvind Kumar
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Matthew J Christmas
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Hiram Clawson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | - Mareike C Janiak
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Martin Kuhlwilm
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna, Austria
| | - Joseph D Orkin
- Département d'Anthropologie, Université de Montréal, Montréal, Quebec, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Lidia Agueda
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Julie Blanc
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Brazil
- Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia - RedeFauna, Manaus, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica-ComFauna, Iquitos, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Brazil
- Department of Biology, Trinity University, San Antonio, TX, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX, USA
| | | | - Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Phoenix, AZ, USA
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
- School of Geosciences, Edinburgh, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, Göttingen, Germany
| | - Ivo Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kevin C Wang
- Department of Cancer Biology, Stanford University, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
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6
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Harris RA, Raveendran M, Warren W, LaDeana HW, Tomlinson C, Graves-Lindsay T, Green RE, Schmidt JK, Colwell JC, Makulec AT, Cole SA, Cheeseman IH, Ross CN, Capuano S, Eichler EE, Levine JE, Rogers J. Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets ( Callithrix jacchus). Genes (Basel) 2023; 14:2185. [PMID: 38137007 PMCID: PMC10742769 DOI: 10.3390/genes14122185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
The common marmoset (Callithrix jacchus) is one of the most widely used nonhuman primate models of human disease. Owing to limitations in sequencing technology, early genome assemblies of this species using short-read sequencing suffered from gaps. In addition, the genetic diversity of the species has not yet been adequately explored. Using long-read genome sequencing and expert annotation, we generated a high-quality genome resource creating a 2.898 Gb marmoset genome in which most of the euchromatin portion is assembled contiguously (contig N50 = 25.23 Mbp, scaffold N50 = 98.2 Mbp). We then performed whole genome sequencing on 84 marmosets sampling the genetic diversity from several marmoset research centers. We identified a total of 19.1 million single nucleotide variants (SNVs), of which 11.9 million can be reliably mapped to orthologous locations in the human genome. We also observed 2.8 million small insertion/deletion variants. This dataset includes an average of 5.4 million SNVs per marmoset individual and a total of 74,088 missense variants in protein-coding genes. Of the 4956 variants orthologous to human ClinVar SNVs (present in the same annotated gene and with the same functional consequence in marmoset and human), 27 have a clinical significance of pathogenic and/or likely pathogenic. This important marmoset genomic resource will help guide genetic analyses of natural variation, the discovery of spontaneous functional variation relevant to human disease models, and the development of genetically engineered marmoset disease models.
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Affiliation(s)
- R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
| | - Wes Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;
| | - Hillier W. LaDeana
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98104, USA; (H.W.L.); (E.E.E.)
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA; (C.T.); (T.G.-L.)
| | - Tina Graves-Lindsay
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA; (C.T.); (T.G.-L.)
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA;
| | - Jenna K. Schmidt
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Julia C. Colwell
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Allison T. Makulec
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Shelley A. Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Ian H. Cheeseman
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Corinna N. Ross
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.A.C.); (I.H.C.); (C.N.R.)
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98104, USA; (H.W.L.); (E.E.E.)
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jon E. Levine
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA; (J.K.S.); (J.C.C.); (A.T.M.); (S.C.III); (J.E.L.)
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; (R.A.H.); (M.R.)
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7
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Harris RA, Bush AH, Eagar TN, Qian J, Greenwood MP, Opekun AR, Baldassano R, Guthery SL, Noe JD, Otley A, Rosh JR, Kugathasan S, Kellermayer R. Exome Sequencing Implicates DGKZ , ESRRA , and GXYLT1 for Modulating Granuloma Formation in Crohn Disease. J Pediatr Gastroenterol Nutr 2023; 77:354-357. [PMID: 37347142 PMCID: PMC10528115 DOI: 10.1097/mpg.0000000000003873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/23/2023]
Abstract
Non-caseating granulomas may indicate a more aggressive phenotype of Crohn disease (CD). Genetic associations of granulomatous CD (GCD) may help elucidate disease pathogenesis. Whole-exome sequencing was performed on peripheral blood-derived DNA from 17 pediatric patients with GCD and 19 with non-GCD (NGCD), and from an independent validation cohort of 44 GCD and 19 NGCD cases. PLINK (a tool set for whole-genome association and population-based linkage analyses) analysis was used to identify single nucleotide polymorphisms (SNPs) differentiating between groups, and subgroup allele frequencies were also compared to a public genomic database (gnomAD). The Combined Annotation Dependent Depletion scoring tool was used to predict deleteriousness of SNPs. Human leukocyte antigen (HLA) haplotype findings were compared to a control group (n = 8496). PLINK-based analysis between GCD and NGCD groups did not find consistently significant hits. gnomAD control comparisons, however, showed consistent subgroup associations with DGKZ , ESRRA , and GXYLT1 , genes that have been implicated in mammalian granulomatous inflammation. Our findings may guide future research and precision medicine.
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Affiliation(s)
- R. Alan Harris
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
- contributed equally
| | - Allyson H Bush
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
- contributed equally
| | - Todd N Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Justin Qian
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
| | - Michael P Greenwood
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Antone R Opekun
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology and Nutrition, University of Pennsylvania, Children’s Hospital of Philadelphia, PA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah and Intermountain Primary Children’s Hospital, Salt Lake City, UT
| | - Joshua D Noe
- Department of Pediatrics, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI
| | - Anthony Otley
- IWK Health/Dalhousie University, Halifax, Nova Scotia, Canada
| | - Joel R. Rosh
- Goryeb Children’s Hospital/Atlantic Children’s Health, Morristown, NJ
| | - Subra Kugathasan
- Departments of Pediatrics and Human Genetics at Emory University School of Medicine, Atlanta, GA
| | - Richard Kellermayer
- Department of Pediatrics, Section of Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX
- Children’s Nutrition and Research Center, Houston, TX
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8
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Harris RA, McAllister JM, Strauss JF. Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome. Int J Mol Sci 2023; 24:10611. [PMID: 37445796 DOI: 10.3390/ijms241310611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by hyperandrogenemia of ovarian thecal cell origin, resulting in anovulation/oligo-ovulation and infertility. Our previous studies established that ovarian theca cells isolated and propagated from ovaries of normal ovulatory women and women with PCOS have distinctive molecular and cellular signatures that underlie the increased androgen biosynthesis in PCOS. To evaluate differences between gene expression in single-cells from passaged cultures of theca cells from ovaries of normal ovulatory women and women with PCOS, we performed single-cell RNA sequencing (scRNA-seq). Results from these studies revealed differentially expressed pathways and genes involved in the acquisition of cholesterol, the precursor of steroid hormones, and steroidogenesis. Bulk RNA-seq and microarray studies confirmed the theca cell differential gene expression profiles. The expression profiles appear to be directed largely by increased levels or activity of the transcription factors SREBF1, which regulates genes involved in cholesterol acquisition (LDLR, LIPA, NPC1, CYP11A1, FDX1, and FDXR), and GATA6, which regulates expression of genes encoding steroidogenic enzymes (CYP17A1) in concert with other differentially expressed transcription factors (SP1, NR5A2). This study provides insights into the molecular mechanisms underlying the hyperandrogenemia associated with PCOS and highlights potential targets for molecular diagnosis and therapeutic intervention.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jan M McAllister
- Department of Pathology, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergman J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science 2023; 380:eabn8153. [PMID: 37262153 DOI: 10.1126/science.abn8153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/27/2022] [Indexed: 06/03/2023]
Abstract
Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.
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Affiliation(s)
- Erik F Sørensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Claudia Fontsere
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Lakshmi Seshadri
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Christina M Bergey
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew S Burrell
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Jane E Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Kenneth L Chiou
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | | | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Marie-Claude Gingras
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Kyle K-H Farh
- Artificial Intelligence Lab, Illumina Inc., San Diego, CA 92122, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluis Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri i Reixac 4, 08028 Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, Edifici ICTA-ICP, cl Columnes s/n, 08193 Cerdanyola del Valles, Barcelona, Spain
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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10
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Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, Schraiber JG, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, Valsecchi J, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin AD, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Rogers J, Farh KKH, Marques Bonet T. A global catalog of whole-genome diversity from 233 primate species. Science 2023; 380:906-913. [PMID: 37262161 DOI: 10.1126/science.abn7829] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/06/2023] [Indexed: 06/03/2023]
Abstract
The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
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Affiliation(s)
- Lukas F K Kuderna
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria
| | - Joseph D Orkin
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
| | | | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA
| | | | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
| | - João Valsecchi
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, Peru
| | - Malu Messias
- Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil
| | | | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar
| | - Clifford J Jolly
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA
| | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA
| | | | - Sree Kanthaswamy
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA
| | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Esther Lizano
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Tomas Marques Bonet
- IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain
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11
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich ASD, Fiziev PP, Kuderna LFK, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rousselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath JE, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Bataillon T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O'Donnell-Luria A, Rehm HL, Xu J, Rogers J, Marques-Bonet T, Farh KKH. The landscape of tolerated genetic variation in humans and primates. Science 2023; 380:eabn8153. [PMID: 37262156 DOI: 10.1126/science.abn8197] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/22/2023] [Indexed: 06/03/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Joshua G Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | | | - Petko P Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Balick
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mareike C Janiak
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Joseph D Orkin
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d'anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
| | | | - Julie E Horvath
- North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabrício Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah, Salt Lake City, UT 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para, Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia - RedeFauna, Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica - ComFauna, Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação "Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia, Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N F da Silva
- Instituto Nacional de Pesquisas da Amazonia, Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso, Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University, San Antonio, TX 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Clément J Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christian Abee
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joe H Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University, New Haven, CT 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | - Fekadu Shiferaw
- Guinea Worm Eradication Program, The Carter Center Ethiopia, PoB 16316, Addis Ababa 1000, Ethiopia
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Women's Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China
| | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald - Insei Riems, Germany
| | - Minh D Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature, 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore 168582, Republic of Singapore
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
- Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, 08010 Barcelona, Spain
| | - Amanda Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
- Department of Medical Genetics, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | | | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Jean P Boubli
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shamil Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, MA, 02142, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA, 94404, USA
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12
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Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, Storer JM, Kuhlwilm M, Fontsere C, Seshadri L, Bergey CM, Burrell AS, Bergmann J, Phillips-Conroy JE, Shiferaw F, Chiou KL, Chuma IS, Keyyu JD, Fischer J, Gingras MC, Salvi S, Doddapaneni H, Schierup MH, Batzer MA, Jolly CJ, Knauf S, Zinner D, Farh KKH, Marques-Bonet T, Munch K, Roos C, Rogers J. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. bioRxiv 2023:2023.05.02.539112. [PMID: 37205419 PMCID: PMC10187195 DOI: 10.1101/2023.05.02.539112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes. One-Sentence Summary Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.
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Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, Yang Y, Dietrich A, Fiziev P, Kuderna L, Sundaram L, Wu Y, Adhikari A, Field Y, Chen C, Batzoglou S, Aguet F, Lemire G, Reimers R, Balick D, Janiak MC, Kuhlwilm M, Orkin JD, Manu S, Valenzuela A, Bergman J, Rouselle M, Silva FE, Agueda L, Blanc J, Gut M, de Vries D, Goodhead I, Harris RA, Raveendran M, Jensen A, Chuma IS, Horvath J, Hvilsom C, Juan D, Frandsen P, de Melo FR, Bertuol F, Byrne H, Sampaio I, Farias I, do Amaral JV, Messias M, da Silva MNF, Trivedi M, Rossi R, Hrbek T, Andriaholinirina N, Rabarivola CJ, Zaramody A, Jolly CJ, Phillips-Conroy J, Wilkerson G, Abee C, Simmons JH, Fernandez-Duque E, Kanthaswamy S, Shiferaw F, Wu D, Zhou L, Shao Y, Zhang G, Keyyu JD, Knauf S, Le MD, Lizano E, Merker S, Navarro A, Batallion T, Nadler T, Khor CC, Lee J, Tan P, Lim WK, Kitchener AC, Zinner D, Gut I, Melin A, Guschanski K, Schierup MH, Beck RMD, Umapathy G, Roos C, Boubli JP, Lek M, Sunyaev S, O’Donnell A, Rehm H, Xu J, Rogers J, Marques-Bonet T, Kai-How Farh K. The landscape of tolerated genetic variation in humans and primates. bioRxiv 2023:2023.05.01.538953. [PMID: 37205491 PMCID: PMC10187174 DOI: 10.1101/2023.05.01.538953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence Summary Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.
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Affiliation(s)
- Hong Gao
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Tobias Hamp
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeffrey Ede
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Joshua G. Schraiber
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Jeremy McRae
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
| | - Yanshen Yang
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Anastasia Dietrich
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Petko Fiziev
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Lukas Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Laksshman Sundaram
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yibing Wu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Aashish Adhikari
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Yair Field
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Chen Chen
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Serafim Batzoglou
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Francois Aguet
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
| | - Gabrielle Lemire
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Rebecca Reimers
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Daniel Balick
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Martin Kuhlwilm
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna; Djerassiplatz 1, 1030, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna; 1030, Vienna, Austria
| | - Joseph D. Orkin
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Département d’anthropologie, Université de Montréal; 3150 Jean-Brillant, Montréal, QC, H3T 1N8, Canada
| | - Shivakumara Manu
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Alejandro Valenzuela
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Aarhus University; Aarhus, 8000, Denmark
| | | | - Felipe Ennes Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development; Estrada da Bexiga 2584, Tefé, Amazonas, CEP 69553-225, Brazil
- Faculty of Sciences, Department of Organismal Biology, Unit of Evolutionary Biology and Ecology, Université Libre de Bruxelles (ULB); Avenue Franklin D. Roosevelt 50, 1050, Brussels, Belgium
| | - Lidia Agueda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Ian Goodhead
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
| | | | - Julie Horvath
- North Carolina Museum of Natural Sciences; Raleigh, North Carolina, 27601, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University; Durham, North Carolina , 27707, USA
- Department of Biological Sciences, North Carolina State University; Raleigh, North Carolina , 27695, USA
- Department of Evolutionary Anthropology, Duke University; Durham, North Carolina , 27708, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | | | - Fabricio Bertuol
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - Hazel Byrne
- Department of Anthropology, University of Utah; Salt Lake City, Utah, 84102, USA
| | - Iracilda Sampaio
- Universidade Federal do Para; Guamá, Belém - PA, 66075-110, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
| | - João Valsecchi do Amaral
- Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development; Tefé, Amazonas, 69553-225, Brazil
- Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna; Manaus, Amazonas, 69080-900, Brazil
- Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna; Iquitos, Loreto, 16001, Peru
| | - Mariluce Messias
- Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
- PPGREN - Programa de Pós-Graduação “Conservação e Uso dos Recursos Naturais and BIONORTE - Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Rede BIONORTE, Universidade Federal de Rondonia; Porto Velho, Rondônia, 78900-000, Brazil
| | - Maria N. F. da Silva
- Instituto Nacional de Pesquisas da Amazonia; Petrópolis, Manaus - AM, 69067-375, Brazil
| | - Mihir Trivedi
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Rogerio Rossi
- Universidade Federal do Mato Grosso; Boa Esperança, Cuiabá - MT, 78060-900, Brazil
| | - Tomas Hrbek
- Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL); Manaus, Amazonas, 69080-900, Brazil
- Department of Biology, Trinity University; San Antonio, Texas, 78212, USA
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga; Mahajanga, 401, Madagascar
| | | | | | - Gregory Wilkerson
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | | | - Joe H. Simmons
- Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center; Houston, Texas, 77030, USA
| | - Eduardo Fernandez-Duque
- Yale University; New Haven, Connecticut, 06520, USA
- Universidad Nacional de Formosa, Argentina Fundacion ECO, Formosa, Argentina
| | | | | | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Long Zhou
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen; Copenhagen, DK-2100, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Liangzhu Laboratory, Zhejiang University Medical Center; 1369 West Wenyi Road, Hangzhou, 311121, China
- Women’s Hospital, School of Medicine, Zhejiang University; 1 Xueshi Road, Shangcheng District, Hangzhou, 310006, China
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Head Office; P.O.Box 661, Arusha, Tanzania
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health; 17493 Greifswald - Isle of Riems, Germany
| | - Minh D. Le
- Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University; Hanoi, 100000, Vietnam
| | - Esther Lizano
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart; 70191 Stuttgart, Germany
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Av. Doctor Aiguader, N88, Barcelona, 08003, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation; C. Wellington 30, Barcelona, 08005, Spain
| | - Thomas Batallion
- Bioinformatics Research Centre, Aarhus University; Aarhus, 8000, Denmark
| | - Tilo Nadler
- Cuc Phuong Commune; Nho Quan District, Ninh Binh Province, 430000, Vietnam
| | - Chiea Chuen Khor
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
| | - Jessica Lee
- Mandai Nature; 80 Mandai Lake Road, Singapore 729826, Republic of Singapore
| | - Patrick Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine (PRISM); Singapore 168582, Republic of Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School; Singapore 168582, Republic of Singapore
- SingHealth Duke-NUS Genomic Medicine Centre; Singapore 168582, Republic of Singapore
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland; Chambers Street, Edinburgh, EH1 1JF, UK
- School of Geosciences, University of Edinburgh; Drummond Street, Edinburgh, EH8 9XP, UK
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research; 37077 Göttingen, Germany
- Department of Primate Cognition, Georg-August-Universität Göttingen; 37077 Göttingen, Germany
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Amanda Melin
- Leibniz Science Campus Primate Cognition; 37077 Göttingen, Germany
- Department of Anthropology & Archaeology and Department of Medical Genetics
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University; SE-75236, Uppsala, Sweden
- Alberta Children’s Hospital Research Institute; University of Calgary; 2500 University Dr NW T2N 1N4, Calgary, Alberta, Canada
| | | | - Robin M. D. Beck
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Govindhaswamy Umapathy
- Academy of Scientific and Innovative Research (AcSIR); Ghaziabad, 201002, India
- Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology; Hyderabad, 500007, India
| | - Christian Roos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH8 9XP, UK
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford; Salford, M5 4WT, United Kingdom
| | - Monkol Lek
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research; Kellnerweg 4, 37077 Göttingen, Germany
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Genetics, Yale School of Medicine; New Haven, Connecticut, 06520, USA
| | - Anne O’Donnell
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Heidi Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Boston, Massachusetts, 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - Jinbo Xu
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
- Toyota Technological Institute at Chicago; Chicago, Illinois, 60637, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, Texas, 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC); PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST); Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Pg. Luís Companys 23, Barcelona, 08010, Spain
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc.; Foster City, California, 94404, USA
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Alan Harris R, Archer KJ, Goodarzi MO, York TP, Rogers J, Dunaif A, McAllister JM, Strauss JF. Loci on chromosome 12q13.2 encompassing ERBB3, PA2G4 and RAB5B are associated with polycystic ovary syndrome. Gene 2023; 852:147062. [PMID: 36423778 PMCID: PMC9811427 DOI: 10.1016/j.gene.2022.147062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Polycystic ovary syndrome (PCOS) is characterized by hyperandrogenemia of ovarian theca cell origin. We report significant association of androgen production with 15 single nucleotide variants (SNVs) identified by exome sequencing of theca cells from women with PCOS and normal ovulatory women. Ten SNVs are located within a 150 kbp region on 12q13.2 which encompasses loci identified in PCOS genome-wide association studies (GWAS) and contains PCOS candidate genes ERBB3 and RAB5B. The region also contains PA2G4 which encodes a transcriptional corepressor of androgen receptor and androgen receptor-regulated genes. PA2G4 has not previously been recognized as related to PCOS in published GWAS studies. Two of the SNVs are predicted to have functional consequences (ERBB3 missense SNV, PA2G4 promoter SNV). PA2G4 interacts with the ERBB3 cytoplasmic domain containing the missense variant, suggesting a potential signaling pathway disruption that could lead to the PCOS ovarian phenotype. Single cell RNA sequencing of theca cells showed significantly less expression of PA2G4 after forskolin treatment in PCOS cells compared to normal cells (padj = 3.82E-30) and in cells heterozygous for the PA2G4 promoter SNV compared to those without the SNV (padj = 2.16E-11). This is consistent with a functional effect of the PA2G4 promoter SNV. No individual SNV was significantly associated with PCOS in an independent family cohort, but a haplotype with minor alleles of three SNVs was found preferentially in women with PCOS. These findings suggest a functional role for 12q13.2 variants in PCOS and implicate variants in ERBB3 and PA2G4 in the pathophysiology of PCOS.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA.
| | - Kellie J Archer
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH 43210 USA.
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA.
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298 USA; Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA.
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA.
| | - Andrea Dunaif
- Division of Endocrinology, Diabetes and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA.
| | - Jan M McAllister
- Department of Pathology, Penn State Hershey College of Medicine, Hershey, PA 17033 USA.
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298 USA; Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA.
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15
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Paulin LF, Raveendran M, Harris RA, Rogers J, von Haeseler A, Sedlazeck FJ. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics 2023; 24:23. [PMID: 36670361 PMCID: PMC9854228 DOI: 10.1186/s12859-022-05046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Recent population studies are ever growing in number of samples to investigate the diversity of a population or species. These studies reveal new polymorphism that lead to important insights into the mechanisms of evolution, but are also important for the interpretation of these variations. Nevertheless, while the full catalog of variations across entire species remains unknown, we can predict which regions harbor additional not yet detected variations and investigate their properties, thereby enhancing the analysis for potentially missed variants. RESULTS To achieve this we developed SVhound ( https://github.com/lfpaulin/SVhound ), which based on a population level SVs dataset can predict regions that harbor unseen SV alleles. We tested SVhound using subsets of the 1000 genomes project data and showed that its correlation (average correlation of 2800 tests r = 0.7136) is high to the full data set. Next, we utilized SVhound to investigate potentially missed or understudied regions across 1KGP and CCDG. Lastly we also apply SVhound on a small and novel SV call set for rhesus macaque (Macaca mulatta) and discuss the impact and choice of parameters for SVhound. CONCLUSIONS SVhound is a unique method to identify potential regions that harbor hidden diversity in model and non model organisms and can also be potentially used to ensure high quality of SV call sets.
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Affiliation(s)
- Luis F Paulin
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
- Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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16
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Wang RJ, Peña-Garcia Y, Bibby MG, Raveendran M, Harris RA, Jansen HT, Robbins CT, Rogers J, Kelley JL, Hahn MW. Examining the effects of hibernation on germline mutation rates in grizzly bears. Genome Biol Evol 2022; 14:6731088. [PMID: 36173788 PMCID: PMC9596377 DOI: 10.1093/gbe/evac148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
A male mutation bias is observed across vertebrates, and, where data are available, this bias is accompanied by increased per-generation mutation rates with parental age. While continuing mitotic cell division in the male germline post puberty has been proposed as the major cellular mechanism underlying both patterns, little direct evidence for this role has been found. Understanding the evolution of the per-generation mutation rate among species requires that we identify the molecular mechanisms that change between species. Here, we study the per-generation mutation rate in an extended pedigree of the brown (grizzly) bear, Ursus arctos horribilis. Brown bears hibernate for one-third of the year, a period during which spermatogenesis slows or stops altogether. The reduction of spermatogenesis is predicted to lessen the male mutation bias and to lower the per-generation mutation rate in this species. However, using whole-genome sequencing, we find that both male bias and per-generation mutation rates are highly similar to that expected for a non-hibernating species. We also carry out a phylogenetic comparison of substitution rates along the lineage leading to brown bear and panda (a non-hibernating species) and find no slowing of the substitution rate in the hibernator. Our results contribute to accumulating evidence that suggests that male germline cell division is not the major determinant of mutation rates and mutation biases. The results also provide a quantitative basis for improved estimates of the timing of carnivore evolution.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Madeleine G Bibby
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.,School of the Environment, Washington State University, Pullman, WA 99164, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA; E-mail:
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.,Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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17
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Wang RJ, Raveendran M, Harris RA, Murphy WJ, Lyons LA, Rogers J, Hahn MW. De novo Mutations in Domestic Cat are Consistent with an Effect of Reproductive Longevity on Both the Rate and Spectrum of Mutations. Mol Biol Evol 2022; 39:msac147. [PMID: 35771663 PMCID: PMC9290555 DOI: 10.1093/molbev/msac147] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The mutation rate is a fundamental evolutionary parameter with direct and appreciable effects on the health and function of individuals. Here, we examine this important parameter in the domestic cat, a beloved companion animal as well as a valuable biomedical model. We estimate a mutation rate of 0.86 × 10-8 per bp per generation for the domestic cat (at an average parental age of 3.8 years). We find evidence for a significant paternal age effect, with more mutations transmitted by older sires. Our analyses suggest that the cat and the human have accrued similar numbers of mutations in the germline before reaching sexual maturity. The per-generation mutation rate in the cat is 28% lower than what has been observed in humans, but is consistent with the shorter generation time in the cat. Using a model of reproductive longevity, which takes into account differences in the reproductive age and time to sexual maturity, we are able to explain much of the difference in per-generation rates between species. We further apply our reproductive longevity model in a novel analysis of mutation spectra and find that the spectrum for the cat resembles the human mutation spectrum at a younger age of reproduction. Together, these results implicate changes in life-history as a driver of mutation rate evolution between species. As the first direct observation of the paternal age effect outside of rodents and primates, our results also suggest a phenomenon that may be universal among mammals.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, USA
- Department of Computer Science, Indiana University, Bloomington, IN, USA
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18
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Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny D, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience 2022; 11:6594469. [PMID: 35640223 PMCID: PMC9155146 DOI: 10.1093/gigascience/giac039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/03/2021] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was generated in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and greater continuity. FINDINGS Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gb, similar to the 2.50-Gb length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity, with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein-coding genes and 10,459 noncoding genes are annotated in BCM_Maur_2.0 compared to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where ∼17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0, in which the number of unresolved bases is reduced to 3.00%. CONCLUSIONS Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dustin T Lyfoung
- Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Trent M Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA,Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA,Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - Jeffrey Rogers
- Correspondence address. Jeffrey Rogers, Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Tel.: 713-798-7783; E-mail:
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19
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Ozirmak Lermi N, Gray SB, Bowen CM, Reyes-Uribe L, Dray BK, Deng N, Harris RA, Raveendran M, Benavides F, Hodo CL, Taggart MW, Colbert Maresso K, Sinha KM, Rogers J, Vilar E. Comparative molecular genomic analyses of a spontaneous rhesus macaque model of mismatch repair-deficient colorectal cancer. PLoS Genet 2022; 18:e1010163. [PMID: 35446842 PMCID: PMC9064097 DOI: 10.1371/journal.pgen.1010163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 05/03/2022] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
Colorectal cancer (CRC) remains the third most common cancer in the US with 15% of cases displaying Microsatellite Instability (MSI) secondary to Lynch Syndrome (LS) or somatic hypermethylation of the MLH1 promoter. A cohort of rhesus macaques from our institution developed spontaneous mismatch repair deficient (MMRd) CRC with a notable fraction harboring a pathogenic germline mutation in MLH1 (c.1029C
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Affiliation(s)
- Nejla Ozirmak Lermi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Stanton B. Gray
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles M. Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Laura Reyes-Uribe
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Beth K. Dray
- Charles River Laboratories, Ashland, Ohio, United States of America
| | - Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Carolyn L. Hodo
- Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Melissa W. Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen Colbert Maresso
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Krishna M. Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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20
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Gunter C, Harris RA, Kovacs-Balint Z, Raveendran M, Michopoulos V, Bachevalier J, Raper J, Sanchez MM, Rogers J. Heritability of social behavioral phenotypes and preliminary associations with autism spectrum disorder risk genes in rhesus macaques: A whole exome sequencing study. Autism Res 2022; 15:447-463. [PMID: 35092647 PMCID: PMC8930433 DOI: 10.1002/aur.2675] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/15/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
Abstract
Nonhuman primates and especially rhesus macaques (Macaca mulatta) have been indispensable animal models for studies of various aspects of neurobiology, developmental psychology, and other aspects of neuroscience. While remarkable progress has been made in our understanding of influences on atypical human social behavior, such as that observed in autism spectrum disorders (ASD), many significant questions remain. Improved understanding of the relationships among variation in specific genes and variation in expressed social behavior in a nonhuman primate would benefit efforts to investigate risk factors, developmental mechanisms, and potential therapies for behavioral disorders including ASD. To study genetic influences on key aspects of social behavior and interactions-individual competence and/or motivation for specific aspects of social behavior-we quantified individual variation in social interactions among juvenile rhesus macaques using both a standard macaque ethogram and a macaque-relevant modification of the human Social Responsiveness Scale. Our analyses demonstrate that various aspects of juvenile social behavior exhibit significant genetic heritability, with estimated quantitative genetic effects similar to that described for ASD in human children. We also performed exome sequencing and analyzed variants in 143 genes previously suggested to influence risk for human ASD. We find preliminary evidence for genetic association between specific variants and both individual behaviors and multi-behavioral factor scores. To our knowledge, this is the first demonstration that spontaneous social behaviors performed by free-ranging juvenile rhesus macaques display significant genetic heritability and then to use exome sequencing data to examine potential macaque genetic associations in genes associated with human ASD.
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Affiliation(s)
- Chris Gunter
- Marcus Autism Center, Children’s Healthcare of Atlanta, Atlanta, GA, USA,Departments of Pediatrics Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Vasiliki Michopoulos
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA,Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Jocelyne Bachevalier
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA,Department of Psychology, Emory University, Atlanta, GA, USA
| | - Jessica Raper
- Departments of Pediatrics Human Genetics, Emory University School of Medicine, Atlanta, GA, USA,Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Mar M. Sanchez
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA,Department of Psychiatry & Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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21
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Smith LM, Ladner JT, Hodara VL, Parodi LM, Harris RA, Callery JE, Lai Z, Zou Y, Raveedran M, Rogers J, Giavedoni LD. Multiplexed Simian Immunodeficiency Virus-Specific Paired RNA-Guided Cas9 Nickases Inactivate Proviral DNA. J Virol 2021; 95:e0088221. [PMID: 34549979 PMCID: PMC8577357 DOI: 10.1128/jvi.00882-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
Human and simian immunodeficiency virus (HIV and SIV) infections establish lifelong reservoirs of cells harboring an integrated proviral genome. Genome editing CRISPR-associated Cas9 nucleases, combined with SIV-specific guiding RNA (gRNA) molecules, inactivate integrated provirus DNA in vitro and in animal models. We generated RNA-guided Cas9 nucleases (RGNu) and nickases (RGNi) targeting conserved SIV regions with no homology in the human or rhesus macaque genome. Assays in cells cotransfected with SIV provirus and plasmids coding for RGNus identified SIV long terminal repeat (LTR), trans-activation response (TAR) element, and ribosome slip site (RSS) regions as the most effective at virus suppression; RGNi targeting these regions inhibited virus production significantly. Multiplex plasmids that coexpressed these three RGNu (Nu3), or six (three pairs) RGNi (Ni6), were more efficient at virus suppression than any combination of individual RGNu and RGNi plasmids. Both Nu3 and Ni6 plasmids were tested in lymphoid cells chronically infected with SIVmac239, and whole-genome sequencing was used to determine on- and off-target mutations. Treatment with these all-in-one plasmids resulted in similar levels of mutations of viral sequences from the cellular genome; Nu3 induced indels at the 3 SIV-specific sites, whereas for Ni6 indels were present at the LTR and TAR sites. Levels of off-target effects detected by two different algorithms were indistinguishable from background mutations. In summary, we demonstrate that Cas9 nickase in association with gRNA pairs can specifically eliminate parts of the integrated provirus DNA; also, we show that careful design of an all-in-one plasmid coding for 3 gRNAs and Cas9 nuclease inhibits SIV production with undetectable off-target mutations, making these tools a desirable prospect for moving into animal studies. IMPORTANCE Our approach to HIV cure, utilizing the translatable SIV/rhesus macaque model system, aims at provirus inactivation and its removal with the least possible off-target side effects. We developed single molecules that delivered either three truncated SIV-specific gRNAs along with Cas9 nuclease or three pairs of SIV-specific gRNAs (six individual gRNAs) along with Cas9 nickase to enhance efficacy of on-target mutagenesis. Whole-genome sequencing demonstrated effective SIV sequence mutation and inactivation and the absence of demonstrable off-target mutations. These results open the possibility to employ Cas9 variants that introduce single-strand DNA breaks to eliminate integrated proviral DNA.
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Affiliation(s)
- Lisa M. Smith
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UT Health San Antonio, San Antonio, Texas, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Vida L. Hodara
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Laura M. Parodi
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jessica E. Callery
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Zhao Lai
- Department of Molecular Medicine, UT Health San Antonio, San Antonio, Texas, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas, USA
| | - Yi Zou
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, Texas, USA
| | - Muthuswamy Raveedran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Luis D. Giavedoni
- Host-Pathogen Interactions Program and Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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22
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Zhou T, Patel K, Harris RA, Seghers V, Walsh SM, Rodriguez R, Kellermayer R, Wu H. SULT1A1 and SULT1A2 Associated Extensive Prolapse-Type Inflammatory Polyposis in Crohn's Colitis. Ann Clin Lab Sci 2021; 51:868-874. [PMID: 34921041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mucosal prolapse syndrome most commonly involves the rectum and presents as solitary rectal ulcer syndrome and proctitis cystica profunda. Symptoms and endoscopic appearances are nonspecific. Histologically, mucosal prolapse is characterized by fibromuscular obliteration of the lamina propria, and displacement of crypts into submucosa and muscularis mucosae. Mucosal prolapse presenting as polyposis is rare and has only been reported involving the rectosigmoid colon. In this report, we describe a case of mucosal prolapse syndrome presenting as diffuse polyposis and colitis cystica profunda involving the hepatic, splenic flexures and descending colon in a teenage boy suffering from refractory fibrostenosing Crohn's disease. This patient was found to have possibly deleterious homozygous single nucleotide polymorphisms in both SULT1A1 and SULT1A2 genes within a unique polygenic variation of altered cell adhesion.
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Affiliation(s)
- Ting Zhou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Kalyani Patel
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
- Department of Pathology & Laboratory Medicine, Texas Children's Hospital, Houston, TX, USA
| | - R Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Victor Seghers
- Department of Radiology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Seema M Walsh
- Section of Gastroenterology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Ruben Rodriguez
- Department of Surgery, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - Richard Kellermayer
- Section of Gastroenterology, Department of Pediatrics, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
- USDA ARS Children's Nutrition and Research Center, Houston, TX, USA
| | - Hao Wu
- Department of Pathology, Yale New Haven Hospital and Yale College of Medicine, New Haven, CT, USA
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23
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Thomas GWC, Wang RJ, Nguyen J, Alan Harris R, Raveendran M, Rogers J, Hahn MW. Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques. Mol Biol Evol 2021; 38:1460-1471. [PMID: 33226085 PMCID: PMC8042740 DOI: 10.1093/molbev/msaa303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations play a key role in the development of disease in an individual and the evolution of traits within species. Recent work in humans and other primates has clarified the origins and patterns of single-nucleotide variants, showing that most arise in the father’s germline during spermatogenesis. It remains unknown whether larger mutations, such as deletions and duplications of hundreds or thousands of nucleotides, follow similar patterns. Such mutations lead to copy-number variation (CNV) within and between species, and can have profound effects by deleting or duplicating genes. Here, we analyze patterns of CNV mutations in 32 rhesus macaque individuals from 14 parent–offspring trios. We find the rate of CNV mutations per generation is low (less than one per genome) and we observe no correlation between parental age and the number of CNVs that are passed on to offspring. We also examine segregating CNVs within the rhesus macaque sample and compare them to a similar data set from humans, finding that both species have far more segregating deletions than duplications. We contrast this with long-term patterns of gene copy-number evolution between 17 mammals, where the proportion of deletions that become fixed along the macaque lineage is much smaller than the proportion of segregating deletions. These results suggest purifying selection acting on deletions, such that the majority of them are removed from the population over time. Rhesus macaques are an important biomedical model organism, so these results will aid in our understanding of this species and the disease models it supports.
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Affiliation(s)
- Gregg W C Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Richard J Wang
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jelena Nguyen
- Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, USA.,Department of Computer Science, Indiana University, Bloomington, IN, USA
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24
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Alan Harris R, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KK, Rogers J, Marques‐Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol 2021; 83:e23255. [PMID: 33792947 PMCID: PMC8250314 DOI: 10.1002/ajp.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
- Department of Medical GeneticsUniversity of CalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryAlbertaCanada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Mareike C. Janiak
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Frank Marrone
- Department of ChemistryNew York UniversityNew YorkUSA
| | - Hasinala Ramangason
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Julie E. Horvath
- Genomics & Microbiology Research LaboratoryNorth Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth CarolinaUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGöettingenGermany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of GeosciencesUniversity of EdinburghEdinburghUK
| | - Chiea Chuen Khor
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- Singapore Eye Research InstituteSingapore National Eye CentreSingapore
| | - Weng Khong Lim
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- SingHealth Duke‐NUS Genomic Medicine CentreSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary ServicesWildlife Reserves SingaporeSingapore
| | - Patrick Tan
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Govindhaswamy Umapathy
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh Binh ProvinceVietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGoettingenGermany
- Leibniz Science Campus Primate CognitionGoettingenGermany
- Department of Primate CognitionGeorg‐August‐University, GoettingenGermany
| | - Minh D. Le
- Department of Environmental Ecology, University of Science and Central Institute for Natural Resources and Environmental StudiesVietnam National UniversityHanoiVietnam
| | - Sivakumara Manu
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Erich D. Jarvis
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Laboratory of Neurogenetics of LanguageThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Olivier Fedrigo
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming Natural History Museum of Zoology, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- China National GenebankBGI‐ShenzhenShenzhenChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Tomas Marques‐Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | | | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
- New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
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25
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Guevara EE, Webster TH, Lawler RR, Bradley BJ, Greene LK, Ranaivonasy J, Ratsirarson J, Harris RA, Liu Y, Murali S, Raveendran M, Hughes DST, Muzny DM, Yoder AD, Worley KC, Rogers J. Comparative genomic analysis of sifakas ( Propithecus) reveals selection for folivory and high heterozygosity despite endangered status. Sci Adv 2021; 7:7/17/eabd2274. [PMID: 33893095 PMCID: PMC8064638 DOI: 10.1126/sciadv.abd2274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/08/2021] [Indexed: 05/12/2023]
Abstract
Sifakas (genus Propithecus) are critically endangered, large-bodied diurnal lemurs that eat leaf-based diets and show corresponding anatomical and microbial adaptations to folivory. We report on the genome assembly of Coquerel's sifaka (P. coquereli) and the resequenced genomes of Verreaux's (P. verreauxi), the golden-crowned (P. tattersalli), and the diademed (P. diadema) sifakas. We find high heterozygosity in all sifakas compared with other primates and endangered mammals. Demographic reconstructions nevertheless suggest declines in effective population size beginning before human arrival on Madagascar. Comparative genomic analyses indicate pervasive accelerated evolution in the ancestral sifaka lineage affecting genes in several complementary pathways relevant to folivory, including nutrient absorption and xenobiotic and fatty acid metabolism. Sifakas show convergent evolution at the level of the pathway, gene family, gene, and amino acid substitution with other folivores. Although sifakas have relatively generalized diets, the physiological challenges of habitual folivory likely led to strong selection.
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Affiliation(s)
- Elaine E Guevara
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Timothy H Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA
| | - Richard R Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, VA 22807, USA
| | - Brenda J Bradley
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA
| | - Lydia K Greene
- Duke Lemur Center, Duke University, Durham, NC 27705, USA
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Jeannin Ranaivonasy
- Département Agroécologie, Biodiversité et Changement Climatique, ESSA, University of Antananarivo, Antananarivo, Madagascar
| | - Joelisoa Ratsirarson
- Département Agroécologie, Biodiversité et Changement Climatique, ESSA, University of Antananarivo, Antananarivo, Madagascar
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shwetha Murali
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Donna M Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Kim C Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
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26
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Harris RA, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KKH, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. bioRxiv 2021:2021.02.03.429540. [PMID: 33564767 PMCID: PMC7872355 DOI: 10.1101/2021.02.03.429540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Canada
- Department of Medical Genetics, University of Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford, United Kingdom
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Frank Marrone
- Department of Chemistry, New York University, United States
| | | | - Julie E. Horvath
- Genomics & Microbiology Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göettingen, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Govindhaswamy Umapathy
- CSIR-Laboratory for the Conservation of Endangered Species, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz Science Campus Primate Cognition, Goettingen, Germany
- Department of Primate Cognition, Georg-August-University, Goettingen, Germany
| | - Steig E. Johnson
- Department of Anthropology and Archaeology, University of Calgary, Canada
| | - Erich D. Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Tomas Marques-Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - James P. Higham
- Department of Anthropology, New York University, United States
- New York Consortium in Evolutionary Primatology, New York, United States
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27
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Petty LE, Phillippi-Falkenstein K, Kubisch HM, Raveendran M, Harris RA, Vallender EJ, Huff CD, Bohm RP, Rogers J, Below JE. Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta). Mol Ecol Resour 2021; 21:1333-1346. [PMID: 33386679 PMCID: PMC8247968 DOI: 10.1111/1755-0998.13317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/30/2022]
Abstract
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide data have improved our ability to determine kinship and reconstruct pedigrees in humans. However, methods for reconstructing complex pedigree structures and estimating distant relatedness (beyond third‐degree) have not been widely applied to other species. We sequenced the genomes of 150 male rhesus macaques from the Tulane National Primate Research Center colony to estimate pairwise relatedness, reconstruct closely related pedigrees, estimate more distant relationships and augment colony records. Methods for determining relatedness developed for human genetic data were applied and evaluated in the analysis of nonhuman primates, including identity‐by‐descent‐based methods for pedigree reconstruction and shared segment‐based inference of more distant relatedness. We compared the genotype‐based pedigrees and estimated relationships to available colony pedigree records and found high concordance (95.5% agreement) between expected and identified relationships for close relatives. In addition, we detected distant relationships not captured in colony records, including some as distant as twelfth‐degree. Furthermore, while deep sequence coverage is preferable, we show that this approach can also provide valuable information when only low‐coverage (5×) sequence data is available. Our findings demonstrate the value of these methods for determination of relatedness in various animal populations, with diverse applications to conservation biology, evolutionary and ecological research and biomedical studies.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - H Michael Kubisch
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J Vallender
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA.,Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rudolf P Bohm
- Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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28
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Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science 2021; 370:370/6523/eabc6617. [PMID: 33335035 DOI: 10.1126/science.abc6617] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022]
Abstract
The rhesus macaque (Macaca mulatta) is the most widely studied nonhuman primate (NHP) in biomedical research. We present an updated reference genome assembly (Mmul_10, contig N50 = 46 Mbp) that increases the sequence contiguity 120-fold and annotate it using 6.5 million full-length transcripts, thus improving our understanding of gene content, isoform diversity, and repeat organization. With the improved assembly of segmental duplications, we discovered new lineage-specific genes and expanded gene families that are potentially informative in studies of evolution and disease susceptibility. Whole-genome sequencing (WGS) data from 853 rhesus macaques identified 85.7 million single-nucleotide variants (SNVs) and 10.5 million indel variants, including potentially damaging variants in genes associated with human autism and developmental delay, providing a framework for developing noninvasive NHP models of human disease.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA. .,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65211, USA.,Institute of Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marina Haukness
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Shwetha C Murali
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jason Fernandes
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jessica M Storer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.,Institue for Systems Biology, Seattle, WA 98109, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Yafei Mao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - David Gordon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth DeVogelaere
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark Diekhans
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jerilyn A Walker
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Peter A Audano
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Ludovica Mercuri
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | | | | | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Betsy Ferguson
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR 97006, USA
| | | | - Louis Picker
- Oregon National Primate Research Center and Vaccine and Gene Therapy Institute, Oregon Health Sciences University, Beaverton, OR 97006, USA
| | - Ned H Kalin
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53719, USA
| | - Douglas Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jon Levine
- Department of Neuroscience, University of Wisconsin, Madison, WI 53175, USA.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA
| | - David H Abbott
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.,Department of Obstetrics and Gynecology, Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
| | - Stanton B Gray
- The University of Texas MD Anderson Cancer Center, Michale E. Keeling Center for Comparative Medicine and Research, Bastrop, TX 78602, USA
| | - Mar M Sanchez
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30329, USA
| | | | - Joseph W Kemnitz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53171, USA.,Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.,Department of Ophthalmology and Vision Science, School of Medicine, University of California-Davis, Davis, CA 95817, USA
| | | | - Erin L Kinnally
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - John P Capitanio
- California National Primate Research Center, Davis, CA 95616, USA.,Department of Psychology, University of California, Davis, CA 95616, USA
| | - J H Pate Skene
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael Platt
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute and Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mario Ventura
- Department of Biology, University of Bari 'Aldo Moro', 70125 Bari, Italy
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Benedict Paten
- Computational Genomics Laboratory, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Grantham EK, Warden AS, McCarthy GS, DaCosta A, Mason S, Blednov Y, Mayfield RD, Harris RA. Role of toll-like receptor 7 (TLR7) in voluntary alcohol consumption. Brain Behav Immun 2020; 89:423-432. [PMID: 32726684 PMCID: PMC7572874 DOI: 10.1016/j.bbi.2020.07.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/09/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022] Open
Abstract
Overactivation of neuroimmune signaling has been linked to excessive ethanol consumption. Toll-like receptors (TLRs) are a major component of innate immune signaling and initiate anti- and pro-inflammatory responses via intracellular signal transduction cascades. TLR7 is upregulated in post-mortem brain tissue from humans with alcohol use disorder (AUD) and animals with prior exposure to ethanol. Despite this evidence, the role of TLR7 in the regulation of voluntary ethanol consumption has not been studied. We test the hypothesis that TLR7 activation regulates voluntary ethanol drinking behavior by administering a TLR7 agonist (R848) during an intermittent access drinking procedure in mice. Acute activation of TLR7 reduced ethanol intake, preference, and total fluid intake due, at least in part, to an acute sickness response. However, chronic pre-treatment with R848 resulted in tolerance to the adverse effects of the drug and a subsequent increase in ethanol consumption. To determine the molecular machinery that mediates these behavioral changes, we evaluated gene expression after acute and chronic TLR7 activation. We found that acute TLR7 activation produces brain region specific changes in expression of immune pathway genes, whereas chronic TLR7 activation causes downregulation of TLRs and blunted cytokine induction, suggesting molecular tolerance. Our results demonstrate a novel role for TLR7 signaling in regulating voluntary ethanol consumption. Taken together, our findings suggest TLR7 may be a viable target for development of therapies to treat AUD.
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Affiliation(s)
- E K Grantham
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA.
| | - A S Warden
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - G S McCarthy
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - A DaCosta
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA
| | - S Mason
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA
| | - Y Blednov
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA
| | - R D Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
| | - R A Harris
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, 2500 Speedway, Stop 14800, Austin, TX 78712, USA; Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712, USA
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Xue C, Rustagi N, Liu X, Raveendran M, Harris RA, Venkata MG, Rogers J, Yu F. Reduced meiotic recombination in rhesus macaques and the origin of the human recombination landscape. PLoS One 2020; 15:e0236285. [PMID: 32841250 PMCID: PMC7447010 DOI: 10.1371/journal.pone.0236285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Characterizing meiotic recombination rates across the genomes of nonhuman primates is important for understanding the genetics of primate populations, performing genetic analyses of phenotypic variation and reconstructing the evolution of human recombination. Rhesus macaques (Macaca mulatta) are the most widely used nonhuman primates in biomedical research. We constructed a high-resolution genetic map of the rhesus genome based on whole genome sequence data from Indian-origin rhesus macaques. The genetic markers used were approximately 18 million SNPs, with marker density 6.93 per kb across the autosomes. We report that the genome-wide recombination rate in rhesus macaques is significantly lower than rates observed in apes or humans, while the distribution of recombination across the macaque genome is more uniform. These observations provide new comparative information regarding the evolution of recombination in primates.
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Affiliation(s)
- Cheng Xue
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (FY); (JR); (CX)
| | - Navin Rustagi
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiaoming Liu
- USF Genomics & College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (FY); (JR); (CX)
| | - Fuli Yu
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (FY); (JR); (CX)
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Wang RJ, Thomas GWC, Raveendran M, Harris RA, Doddapaneni H, Muzny DM, Capitanio JP, Radivojac P, Rogers J, Hahn MW. Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability. Genome Res 2020; 30:826-834. [PMID: 32461224 PMCID: PMC7370888 DOI: 10.1101/gr.255174.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Mutation is the ultimate source of all genetic novelty and the cause of heritable genetic disorders. Mutational burden has been linked to complex disease, including neurodevelopmental disorders such as schizophrenia and autism. The rate of mutation is a fundamental genomic parameter and direct estimates of this parameter have been enabled by accurate comparisons of whole-genome sequences between parents and offspring. Studies in humans have revealed that the paternal age at conception explains most of the variation in mutation rate: Each additional year of paternal age in humans leads to approximately 1.5 additional inherited mutations. Here, we present an estimate of the de novo mutation rate in the rhesus macaque (Macaca mulatta) using whole-genome sequence data from 32 individuals in four large pedigrees. We estimated an average mutation rate of 0.58 × 10−8 per base pair per generation (at an average parental age of 7.5 yr), much lower than found in direct estimates from great apes. As in humans, older macaque fathers transmit more mutations to their offspring, increasing the per generation mutation rate by 4.27 × 10−10 per base pair per year. We found that the rate of mutation accumulation after puberty is similar between macaques and humans, but that a smaller number of mutations accumulate before puberty in macaques. We additionally investigated the role of paternal age on offspring sociability, a proxy for normal neurodevelopment, by studying 203 male macaques in large social groups.
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Affiliation(s)
- Richard J Wang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - John P Capitanio
- California National Primate Research Center, University of California-Davis, Davis, California 95616, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA.,Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.,Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
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Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 2020; 16:e1008742. [PMID: 32392208 PMCID: PMC7241854 DOI: 10.1371/journal.pgen.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 05/21/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.
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Affiliation(s)
- Marina Brasó-Vives
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Inna S. Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Diego A. Hartasánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Farré
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Marcos Fernandez-Callejo
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Douglas L. Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Belen Lorente-Galdos
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
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Harris RA, Raveendran M, Worley KC, Rogers J. Unusual sequence characteristics of human chromosome 19 are conserved across 11 nonhuman primates. BMC Evol Biol 2020; 20:33. [PMID: 32106815 PMCID: PMC7045612 DOI: 10.1186/s12862-020-1595-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/11/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Human chromosome 19 has many unique characteristics including gene density more than double the genome-wide average and 20 large tandemly clustered gene families. It also has the highest GC content of any chromosome, especially outside gene clusters. The high GC content and concomitant high content of hypermutable CpG sites raises the possibility chromosome 19 exhibits higher levels of nucleotide diversity both within and between species, and may possess greater variation in DNA methylation that regulates gene expression. RESULTS We examined GC and CpG content of chromosome 19 orthologs across representatives of the primate order. In all 12 primate species with suitable genome assemblies, chromosome 19 orthologs have the highest GC content of any chromosome. CpG dinucleotides and CpG islands are also more prevalent in chromosome 19 orthologs than other chromosomes. GC and CpG content are generally higher outside the gene clusters. Intra-species variation based on SNPs in human common dbSNP, rhesus, crab eating macaque, baboon and marmoset datasets is most prevalent on chromosome 19 and its orthologs. Inter-species comparisons based on phyloP conservation show accelerated nucleotide evolution for chromosome 19 promoter flanking and enhancer regions. These same regulatory regions show the highest CpG density of any chromosome suggesting they possess considerable methylome regulatory potential. CONCLUSIONS The pattern of high GC and CpG content in chromosome 19 orthologs, particularly outside gene clusters, is present from human to mouse lemur representing 74 million years of primate evolution. Much CpG variation exists both within and between primate species with a portion of this variation occurring in regulatory regions.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA.
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Mail Stop: BCM226, Houston, TX, 77030, USA
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Caskey JR, Wiseman RW, Karl JA, Baker DA, Lee T, Maddox RJ, Raveendran M, Harris RA, Hu J, Muzny DM, Rogers J, O'Connor DH. MHC genotyping from rhesus macaque exome sequences. Immunogenetics 2019; 71:531-544. [PMID: 31321455 PMCID: PMC6790296 DOI: 10.1007/s00251-019-01125-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/02/2019] [Indexed: 02/03/2023]
Abstract
Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.
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Affiliation(s)
- John R Caskey
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Taylor Lee
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Robert J Maddox
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | | | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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Antony KM, Kazembe PN, Pace RM, Levison J, Mlotha-Namarika J, Phiri H, Chiudzu G, Harris RA, Aagaard J, Twyman N, Ramin SM, Raine SP, Belfort MA, Aagaard KM. Population-Based Estimation of Dental Caries and Periodontal Disease Rates of Gravid and Recently Postpartum Women in Lilongwe, Malawi. AJP Rep 2019; 9:e268-e274. [PMID: 31435488 PMCID: PMC6702028 DOI: 10.1055/s-0039-1695003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 06/15/2019] [Indexed: 11/29/2022] Open
Abstract
Objectives The objective of this study was to determine the rate of dental caries and periodontal disease among gravid and recently postpartum women at five delivery centers within and surrounding Lilongwe, Malawi. Study Design We partnered with obstetric specialists, community health workers, and dentists to perform dental history interviews and dental examinations during the study period from December 2012 to May 2014. Dental examinations were performed according to World Health Organization standards to assess periodontal and oral health status. Results Among the 387 gravid and recently postpartum women, the rate of dental caries was 69.3% and the rate of composite dental disease (caries and periodontal disease) was 76.7%. The majority (69.5%) of women examined had a decayed-missing-filled (DMF) index greater than or equal to one; the average DMF Index was 2.48. The majority of women had never seen a dentist (62.8%). However, most did perform oral hygiene, two or more times per day (90.2%); most women reported brushing with toothpaste (88.1%). Conclusion When assessing this population for dental caries and periodontal disease, the rate of dental disease was high. Therefore, this may be an ideal setting to test for impactful interventions aimed at reducing caries and periodontal disease.
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Affiliation(s)
- Kathleen M Antony
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas.,Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, One Baylor College of Medicine, Houston, Texas.,Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Peter N Kazembe
- Department of Pediatrics, Baylor College of Medicine Children's Clinical Center of Excellence, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Ryan M Pace
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | - Judy Levison
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | | | - Henry Phiri
- Department of Obstetrics and Gynecology, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Grace Chiudzu
- Department of Obstetrics and Gynecology, Kamuzu Central Hospital, Lilongwe, Malawi
| | - R Alan Harris
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | | | - Nicholas Twyman
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | - Susan M Ramin
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas.,Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, One Baylor College of Medicine, Houston, Texas.,American Board of Obstetrics and Gynecology, 2915 Vine Street, Dallas, Texas
| | - Susan P Raine
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas
| | - Michael A Belfort
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas.,Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, One Baylor College of Medicine, Houston, Texas
| | - Kjersti M Aagaard
- Department of Obstetrics and Gynecology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas.,Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, One Baylor College of Medicine, Houston, Texas
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Hao G, Pollock NK, Harris RA, Gutin B, Su S, Wang X. Associations between muscle mass, physical activity and dietary behaviour in adolescents. Pediatr Obes 2019; 14:e12471. [PMID: 30280506 DOI: 10.1111/ijpo.12471] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 07/12/2018] [Accepted: 07/30/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND AND OBJECTIVES Investigations in older individuals suggest that adequate nutrition and physical activity are particularly important to skeletal muscle health; however, data in adolescents are scant and equivocal. The objective was to determine the associations among diet, physical activity and skeletal muscle mass in adolescents. METHODS We assessed diet with four to seven 24-h recalls and physical activity by accelerometry in 640 adolescents. Using total body measures of fat-free soft tissue mass and fat mass assessed by dual-energy X-ray absorptiometry, the skeletal muscle mass index (SMMI) was derived by adjusting fat-free soft tissue mass for fat mass in addition to height. RESULTS Skeletal muscle mass index (SMMI) was negatively associated with consumption of sugar-sweetened beverages (standardized beta coefficient [β] = -0.10, P = 0.001) and saturated fats (β = -0.28, P < 0.001). SMMI was positively associated with physical activity (moderate + vigorous) (β = 0.20, P < 0.001). In further analysis, we observed a significant interaction between physical activity and sugar-sweetened beverage intake on SMMI (P = 0.002). CONCLUSION Our study in adolescence suggests that physical activity and consumption of both sugar-sweetened beverages and saturated fats are associated with skeletal muscle mass. More importantly, our findings suggest that sugar-sweetened beverage intake may attenuate the beneficial effects of physical activity on skeletal muscle mass.
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Affiliation(s)
- G Hao
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - N K Pollock
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - R A Harris
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - B Gutin
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - S Su
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - X Wang
- Georgia Prevention Institute, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
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Moshiri A, Chen R, Kim S, Harris RA, Li Y, Raveendran M, Davis S, Liang Q, Pomerantz O, Wang J, Garzel L, Cameron A, Yiu G, Stout JT, Huang Y, Murphy CJ, Roberts J, Gopalakrishna KN, Boyd K, Artemyev NO, Rogers J, Thomasy SM. A nonhuman primate model of inherited retinal disease. J Clin Invest 2019; 129:863-874. [PMID: 30667376 PMCID: PMC6355306 DOI: 10.1172/jci123980] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/15/2018] [Indexed: 12/30/2022] Open
Abstract
Inherited retinal degenerations are a common cause of untreatable blindness worldwide, with retinitis pigmentosa and cone dystrophy affecting approximately 1 in 3500 and 1 in 10,000 individuals, respectively. A major limitation to the development of effective therapies is the lack of availability of animal models that fully replicate the human condition. Particularly for cone disorders, rodent, canine, and feline models with no true macula have substantive limitations. By contrast, the cone-rich macula of a nonhuman primate (NHP) closely mirrors that of the human retina. Consequently, well-defined NHP models of heritable retinal diseases, particularly cone disorders that are predictive of human conditions, are necessary to more efficiently advance new therapies for patients. We have identified 4 related NHPs at the California National Primate Research Center with visual impairment and findings from clinical ophthalmic examination, advanced retinal imaging, and electrophysiology consistent with achromatopsia. Genetic sequencing confirmed a homozygous R565Q missense mutation in the catalytic domain of PDE6C, a cone-specific phototransduction enzyme associated with achromatopsia in humans. Biochemical studies demonstrate that the mutant mRNA is translated into a stable protein that displays normal cellular localization but is unable to hydrolyze cyclic GMP (cGMP). This NHP model of a cone disorder will not only serve as a therapeutic testing ground for achromatopsia gene replacement, but also for optimization of gene editing in the macula and of cone cell replacement in general.
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Affiliation(s)
- Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, UC Davis, Sacramento, California, USA
| | - Rui Chen
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, and.,Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Soohyun Kim
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, and
| | - Yumei Li
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, and
| | | | - Sarah Davis
- California National Primate Research Center, Davis, California, USA
| | - Qingnan Liang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ori Pomerantz
- California National Primate Research Center, Davis, California, USA
| | - Jun Wang
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, and
| | - Laura Garzel
- California National Primate Research Center, Davis, California, USA
| | - Ashley Cameron
- California National Primate Research Center, Davis, California, USA
| | - Glenn Yiu
- Department of Ophthalmology & Vision Science, School of Medicine, UC Davis, Sacramento, California, USA
| | - J Timothy Stout
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, Texas, USA
| | | | - Christopher J Murphy
- Department of Ophthalmology & Vision Science, School of Medicine, UC Davis, Sacramento, California, USA.,Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA.,EyeKor Inc., Madison, Wisconsin, USA
| | - Jeffrey Roberts
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA.,California National Primate Research Center, Davis, California, USA
| | | | - Kimberly Boyd
- Department of Molecular Physiology and Biophysics, and
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, and.,Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, and
| | - Sara M Thomasy
- Department of Ophthalmology & Vision Science, School of Medicine, UC Davis, Sacramento, California, USA.,Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
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Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC. The comparative genomics and complex population history of Papio baboons. Sci Adv 2019; 5:eaau6947. [PMID: 30854422 PMCID: PMC6401983 DOI: 10.1126/sciadv.aau6947] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/06/2018] [Indexed: 05/26/2023]
Abstract
Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.
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Affiliation(s)
- Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Kalle Leppälä
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Georgios Athanasiadis
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Jade Cheng
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, CF Møllers Alle 8, DK-8000 Aarhus, Denmark
| | - Jerilyn A. Walker
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Miriam K. Konkel
- Department of Genetics and Biochemistry, 105 Collings Street, Clemson University, Clemson, SC 29634, USA
| | - Vallmer Jordan
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Cody J. Steely
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Thomas O. Beckstrom
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Christina Bergey
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
- Departments of Anthropology and Biology, Pennsylvania State University, 514 Carpenter Building, University Park, PA 16802, USA
| | - Andrew Burrell
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
| | - Dominik Schrempf
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Maximillian Kothe
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Gisela H. Kopp
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
- Department of Biology, University of Konstanz, Universitätsstr. 10, 78467 Konstanz, Germany
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Am Obstberg 1, 78315 Radolfzell, Germany
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha Murali
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Fergal J. Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Laura Cox
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military Drive, San Antonio, TX 78227, USA
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, 475 Vine Street, Winston-Salem, NC 27101, USA
| | - James Else
- Department of Pathology and Laboratory Medicine and Yerkes Primate Research Center, 954 Gatewood Road, Emory University, Atlanta, GA 30322, USA
| | - Todd Disotell
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jane Phillips-Conroy
- Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
- Department of Anthropology, Washington University, McMillan Hall, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
- Howard Hughes Medical Institute, University of Washington, 3720 15th Avenue NE, S413C, Box 355065, Seattle, WA 98195-5065, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader, 88. 08003, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institut Catala de Paleontologia Miquel Crusafont, Universitat Autonoma de Barcelona, c/de les Columnes, s/n. Campus de la UAB. 08193–Cerdanyola del Vallès, Barcelona, Spain
| | - Carolin Kosiol
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Veterinärplatz 11210 Vienna, Austria
- Centre for Biological Diversity, School of Biology, University of St. Andrews, Dyers Brae House, Greenside Place, St Andrews, Fife, KY16 9TH, UK
| | - Mark A. Batzer
- Department of Biological Sciences, 202 Life Sciences Building, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Matthew W. Hahn
- Department of Biology and Department of Computer Science, Indiana University, 1001 E. 3rd Street, Bloomington, IN 47405, USA
| | - Jenny Tung
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Duke Population Research Institute, Duke University, Box 90989, Durham, NC 27708, USA
- Institute of Primate Research, P.O. Box 24481, Nairobi, Kenya
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany
| | - Clifford J. Jolly
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Kim C. Worley
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Yang T, Xu G, Newton PT, Chagin AS, Mkrtchian S, Carlström M, Zhang XM, Harris RA, Cooter M, Berger M, Maddipati KR, Akassoglou K, Terrando N. Maresin 1 attenuates neuroinflammation in a mouse model of perioperative neurocognitive disorders. Br J Anaesth 2018; 122:350-360. [PMID: 30770053 PMCID: PMC6396737 DOI: 10.1016/j.bja.2018.10.062] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/15/2022] Open
Abstract
Background Resolution of inflammation is an active and dynamic process after surgery. Maresin 1 (MaR1) is one of a growing number of specialised pro-resolving lipids biosynthesised by macrophages that regulates acute inflammation. We investigated the effects of MaR1 on postoperative neuroinflammation, macrophage activity, and cognitive function in mice. Methods Adult male C57BL/6 (n=111) and Ccr2RFP/+Cx3cr1GFP/+ (n=54) mice were treated with MaR1 before undergoing anaesthesia and orthopaedic surgery. Systemic inflammatory changes, bone healing, neuroinflammation, and cognition were assessed at different time points. MaR1 protective effects were also evaluated using bone marrow derived macrophage cultures. Results MaR1 exerted potent systemic anti-inflammatory effects without impairing fracture healing. Prophylaxis with MaR1 prevented surgery-induced glial activation and opening of the blood–brain barrier. In Ccr2RFP/+Cx3cr1GFP/+ mice, fewer infiltrating macrophages were detected in the hippocampus after surgery with MaR1 prophylaxis, which resulted in improved memory function. MaR1 treatment also reduced expression of pro-inflammatory cell surface markers and cytokines by in vitro cultured macrophages. MaR1 was detectable in the cerebrospinal fluid of older adults before and after surgery. Conclusions MaR1 exerts distinct anti-inflammatory and pro-resolving effects through regulation of macrophage infiltration, NF-κB signalling, and cytokine release after surgery. Future studies on the use of pro-resolving lipid mediators may inform novel approaches to treat neuroinflammation and postoperative neurocognitive disorders.
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Affiliation(s)
- T Yang
- Department of Physiology and Pharmacology, Stockholm, Sweden; Department of Medicine, Division of Nephrology, Durham, NC, USA
| | - G Xu
- Department of Physiology and Pharmacology, Stockholm, Sweden
| | - P T Newton
- Department of Physiology and Pharmacology, Stockholm, Sweden
| | - A S Chagin
- Department of Physiology and Pharmacology, Stockholm, Sweden; Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - S Mkrtchian
- Department of Physiology and Pharmacology, Stockholm, Sweden
| | - M Carlström
- Department of Physiology and Pharmacology, Stockholm, Sweden
| | - X-M Zhang
- Applied Immunology & Immunotherapy, Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - R A Harris
- Applied Immunology & Immunotherapy, Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - M Cooter
- Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - M Berger
- Center for Cognitive Neuroscience, Center for the Study of Aging & Human Development, Durham, NC, USA; Center for the Study of Aging & Human Development, Durham, NC, USA; Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA
| | - K R Maddipati
- Department of Pathology-Bioactive Lipids Research Program, Wayne State University, Detroit, MI, USA
| | - K Akassoglou
- Gladstone Institutes, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - N Terrando
- Department of Physiology and Pharmacology, Stockholm, Sweden; Center for Translational Pain Medicine, Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA; Department of Anesthesiology, Duke University Medical Center, Durham, NC, USA.
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40
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Erickson EK, Grantham EK, Warden AS, Harris RA. Neuroimmune signaling in alcohol use disorder. Pharmacol Biochem Behav 2018; 177:34-60. [PMID: 30590091 DOI: 10.1016/j.pbb.2018.12.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/25/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023]
Abstract
Alcohol use disorder (AUD) is a widespread disease with limited treatment options. Targeting the neuroimmune system is a new avenue for developing or repurposing effective pharmacotherapies. Alcohol modulates innate immune signaling in different cell types in the brain by altering gene expression and the molecular pathways that regulate neuroinflammation. Chronic alcohol abuse may cause an imbalance in neuroimmune function, resulting in prolonged perturbations in brain function. Likewise, manipulating the neuroimmune system may change alcohol-related behaviors. Psychiatric disorders that are comorbid with AUD, such as post-traumatic stress disorder, major depressive disorder, and other substance use disorders, may also have underlying neuroimmune mechanisms; current evidence suggests that convergent immune pathways may be involved in AUD and in these comorbid disorders. In this review, we provide an overview of major neuroimmune cell-types and pathways involved in mediating alcohol behaviors, discuss potential mechanisms of alcohol-induced neuroimmune activation, and present recent clinical evidence for candidate immune-related drugs to treat AUD.
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Affiliation(s)
- Emma K Erickson
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712-01095, USA.
| | - Emily K Grantham
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712-01095, USA
| | - Anna S Warden
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712-01095, USA
| | - R A Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712-01095, USA
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41
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Schmidtke D, Lempp C, Dubicanac M, Radespiel U, Zimmermann E, Baumgärtner W, Kästner S, Meier M, Balkema-Buschmann A, Harris RA, Raveendran M, Muzny DM, Worley KC, Rogers J. Spontaneous Spongiform Brainstem Degeneration in a Young Mouse Lemur ( Microcebus murinus) with Conspicuous Behavioral, Motor, Growth, and Ocular Pathologies. Comp Med 2018; 68:489-495. [PMID: 30486920 DOI: 10.30802/aalas-cm-18-000019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here we report a case of severe growth retardation and neurologic abnormalities in a female gray mouse lemur (Microcebus murinus), a small NHP species for which the genomic sequence recently became available. The female lemur we present here died on postnatal day 125. This lemur had impaired development of motor skills and showed severe ataxia and tremors. In addition, hearing seemed normal whereas ophthalmic examination revealed incipient bilateral cataracts, abnormal pigmentation in the lens of the left eye, and a missing optokinetic nystagmus, which indicated impaired vision. Most prominently, the lemur showed severe growth retardation. Necropsy revealed maldevelopment of the left reproductive organs and unilateral dilation of the right lateral ventricle, which was confirmed on brain MRI. Brain histology further revealed large, bilateral areas of vacuolation within the brainstem, but immunohistochemistry indicated no sign of pathologic prion protein deposition. Full genomic sequencing of the lemur revealed a probably pathologic mutation in LARGE2 of the LARGE gene family, which has been associated with congenital muscular dystrophies. However, potentially functional mutations in other genes were also present. The observed behavioral and motor signs in the presented animal might have been linked to spongiform degeneration and resulting brainstem dysfunction and progressive muscle weakness. The macroscopic developmental abnormalities and ophthalmic findings might be genetic in origin and linked to the mutation in LARGE2.
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Affiliation(s)
- Daniel Schmidtke
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany; Center for Neuroscience Systems Hannover, Hannover, Lower Saxony, Germany.
| | - Charlotte Lempp
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Marko Dubicanac
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Elke Zimmermann
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany; Center for Neuroscience Systems Hannover, Hannover, Lower Saxony, Germany
| | - Wolfgang Baumgärtner
- Center for Neuroscience Systems Hannover, Hannover, Lower Saxony, Germany; Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Sabine Kästner
- Small Animal Clinic, University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
| | - Martin Meier
- Imaging Center, Institute of Laboratory Animal Science, Hannover Medical School, Hannover, Lower Saxony, Germany
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, FriedrichLoeffler-Institute, Federal Research Institute for Animal Health, Greifswald, Mecklenburg Western Pomerania, Germany
| | - R Alan Harris
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Muthuswamy Raveendran
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jeffrey Rogers
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
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42
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Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science 2018; 361:eaar3146. [PMID: 30139913 PMCID: PMC6198826 DOI: 10.1126/science.aar3146] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/07/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in 71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes revealed sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, which is defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provided a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.
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Affiliation(s)
- Vitor Onuchic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Eugene Lurie
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Ivenise Carrero
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Piotr Pawliczek
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Ronak Y Patel
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Zhuoyi Huang
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Robert C Altshuler
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhizhuo Zhang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - R Alan Harris
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Cristian Coarfa
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
| | - Lillian Ashmore
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
| | - Jessica W Bertol
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Walid D Fakhouri
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Fuli Yu
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Manolis Kellis
- NIH Roadmap Epigenomics Project
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Aleksandar Milosavljevic
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA.
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Epigenome Center, Baylor College of Medicine, Houston, TX, USA
- NIH Roadmap Epigenomics Project
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43
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Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. Reproductive Longevity Predicts Mutation Rates in Primates. Curr Biol 2018; 28:3193-3197.e5. [PMID: 30270182 DOI: 10.1016/j.cub.2018.08.050] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10-8 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.
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Affiliation(s)
- Gregg W C Thomas
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
| | - Richard J Wang
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Arthi Puri
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Lawrence E Williams
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christian R Abee
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, 201 Dowman Drive, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University, 201 Dowman Drive, Atlanta, GA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
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44
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Palesch D, Bosinger SE, Tharp GK, Vanderford TH, Paiardini M, Chahroudi A, Johnson ZP, Kirchhoff F, Hahn BH, Norgren RB, Patel NB, Sodora DL, Dawoud RA, Stewart CB, Seepo SM, Harris RA, Liu Y, Raveendran M, Han Y, English A, Thomas GWC, Hahn MW, Pipes L, Mason CE, Muzny DM, Gibbs RA, Sauter D, Worley K, Rogers J, Silvestri G. Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host. Nature 2018; 553:77-81. [PMID: 29300007 PMCID: PMC5843367 DOI: 10.1038/nature25140] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 11/16/2017] [Indexed: 01/08/2023]
Abstract
In contrast to infections with human immunodeficiency virus (HIV) in humans and simian immunodeficiency virus (SIV) in macaques, SIV infection of a natural host, sooty mangabeys (Cercocebus atys), is non-pathogenic despite high viraemia1. Here we sequenced and assembled the genome of a captive sooty mangabey. We conducted genome-wide comparative analyses of transcript assemblies from C. atys and AIDS-susceptible species, such as humans and macaques, to identify candidates for host genetic factors that influence susceptibility. We identified several immune-related genes in the genome of C. atys that show substantial sequence divergence from macaques or humans. One of these sequence divergences, a C-terminal frameshift in the toll-like receptor-4 (TLR4) gene of C. atys, is associated with a blunted in vitro response to TLR-4 ligands. In addition, we found a major structural change in exons 3–4 of the immune-regulatory protein intercellular adhesion molecule 2 (ICAM-2); expression of this variant leads to reduced cell surface expression of ICAM-2. These data provide a resource for comparative genomic studies of HIV and/or SIV pathogenesis and may help to elucidate the mechanisms by which SIV-infected sooty mangabeys avoid AIDS.
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Affiliation(s)
- David Palesch
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Steven E Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30329, USA
| | - Gregory K Tharp
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Thomas H Vanderford
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Mirko Paiardini
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30329, USA
| | - Ann Chahroudi
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30329, USA
| | - Zachary P Johnson
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Robert B Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska, Medical Center, Omaha, Nebraska 68198, USA
| | - Nirav B Patel
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Donald L Sodora
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Reem A Dawoud
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA
| | - Caro-Beth Stewart
- Department of Biological Sciences, University at Albany-State University of New York, Albany, New York 12222, USA
| | - Sara M Seepo
- Department of Biological Sciences, University at Albany-State University of New York, Albany, New York 12222, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gregg W C Thomas
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
| | - Matthew W Hahn
- Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
| | - Lenore Pipes
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Kim Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Guido Silvestri
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30329, USA
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45
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Larsen PA, Harris RA, Liu Y, Murali SC, Campbell CR, Brown AD, Sullivan BA, Shelton J, Brown SJ, Raveendran M, Dudchenko O, Machol I, Durand NC, Shamim MS, Aiden EL, Muzny DM, Gibbs RA, Yoder AD, Rogers J, Worley KC. Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biol 2017; 15:110. [PMID: 29145861 PMCID: PMC5689209 DOI: 10.1186/s12915-017-0439-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/10/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications. Here, we present an iterative approach to hybrid de novo genome assembly that incorporates datasets stemming from multiple genomic technologies and methods. We used this approach to improve the gray mouse lemur (Microcebus murinus) genome from early draft status to a near chromosome-scale assembly. METHODS We used a combination of advanced genomic technologies to iteratively resolve conflicts and super-scaffold the M. murinus genome. RESULTS We improved the M. murinus genome assembly to a scaffold N50 of 93.32 Mb. Whole genome alignments between our primary super-scaffolds and 23 human chromosomes revealed patterns that are congruent with historical comparative cytogenetic data, thus demonstrating the accuracy of our de novo scaffolding approach and allowing assignment of scaffolds to M. murinus chromosomes. Moreover, we utilized our independent datasets to discover and characterize sequences associated with centromeres across the mouse lemur genome. Quality assessment of the final assembly found 96% of mouse lemur canonical transcripts nearly complete, comparable to other published high-quality reference genome assemblies. CONCLUSIONS We describe a new assembly of the gray mouse lemur (Microcebus murinus) genome with chromosome-scale scaffolds produced using a hybrid bioinformatic and sequencing approach. The approach is cost effective and produces superior results based on metrics of contiguity and completeness. Our results show that emerging genomic technologies can be used in combination to characterize centromeres of non-model species and to produce accurate de novo chromosome-scale genome assemblies of complex mammalian genomes.
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Affiliation(s)
- Peter A. Larsen
- Department of Biology, Duke University, Durham, NC 27708 USA
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yue Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Shwetha C. Murali
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Present address: Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | | | - Adam D. Brown
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710 USA
- Present address: Bristol Myers-Squibb, 420 W Round Grove Rd, Lewisville, TX 75067 USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710 USA
| | - Jennifer Shelton
- Kansas State University Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506 USA
- Present address: New York Genome Center, 101 Avenue of the Americas, New York, NY 10013 USA
| | - Susan J. Brown
- Kansas State University Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | | | - Olga Dudchenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 USA
- Department of Computer Science, Rice University, Houston, TX 77005 USA
| | - Ido Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 USA
- Department of Computer Science, Rice University, Houston, TX 77005 USA
| | - Neva C. Durand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 USA
- Department of Computer Science, Rice University, Houston, TX 77005 USA
| | - Muhammad S. Shamim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 USA
- Department of Computer Science, Rice University, Houston, TX 77005 USA
| | - Erez Lieberman Aiden
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 USA
- Department of Computer Science, Rice University, Houston, TX 77005 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708 USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Kim C. Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
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46
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Prall TM, Graham ME, Karl JA, Wiseman RW, Ericsen AJ, Raveendran M, Alan Harris R, Muzny DM, Gibbs RA, Rogers J, O'Connor DH. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics 2017; 69:325-339. [PMID: 28343239 DOI: 10.1007/s00251-017-0977-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/08/2017] [Indexed: 12/25/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS). We also describe a new approach to Macaque Exome Sequencing (MES) and the development of the Rhexome1.0, an adapted target capture reagent that includes macaque-specific capture probe sets. By using sequence reads generated by whole genome sequencing (WGS) and MES to inform primer design, we were able to increase the sensitivity of KIR allele discovery. We demonstrate this increased sensitivity by defining nine novel alleles within a cohort of Mauritian cynomolgus macaques (MCM), a geographically isolated population with restricted KIR genetics that was thought to be completely characterized. Finally, we describe an approach to genotyping KIRs directly from sequence reads generated using WGS/MES reads. The findings presented here expand our understanding of KIR genetics in MCM by associating new genes with all eight KIR haplotypes and demonstrating the existence of at least one KIR3DS gene associated with every haplotype.
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Affiliation(s)
- Trent M Prall
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
| | - Michael E Graham
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA.,Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Adam J Ericsen
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
| | | | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA. .,Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA.
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47
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Harris RA, Grobman ME, Allen MJ, Schachtel J, Rawson NE, Bennett B, Ledyayev J, Hopewell B, Coates JR, Reinero CR, Lever TE. Standardization of a Videofluoroscopic Swallow Study Protocol to Investigate Dysphagia in Dogs. J Vet Intern Med 2017; 31:383-393. [PMID: 28240398 PMCID: PMC5354069 DOI: 10.1111/jvim.14676] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/13/2016] [Accepted: 01/17/2017] [Indexed: 12/30/2022] Open
Abstract
Background Videofluoroscopic swallow study (VFSS) is the gold standard for diagnosis of dysphagia in veterinary medicine but lacks standardized protocols that emulate physiologic feeding practices. Age impacts swallow function in humans but has not been evaluated by VFSS in dogs. Hypothesis/Objectives To develop a protocol with custom kennels designed to allow free‐feeding of 3 optimized formulations of contrast media and diets that address limitations of current VFSS protocols. We hypothesized that dogs evaluated by a free‐feeding VFSS protocol would show differences in objective swallow metrics based on age. Animals Healthy juvenile, adult, and geriatric dogs (n = 24). Methods Prospective, experimental study. Custom kennels were developed to maintain natural feeding behaviors during VFSS. Three food consistencies (thin liquid, pureed food, and dry kibble) were formulated with either iohexol or barium to maximize palatability and voluntary prehension. Dogs were evaluated by 16 swallow metrics and compared across age groups. Results Development of a standardized VFSS protocol resulted in successful collection of swallow data in healthy dogs. No significant differences in swallow metrics were observed among age groups. Substantial variability was observed in healthy dogs when evaluated under these physiologic conditions. Features typically attributed to pathologic states, such as gastric reflux, were seen in healthy dogs. Conclusions and Clinical Importance Development of a VFSS protocol that reflects natural feeding practices may allow emulation of physiology resulting in clinical signs of dysphagia. Age did not result in significant changes in swallow metrics, but additional studies are needed, particularly in light of substantial normal variation.
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Affiliation(s)
- R A Harris
- Department of Communication Science and Disorders, University of Missouri, Columbia, MO
| | - M E Grobman
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, MO
| | - M J Allen
- Department of Otolaryngology-Head and Neck Surgery, University of Missouri School of Medicine, Columbia, MO
| | - J Schachtel
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, MO
| | | | | | | | - B Hopewell
- Department of Otolaryngology-Head and Neck Surgery, University of Missouri School of Medicine, Columbia, MO
| | - J R Coates
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, MO
| | - C R Reinero
- Department of Veterinary Medicine and Surgery, University of Missouri College of Veterinary Medicine, Columbia, MO
| | - T E Lever
- Department of Otolaryngology-Head and Neck Surgery, University of Missouri School of Medicine, Columbia, MO
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48
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Aagaard KM, Lahon A, Suter MA, Arya RP, Seferovic MD, Vogt MB, Hu M, Stossi F, Mancini MA, Harris RA, Kahr M, Eppes C, Rac M, Belfort MA, Park CS, Lacorazza D, Rico-Hesse R. Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication. Sci Rep 2017; 7:41389. [PMID: 28128342 PMCID: PMC5269613 DOI: 10.1038/srep41389] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/29/2016] [Indexed: 02/07/2023] Open
Abstract
Zika virus (ZIKV) is an emerging mosquito-borne (Aedes genus) arbovirus of the Flaviviridae family. Although ZIKV has been predominately associated with a mild or asymptomatic dengue-like disease, its appearance in the Americas has been accompanied by a multi-fold increase in reported incidence of fetal microcephaly and brain malformations. The source and mode of vertical transmission from mother to fetus is presumptively transplacental, although a causal link explaining the interval delay between maternal symptoms and observed fetal malformations following infection has been missing. In this study, we show that primary human placental trophoblasts from non-exposed donors (n = 20) can be infected by primary passage ZIKV-FLR isolate, and uniquely allowed for ZIKV viral RNA replication when compared to dengue virus (DENV). Consistent with their being permissive for ZIKV infection, primary trophoblasts expressed multiple putative ZIKV cell entry receptors, and cellular function and differentiation were preserved. These findings suggest that ZIKV-FLR strain can replicate in human placental trophoblasts without host cell destruction, thereby serving as a likely permissive reservoir and portal of fetal transmission with risk of latent microcephaly and malformations.
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Affiliation(s)
- Kjersti M. Aagaard
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular & Human Genetics at Baylor College of Medicine, Houston, TX, USA
- Department of Molecular & Cellular Biology at Baylor College of Medicine, Houston, TX, USA
- National School for Tropical Medicine at Baylor College of Medicine, Houston, TX, USA
| | - Anismrita Lahon
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Melissa A. Suter
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Ravi P. Arya
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Maxim D. Seferovic
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Megan B. Vogt
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
- Integrative Molecular and Biological Science Program, Baylor College of Medicine, Houston, TX, USA
| | - Min Hu
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Fabio Stossi
- Department of Molecular & Cellular Biology at Baylor College of Medicine, Houston, TX, USA
| | - Michael A. Mancini
- Department of Molecular & Cellular Biology at Baylor College of Medicine, Houston, TX, USA
| | - R. Alan Harris
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular & Human Genetics at Baylor College of Medicine, Houston, TX, USA
| | - Maike Kahr
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Catherine Eppes
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Martha Rac
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Michael A. Belfort
- Departments of Obstetrics & Gynecology, Division of Maternal-Fetal Medicine at Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA
| | - Chun Shik Park
- Department of Pathology & Immunology, Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA.
| | - Daniel Lacorazza
- Department of Pathology & Immunology, Baylor College of Medicine & Texas Children’s Hospital, Houston, TX, USA.
| | - Rebecca Rico-Hesse
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
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Pace RM, Harris RA, Alcott CE, Sullivan EL, Takahashi D, McCurdy CE, Comstock S, Baquero K, Blundell P, Frias AE, Kahr M, Suter M, Wesolowski S, Friedman JE, Grove KL, Aagaard KM. 124: Genomic variants associated with resistance to high fat diet induced obesity in a primate model. Am J Obstet Gynecol 2017. [DOI: 10.1016/j.ajog.2016.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Racusin DA, Pew B, Harris RA, Suter M, Delbeccaro M, Shope C, Hu M, Antony K, Aagaard K. 111: Does your placenta know you're diabetic? A study in placental gene expression. Am J Obstet Gynecol 2017. [DOI: 10.1016/j.ajog.2016.11.1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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