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Fibi-Smetana S, Inglis C, Schuster D, Eberle N, Granados-Soler JL, Liu W, Krohn S, Junghanss C, Nolte I, Taher L, Murua Escobar H. The TiHoCL panel for canine lymphoma: a feasibility study integrating functional genomics and network biology approaches for comparative oncology targeted NGS panel design. Front Vet Sci 2023; 10:1301536. [PMID: 38144469 PMCID: PMC10748409 DOI: 10.3389/fvets.2023.1301536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Targeted next-generation sequencing (NGS) enables the identification of genomic variants in cancer patients with high sensitivity at relatively low costs, and has thus opened the era to personalized human oncology. Veterinary medicine tends to adopt new technologies at a slower pace compared to human medicine due to lower funding, nonetheless it embraces technological advancements over time. Hence, it is reasonable to assume that targeted NGS will be incorporated into routine veterinary practice in the foreseeable future. Many animal diseases have well-researched human counterparts and hence, insights gained from the latter might, in principle, be harnessed to elucidate the former. Here, we present the TiHoCL targeted NGS panel as a proof of concept, exemplifying how functional genomics and network approaches can be effectively used to leverage the wealth of information available for human diseases in the development of targeted sequencing panels for veterinary medicine. Specifically, the TiHoCL targeted NGS panel is a molecular tool for characterizing and stratifying canine lymphoma (CL) patients designed based on human non-Hodgkin lymphoma (NHL) research outputs. While various single nucleotide polymorphisms (SNPs) have been associated with high risk of developing NHL, poor prognosis and resistance to treatment in NHL patients, little is known about the genetics of CL. Thus, the ~100 SNPs featured in the TiHoCL targeted NGS panel were selected using functional genomics and network approaches following a literature and database search that shielded ~500 SNPs associated with, in nearly all cases, human hematologic malignancies. The TiHoCL targeted NGS panel underwent technical validation and preliminary functional assessment by sequencing DNA samples isolated from blood of 29 lymphoma dogs using an Ion Torrent™ PGM System achieving good sequencing run metrics. Our design framework holds new possibilities for the design of similar molecular tools applied to other diseases for which limited knowledge is available and will improve drug target discovery and patient care.
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Affiliation(s)
- Silvia Fibi-Smetana
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Camila Inglis
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Daniela Schuster
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-University, Erlangen, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Nina Eberle
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - José Luis Granados-Soler
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
- UQVETS Small Animal Hospital, School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Wen Liu
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Saskia Krohn
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Christian Junghanss
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Ingo Nolte
- Small Animal Clinic, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-University, Erlangen, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, University of Rostock, Rostock, Germany
| | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, Rostock University Medical Center, University of Rostock, Rostock, Germany
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2
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Song X, Li X, Liu X, Zhang Z, Ding X, Chai Y, Li Z, Wang H, Li J, Liang H, Sun X, Yang G, Qi Z, Chen F, Shi Q, Wang E, Ru B, Lei C, Chen H, Liu W, Huang Y. Copy number variation of the ZNF679 gene in cattle and its association analysis with growth traits. Anim Biotechnol 2023; 34:4680-4686. [PMID: 37093180 DOI: 10.1080/10495398.2023.2185628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Copy number variation (CNV) is an important member of genetic structural variation that exists widely in animal genomes and is between 50 bp and several Mb in length and widely used in research's of animal genetics and breeding. ZNF679 is an important transcription factor, which has been found association with diseases in the human genome many times. This gene has also been found to be associated with cattle growth traits in previous re-sequencing studies. We tested the CNVs of the ZNF679 gene in 809 individuals from 7 Chinese cattle breeds and tested the association between the CNVs and growth traits in 552 individuals from 5 breeds. The results demonstrated the correlation the correlation between the CNVs of the ZNF679 gene and some Chinese cattle (QC cattle and XN cattle) growth traits. To sum up, this study indicated that ZNF679-CNVs can be used as a candidate gene for molecular genetic marker-assisted selection breeding for cattle growth traits to contribute to the development of genetic improvement of Chinese cattle.
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Affiliation(s)
- Xingya Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xinmiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yanan Chai
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Hongli Wang
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan, People's Republic of China
| | - Jungang Li
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan, People's Republic of China
| | - Huifeng Liang
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan, People's Republic of China
| | - Xiaoyan Sun
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan, People's Republic of China
| | - Guojie Yang
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan, People's Republic of China
| | - Zengfang Qi
- Jiaxian Animal Husbandry Bureau, Jiaxian Henan, People's Republic of China
| | - Fuying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi, Xinjiang, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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3
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Igoshin AV, Deniskova TE, Yurchenko AA, Yudin NS, Dotsev AV, Selionova MI, Zinovieva NA, Larkin DM. Copy number variants in genomes of local sheep breeds from Russia. Anim Genet 2021; 53:119-132. [PMID: 34904242 DOI: 10.1111/age.13163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2021] [Indexed: 01/21/2023]
Abstract
Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.
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Affiliation(s)
- A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - T E Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - M I Selionova
- Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, Moscow, 127550, Russia
| | - N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - D M Larkin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Royal Veterinary College, University of London, London, NW1 0TU, UK
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4
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Zhang S, Liu W, Liu X, Du X, Zhang K, Zhang Y, Song Y, Zi Y, Qiu Q, Lenstra JA, Liu J. Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing. Mol Biol Evol 2021; 38:3676-3680. [PMID: 33944937 PMCID: PMC8382902 DOI: 10.1093/molbev/msab134] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72 and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 372,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity, and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.
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Affiliation(s)
- Shangzhe Zhang
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Wenyu Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Xinfeng Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Ke Zhang
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Yang Zhang
- The Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Yongwu Song
- Animal Disease Prevention and Control Center of Gangcha County, Haibei Tibetan Autonomous Prefecture, China
| | - Yunnan Zi
- Animal Husbandry Workstation of Xiahe County, Gannan Tibetan Autonomous Prefecture, China
| | - Qiang Qiu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianquan Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
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5
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Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. Genes (Basel) 2021; 12:genes12060847. [PMID: 34070911 PMCID: PMC8228171 DOI: 10.3390/genes12060847] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 12/27/2022] Open
Abstract
The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named "Tasha" initially published in 2005. Derived from a Sanger whole genome shotgun sequencing approach coupled with limited clone-based sequencing, the initial assembly and subsequent updates have served as the predominant resource for canine genetics for 15 years. While the initial assembly produced a good-quality draft, as with all assemblies produced at the time, it contained gaps, assembly errors and missing sequences, particularly in GC-rich regions, which are found at many promoters and in the first exons of protein-coding genes. Here, we present Dog10K_Boxer_Tasha_1.0, an improved chromosome-level highly contiguous genome assembly of Tasha created with long-read technologies that increases sequence contiguity >100-fold, closes >23,000 gaps of the CanFam3.1 reference assembly and improves gene annotation by identifying >1200 new protein-coding transcripts. The assembly and annotation are available at NCBI under the accession GCF_000002285.5.
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6
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Serres-Armero A, Davis BW, Povolotskaya IS, Morcillo-Suarez C, Plassais J, Juan D, Ostrander EA, Marques-Bonet T. Copy number variation underlies complex phenotypes in domestic dog breeds and other canids. Genome Res 2021; 31:762-774. [PMID: 33863806 PMCID: PMC8092016 DOI: 10.1101/gr.266049.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 02/26/2021] [Indexed: 01/02/2023]
Abstract
Extreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive genome-wide study of structural variation as it relates to breed-specific phenotypes is lacking. We have generated whole genome CNV maps for more than 300 canids. Our data set extends the canine structural variation landscape to more than 100 dog breeds, including novel variants that cannot be assessed using microarray technologies. We have taken advantage of this data set to perform the first CNV-based genome-wide association study (GWAS) in canids. We identify 96 loci that display copy number differences across breeds, which are statistically associated with a previously compiled set of breed-specific morphometrics and disease susceptibilities. Among these, we highlight the discovery of a long-range interaction involving a CNV near MED13L and TBX3, which could influence breed standard height. Integration of the CNVs with chromatin interactions, long noncoding RNA expression, and single nucleotide variation highlights a subset of specific loci and genes with potential functional relevance and the prospect to explain trait variation between dog breeds.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Brian W Davis
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
| | - Inna S Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Carlos Morcillo-Suarez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - David Juan
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, Barcelona 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08201, Spain
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7
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Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen J, Rosen BD, Johnson GS, Rice ES, Hillier LD, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC, Ballard JWO. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 2021; 22:188. [PMID: 33726677 PMCID: PMC7962210 DOI: 10.1186/s12864-021-07493-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/28/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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Affiliation(s)
- Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878 Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - James M. Ferguson
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str, 27 06484 Quedlinburg, Germany
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705 USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211 USA
| | - Edward S. Rice
- Department of Surgery, University of Missouri, Columbia, MO 65211 USA
| | | | - Jillian M. Hammond
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010 Australia
| | - Ozren Bogdanovic
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765 Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
- Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009 Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Wesley C. Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211 Australia
| | - J. William O. Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086 Australia
- School of Biosciences, University of Melbourne, Parkville, Victoria 3052 Australia
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8
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Cayuela H, Dorant Y, Mérot C, Laporte M, Normandeau E, Gagnon-Harvey S, Clément M, Sirois P, Bernatchez L. Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish. Mol Ecol 2021; 30:1624-1641. [PMID: 33565147 DOI: 10.1111/mec.15835] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two types of genomic variation in population genomics studies.
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Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Stéphane Gagnon-Harvey
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Marie Clément
- Center for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial, University of Newfoundland, St. John's, NL, Canada.,Labrador Institute of Memorial University of Newfoundland, Happy Valley-Goose Bay, NL, Canada
| | - Pascal Sirois
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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9
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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] [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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10
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Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 2019; 20:759. [PMID: 31640551 PMCID: PMC6805398 DOI: 10.1186/s12864-019-6141-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. RESULTS We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. CONCLUSIONS This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
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Affiliation(s)
- Marina Solé
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Michela Ablondi
- Department of Veterinary Science, Università di Parma, Parma, Italy
| | - Amrei Binzer-Panchal
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Brandon D Velie
- Faculty of Life and Environmental Science, University of Sydney, Sydney, NSW, Australia
| | - Nina Hollfelder
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.,Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Åsa Viklund
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Isaksson
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Hanna Kultima
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
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11
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Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome. Animals (Basel) 2019; 9:ani9100809. [PMID: 31618984 PMCID: PMC6826909 DOI: 10.3390/ani9100809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Chickens have been bred for meat and egg production as a source of animal protein. With the increase of productivity as the main purpose of domestication, factors such as metabolism and immunity were boosted, which are detectable signs of selection on the genome. This study focused on copy number variation (CNV) to find evidence of domestication on the genome. CNV was detected from whole-genome sequencing of 65 chickens including Red Jungle Fowl, broilers, and layers. After that, CNV region, the overlapping region of CNV between individuals, was made to identify which genomic regions showed copy number differentiation. The 663 domesticated-specific CNV regions were associated with various functions such as metabolism and organ development. Also, by performing population differentiation analyses such as clustering analysis and ANOVA test, we found that there are a lot of genomic regions with different copy number patterns between broilers and layers. This result indicates that different genetic variations can be found, depending on the purpose of artificial selection and provides considerations for future animal breeding. Abstract Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.
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12
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Mortlock SA, Williamson P, Khatkar MS. Copy number variation and variant discovery in Bullmastiff dogs. Anim Genet 2019; 50:177-181. [PMID: 30793343 DOI: 10.1111/age.12754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2018] [Indexed: 01/05/2023]
Abstract
Identification of genomic variants within dogs is important for understanding genetic factors contributing to breed diversity and phenotypic traits. This study aimed to identify sources of variation in the Bullmastiff using high-density signal intensity and whole-genome sequence data. Close to 3000 copy number variants (CNVs) were identified in Bullmastiff dogs using Canine HD BeadChip data. When CNVs were collated, 82 CNV regions (CNVRs) were detected, 50% in transcribed regions encompassing 432 genes. Fifty of the CNVRs detected have not been reported in other breeds and represent potential breed-specific variants. A proportion of the CNVR variants with predicted modifying effects on gene pathways may contribute to breed traits. Approximately 5 million putative variants per dog, inclusive of single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertion and deletions (INDELs), were identified from DNA sequence data on a small number of animals. Identification of genetic variants in the Bullmastiff highlights sources of variation in the breed and molecular markers that will assist in future trait and disease investigations in dogs.
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Affiliation(s)
- S-A Mortlock
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia.,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - P Williamson
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia.,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - M S Khatkar
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia
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13
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Wang GD, Shao XJ, Bai B, Wang J, Wang X, Cao X, Liu YH, Wang X, Yin TT, Zhang SJ, Lu Y, Wang Z, Wang L, Zhao W, Zhang B, Ruan J, Zhang YP. Structural variation during dog domestication: insights from gray wolf and dhole genomes. Natl Sci Rev 2019; 6:110-122. [PMID: 34694297 PMCID: PMC8291444 DOI: 10.1093/nsr/nwy076] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/27/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiu-Juan Shao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bing Bai
- Medical Faculty, Kunming University of Science and Technology, Kunming 650504, China
- Department of Pediatrics, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - Junlong Wang
- College of Pharmacology, Soochow University, Suzhou 215123, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Shao-Jie Zhang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan Lu
- Beijing Zoo, Beijing 100044, China
| | | | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Wenming Zhao
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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14
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Genova F, Longeri M, Lyons LA, Bagnato A, Strillacci MG. First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics 2018; 19:895. [PMID: 30526495 PMCID: PMC6288940 DOI: 10.1186/s12864-018-5297-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023] Open
Abstract
Background Copy Number Variations (CNVs) have becoming very significant variants, representing a major source of genomic variation. CNVs involvement in phenotypic expression and different diseases has been widely demonstrated in humans as well as in many domestic animals. However, genome wide investigation on these structural variations is still missing in Felis catus. The present work is the first CNV mapping from a large data set of Next Generation Sequencing (NGS) data in the domestic cat, performed within the 99 Lives Consortium. Results Reads have been mapped on the reference assembly_6.2 by Maverix Biomics. CNV detection with cn.MOPS and CNVnator detected 592 CNVs. These CNVs were used to obtain 154 CNV Regions (CNVRs) with BedTools, including 62 singletons. CNVRs covered 0.26% of the total cat genome with 129 losses, 19 gains and 6 complexes. Cluster Analysis and Principal Component Analysis of the detected CNVRs showed that breeds tend to cluster together as well as cats sharing the same geographical origins. The 46 genes identified within the CNVRs were annotated. Conclusion This study has improved the genomic characterization of 14 cat breeds and has provided CNVs information that can be used for studies of traits in cats. It can be considered a sound starting point for genomic CNVs identification in this species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F Genova
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy
| | - M Longeri
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy
| | - L A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - A Bagnato
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy
| | | | - M G Strillacci
- Department of Veterinary Medicine, University of Milan, 20122, Milan, Italy.
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15
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Pedigree data indicate rapid inbreeding and loss of genetic diversity within populations of native, traditional dog breeds of conservation concern. PLoS One 2018; 13:e0202849. [PMID: 30208042 PMCID: PMC6135370 DOI: 10.1371/journal.pone.0202849] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/09/2018] [Indexed: 11/19/2022] Open
Abstract
Increasing concern is directed towards genetic diversity of domestic animal populations because strong selective breeding can rapidly deplete genetic diversity of socio-economically valuable animals. International conservation policy identifies minimizing genetic erosion of domesticated animals as a key biodiversity target. We used breeding records to assess potential indications of inbreeding and loss of founder allelic diversity in 12 native Swedish dog breeds, traditional to the country, ten of which have been identified by authorities as of conservation concern. The pedigrees dated back to the mid-1900, comprising 5-11 generations and 350-66,500 individuals per pedigree. We assessed rates of inbreeding and potential indications of loss of genetic variation by measuring inbreeding coefficients and remaining number of founder alleles at five points in time during 1980-2012. We found average inbreeding coefficients among breeds to double-from an average of 0.03 in 1980 to 0.07 in 2012 -in spite of the majority of breeds being numerically large with pedigrees comprising thousands of individuals indicating that such rapid increase of inbreeding should have been possible to avoid. We also found indications of extensive loss of intra-breed variation; on average 70 percent of founder alleles are lost during 1980-2012. Explicit conservation goals for these breeds were not reflected in pedigree based conservation genetic measures; breeding needs to focus more on retaining genetic variation, and supplementary genomic analyses of these breeds are highly warranted in order to find out the extent to which the trends indicated here are reflected over the genomes of these breeds.
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16
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Gómez-Sánchez D, Olalde I, Sastre N, Enseñat C, Carrasco R, Marques-Bonet T, Lalueza-Fox C, Leonard JA, Vilà C, Ramírez O. On the path to extinction: Inbreeding and admixture in a declining grey wolf population. Mol Ecol 2018; 27:3599-3612. [DOI: 10.1111/mec.14824] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Daniel Gómez-Sánchez
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Iñigo Olalde
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Natalia Sastre
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària, Servei Veterinari de Genètica Molecular; Universitat Autònoma de Barcelona; Bellaterra Spain
- Department of Ecology and Evolutionary Biology; UCLA; Los Angeles California
| | | | - Rafael Carrasco
- Departamento de Biologia Animal, Biologia Vegetal y Ecología; Universidad de Jaén (UJA); Jaen Spain
| | - Tomas Marques-Bonet
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Barcelona Spain
- Centro Nacional de Análisis Genómico (CNAG); Barcelona Spain
| | - Carles Lalueza-Fox
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - Oscar Ramírez
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
- Vetgenomics S.L.; Bellaterra Spain
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17
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Zhernakova DV, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Dobrynin P, Yurchenko AA, Shimansky V, Shcherbakova IV, Glotov AS, Valle DL, Tang M, Shin E, Schwarz KB, O'Brien SJ. Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis. PLoS One 2018; 13:e0200423. [PMID: 29995946 PMCID: PMC6040705 DOI: 10.1371/journal.pone.0200423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/26/2018] [Indexed: 12/23/2022] Open
Abstract
A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case’s unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence.
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Affiliation(s)
- Daria V. Zhernakova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
- * E-mail: (DVZ); (SJO)
| | - Sergei Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Nikolay Cherkasov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Mikhail Rotkevich
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Igor Evsyukov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Sviatoslav Sidorov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Andrey A. Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Valentin Shimansky
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Irina V. Shcherbakova
- Research Resource Center for Molecular and Cell Technologies, Research Park, Saint-Petersburg State University, St. Petersburg, Russia
| | - Andrey S. Glotov
- Research Resource Center for Molecular and Cell Technologies, Research Park, Saint-Petersburg State University, St. Petersburg, Russia
| | - David L. Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | | | - Emilia Shin
- Pediatric Liver Center, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Kathleen B. Schwarz
- Pediatric Liver Center, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
- Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
- * E-mail: (DVZ); (SJO)
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18
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Pendleton AL, Shen F, Taravella AM, Emery S, Veeramah KR, Boyko AR, Kidd JM. Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication. BMC Biol 2018; 16:64. [PMID: 29950181 PMCID: PMC6022502 DOI: 10.1186/s12915-018-0535-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Domesticated from gray wolves between 10 and 40 kya in Eurasia, dogs display a vast array of phenotypes that differ from their ancestors, yet mirror other domesticated animal species, a phenomenon known as the domestication syndrome. Here, we use signatures persisting in dog genomes to identify genes and pathways possibly altered by the selective pressures of domestication. RESULTS Whole-genome SNP analyses of 43 globally distributed village dogs and 10 wolves differentiated signatures resulting from domestication rather than breed formation. We identified 246 candidate domestication regions containing 10.8 Mb of genome sequence and 429 genes. The regions share haplotypes with ancient dogs, suggesting that the detected signals are not the result of recent selection. Gene enrichments highlight numerous genes linked to neural crest and central nervous system development as well as neurological function. Read depth analysis suggests that copy number variation played a minor role in dog domestication. CONCLUSIONS Our results identify genes that act early in embryogenesis and can confer phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development as the targets of selection during domestication. These differences reflect the phenotypes of the domestication syndrome, which can be explained by alterations in the migration or activity of neural crest cells during development. We propose that initial selection during early dog domestication was for behavior, a trait influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
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Affiliation(s)
- Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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