1
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Liu X, Lin L, Sinding MHS, Bertola LD, Hanghøj K, Quinn L, Garcia-Erill G, Rasmussen MS, Schubert M, Pečnerová P, Balboa RF, Li Z, Heaton MP, Smith TPL, Pinto RR, Wang X, Kuja J, Brüniche-Olsen A, Meisner J, Santander CG, Ogutu JO, Masembe C, da Fonseca RR, Muwanika V, Siegismund HR, Albrechtsen A, Moltke I, Heller R. Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations. Nat Commun 2024; 15:2921. [PMID: 38609362 PMCID: PMC11014984 DOI: 10.1038/s41467-024-47015-y] [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: 10/31/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.
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Affiliation(s)
- Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, USA
| | - Rui Resende Pinto
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jonas Meisner
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Copenhagen Research Centre for Mental Health, Copenhagen University Hospital, Copenhagen, Denmark
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph O Ogutu
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Rute R da Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research-University of Porto, Porto, Portugal
- Section for Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vincent Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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2
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Balboa RF, Bertola LD, Brüniche-Olsen A, Rasmussen MS, Liu X, Besnard G, Salmona J, Santander CG, He S, Zinner D, Pedrono M, Muwanika V, Masembe C, Schubert M, Kuja J, Quinn L, Garcia-Erill G, Stæger FF, Rakotoarivony R, Henrique M, Lin L, Wang X, Heaton MP, Smith TPL, Hanghøj K, Sinding MHS, Atickem A, Chikhi L, Roos C, Gaubert P, Siegismund HR, Moltke I, Albrechtsen A, Heller R. African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival. Nat Commun 2024; 15:172. [PMID: 38172616 PMCID: PMC10764920 DOI: 10.1038/s41467-023-44105-1] [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: 08/23/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.
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Affiliation(s)
- Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guillaume Besnard
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Jordi Salmona
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shixu He
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Dietmar Zinner
- Cognitive Ecology Laboratory, German 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
| | - Miguel Pedrono
- UMR ASTRE, CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Mikkel Schubert
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anagaw Atickem
- Department of Zoological Sciences, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - Lounès Chikhi
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique (EDB), UMR 5174, CNRS, IRD, Université Toulouse Paul Sabatier, 31062, Toulouse, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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3
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Beiki H, Murdoch BM, Park CA, Kern C, Kontechy D, Becker G, Rincon G, Jiang H, Zhou H, Thorne J, Koltes JE, Michal JJ, Davenport K, Rijnkels M, Ross PJ, Hu R, Corum S, McKay S, Smith TPL, Liu W, Ma W, Zhang X, Xu X, Han X, Jiang Z, Hu ZL, Reecy JM. Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology. Gigascience 2024; 13:giae019. [PMID: 38626724 PMCID: PMC11020238 DOI: 10.1093/gigascience/giae019] [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: 02/11/2023] [Revised: 07/29/2023] [Accepted: 03/27/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUND The accurate identification of the functional elements in the bovine genome is a fundamental requirement for high-quality analysis of data informing both genome biology and genomic selection. Functional annotation of the bovine genome was performed to identify a more complete catalog of transcript isoforms across bovine tissues. RESULTS A total of 160,820 unique transcripts (50% protein coding) representing 34,882 unique genes (60% protein coding) were identified across tissues. Among them, 118,563 transcripts (73% of the total) were structurally validated by independent datasets (PacBio isoform sequencing data, Oxford Nanopore Technologies sequencing data, de novo assembled transcripts from RNA sequencing data) and comparison with Ensembl and NCBI gene sets. In addition, all transcripts were supported by extensive data from different technologies such as whole transcriptome termini site sequencing, RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression, chromatin immunoprecipitation sequencing, and assay for transposase-accessible chromatin using sequencing. A large proportion of identified transcripts (69%) were unannotated, of which 86% were produced by annotated genes and 14% by unannotated genes. A median of two 5' untranslated regions were expressed per gene. Around 50% of protein-coding genes in each tissue were bifunctional and transcribed both coding and noncoding isoforms. Furthermore, we identified 3,744 genes that functioned as noncoding genes in fetal tissues but as protein-coding genes in adult tissues. Our new bovine genome annotation extended more than 11,000 annotated gene borders compared to Ensembl or NCBI annotations. The resulting bovine transcriptome was integrated with publicly available quantitative trait loci data to study tissue-tissue interconnection involved in different traits and construct the first bovine trait similarity network. CONCLUSIONS These validated results show significant improvement over current bovine genome annotations.
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Affiliation(s)
- Hamid Beiki
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Brenda M Murdoch
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - Carissa A Park
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Chandlar Kern
- Department of Animal Science, Pennsylvania State University, PA 16802, USA
| | - Denise Kontechy
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - Gabrielle Becker
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | | | - Honglin Jiang
- Department of Animal and Poultry Sciences, Virginia Tech, VA 24060, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Jacob Thorne
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Jennifer J Michal
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Kimberly Davenport
- Department of Animal and Veterinary and Food Science, University of Idaho, ID 83844, USA
| | - Monique Rijnkels
- Department of Veterinary Integrative Biosciences, Texas A&M University, TX 77843, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Rui Hu
- Department of Animal and Poultry Sciences, Virginia Tech, VA 24060, USA
| | - Sarah Corum
- Zoetis, Parsippany-Troy Hills, NJ 07054, USA
| | | | | | - Wansheng Liu
- Department of Animal Science, Pennsylvania State University, PA 16802, USA
| | - Wenzhi Ma
- Department of Animal Science, Pennsylvania State University, PA 16802, USA
| | - Xiaohui Zhang
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Xiaoqing Xu
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Xuelei Han
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Zhihua Jiang
- Department of Animal Science, Washington State University, WA 99164, USA
| | - Zhi-Liang Hu
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
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4
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Weinroth MD, Clawson ML, Harhay GP, Eppinger M, Harhay DM, Smith TPL, Bono JL. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Front Microbiol 2023; 14:1303387. [PMID: 38169669 PMCID: PMC10758439 DOI: 10.3389/fmicb.2023.1303387] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.
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Affiliation(s)
- Margaret D. Weinroth
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Michael L. Clawson
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Dayna M. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Timothy P. L. Smith
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - James L. Bono
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
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5
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Oppert B, Dossey AT, Chu FC, Šatović-Vukšić E, Plohl M, Smith TPL, Koren S, Olmstead ML, Leierer D, Ragan G, Johnston JS. The Genome of the Yellow Mealworm, Tenebrio molitor: It's Bigger Than You Think. Genes (Basel) 2023; 14:2209. [PMID: 38137031 PMCID: PMC10742464 DOI: 10.3390/genes14122209] [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: 09/30/2023] [Revised: 11/26/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Insects are a sustainable source of protein for human food and animal feed. We present a genome assembly, CRISPR gene editing, and life stage-specific transcriptomes for the yellow mealworm, Tenebrio molitor, one of the most intensively farmed insects worldwide. METHODS Long and short reads and long-range data were obtained from a T. molitor male pupa. Sequencing transcripts from 12 T. molitor life stages resulted in 279 million reads for gene prediction and genetic engineering. A unique plasmid delivery system containing guide RNAs targeting the eye color gene vermilion flanking the muscle actin gene promoter and EGFP marker was used in CRISPR/Cas9 transformation. RESULTS The assembly is approximately 53% of the genome size of 756.8 ± 9.6 Mb, measured using flow cytometry. Assembly was complicated by a satellitome of at least 11 highly conserved satDNAs occupying 28% of the genome. The injection of the plasmid into embryos resulted in knock-out of Tm vermilion and knock-in of EGFP. CONCLUSIONS The genome of T. molitor is longer than current assemblies (including ours) due to a substantial amount (26.5%) of only one highly abundant satellite DNA sequence. Genetic sequences and transformation tools for an insect important to the food and feed industries will promote the sustainable utilization of mealworms and other farmed insects.
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Affiliation(s)
- Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA; (M.L.O.); (G.R.)
| | - Aaron T. Dossey
- All Things Bugs LLC, 755 Research Parkway, Suite 465, Oklahoma City, OK 73130, USA or (A.T.D.); (F.-C.C.)
- Invertebrate Studies Institute, 2211 Snapper Ln, Midwest City, OK 73130, USA
| | - Fu-Chyun Chu
- All Things Bugs LLC, 755 Research Parkway, Suite 465, Oklahoma City, OK 73130, USA or (A.T.D.); (F.-C.C.)
| | - Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (E.Š.-V.); (M.P.)
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (E.Š.-V.); (M.P.)
| | | | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Morgan L. Olmstead
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA; (M.L.O.); (G.R.)
| | - Dewey Leierer
- Department of Molecular Biology and Biophysics, Kansas State University, Manhattan, KS 66506, USA;
| | - Gail Ragan
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, USA; (M.L.O.); (G.R.)
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA;
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Fuller T, Bickhart DM, Koch LM, Kucek LK, Ali S, Mangelson H, Monteros MJ, Hernandez T, Smith TPL, Riday H, Sullivan ML. A reference assembly for the legume cover crop hairy vetch ( Vicia villosa). GigaByte 2023; 2023:gigabyte98. [PMID: 38023065 PMCID: PMC10659084 DOI: 10.46471/gigabyte.98] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
Vicia villosa is an incompletely domesticated annual legume of the Fabaceae family native to Europe and Western Asia. V. villosa is widely used as a cover crop and forage due to its ability to withstand harsh winters. Here, we generated a reference-quality genome assembly (Vvill1.0) from low error-rate long-sequence reads to improve the genetic-based trait selection of this species. Our Vvill1.0 assembly includes seven scaffolds corresponding to the seven estimated linkage groups and comprising approximately 68% of the total genome size of 2.03 Gbp. This assembly is expected to be a useful resource for genetically improving this emerging cover crop species and provide useful insights into legume genomics and plant genome evolution.
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Affiliation(s)
- Tyson Fuller
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Derek M. Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Lisa M. Koch
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Lisa Kissing Kucek
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Shahjahan Ali
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | | | - Maria J. Monteros
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Timothy Hernandez
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Timothy P. L. Smith
- US Meat Animal Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), PO Box 166 (State Spur 18D), Clay Center, NE 68933, USA
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Michael L. Sullivan
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
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7
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Smith TPL, Bickhart DM, Boichard D, Chamberlain AJ, Djikeng A, Jiang Y, Low WY, Pausch H, Demyda-Peyrás S, Prendergast J, Schnabel RD, Rosen BD. The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biol 2023; 24:139. [PMID: 37337218 DOI: 10.1186/s13059-023-02975-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 05/19/2023] [Indexed: 06/21/2023] Open
Abstract
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.
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Affiliation(s)
- Timothy P L Smith
- US Meat Animal Research Center, USDA-ARS, Clay Center, NE, 68933, USA
| | | | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, ILRI Kenya, Nairobi, 30709-00100, Kenya
- Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yu Jiang
- Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling, 712100, China
| | - Wai Y Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland
| | - Sebastian Demyda-Peyrás
- Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, 1900, La Plata, Argentina
- Consejo Superior de Investigaciones Científicas Y Tecnológicas (CONICET), CCT-La Plata, 1900, La Plata, Argentina
| | - James Prendergast
- Centre for Tropical Livestock Genetics and Health, Easter Bush, Midlothian, EH25 9RG, UK
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
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8
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Ren Y, Tseng E, Smith TPL, Hiendleder S, Williams JL, Low WY. Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies. BMC Genomics 2023; 24:108. [PMID: 36915055 PMCID: PMC10012480 DOI: 10.1186/s12864-023-09212-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU). However, the higher cost of Iso-Seq relative to RNA-seq has limited the comparison of both methods. Transcript abundance estimated by RNA-seq and deep Iso-Seq data for fetal liver from two cattle subspecies were compared to evaluate concordance. Inter-sample correlation of gene- and transcript-level abundance was higher within technology than between technologies. Identification of DEGs between the cattle subspecies depended on sequencing method with only 44 genes identified by both that included 6 novel genes annotated by Iso-Seq. There was a pronounced difference between Iso-Seq and RNA-seq results at transcript-level wherein Iso-Seq revealed several magnitudes more transcript abundance and usage differences between subspecies. Factors influencing DEG identification included size selection during Iso-Seq library preparation, average transcript abundance, multi-mapping of RNA-seq reads to the reference genome, and overlapping coordinates of genes. Some DEGs called by RNA-seq alone appear to be sequence duplication artifacts. Among the 44 DEGs identified by both technologies some play a role in immune system, thyroid function and cell growth. Iso-Seq revealed hidden transcriptional complexity in DEGs, DETs and DTU genes between cattle subspecies previously missed by RNA-seq.
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Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia
| | | | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Clay Center, Nebraska, USA
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.,Robinson Research Institute, The University of Adelaide, North Adelaide, Adelaide, SA, 5006, Australia
| | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.,Department of Animal Science, Food and Nutrition, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Adelaide, SA, 5371, Australia.
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9
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Cohen ZP, Perkin LC, Sim SB, Stahlke AR, Geib SM, Childers AK, Smith TPL, Suh C. Insight into weevil biology from a reference quality genome of the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae). G3 (Bethesda) 2023; 13:jkac309. [PMID: 36454104 PMCID: PMC9911062 DOI: 10.1093/g3journal/jkac309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 12/03/2022]
Abstract
The boll weevil, Anthonomus grandis grandis Boheman, is one of the most historically impactful insects due to its near destruction of the US cotton industry in the early 20th century. Contemporary efforts to manage this insect primarily use pheromone baited traps for detection and organophosphate insecticides for control, but this strategy is not sustainable due to financial and environmental costs. We present a high-quality boll weevil genome assembly, consisting of 306 scaffolds with approximately 24,000 annotated genes, as a first step in the identification of gene targets for novel pest control. Gene content and transposable element distribution are similar to those found in other Curculionidae genomes; however, this is the most contiguous and only assembly reported to date for a member in the species-rich genus Anthonomus. Transcriptome profiles across larval, pupal, and adult life stages led to identification of several genes and gene families that could present targets for novel control strategies.
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Affiliation(s)
- Zachary P Cohen
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, 2771 F and B Road, College Station, TX 77845, USA
| | - Lindsey C Perkin
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, 2771 F and B Road, College Station, TX 77845, USA
| | - Sheina B Sim
- Tropical Crop and Commodity Protection Research Unit, U.S. Pacific Basin Agricultural Research Center, USDA, Agricultural Research Service, 64 Nowelo Street, Hilo, HI 96720, USA
| | - Amanda R Stahlke
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, U.S. Pacific Basin Agricultural Research Center, USDA, Agricultural Research Service, 64 Nowelo Street, Hilo, HI 96720, USA
| | - Anna K Childers
- Bee Research Laboratory, Beltsville Agricultural Research Center, USDA, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Timothy P L Smith
- Genetics and Breeding Research Unit, U.S. Meat Animal Research Center, USDA, Agricultural Research Service, State Spur 18D, Clay Center, NE 68933, USA
| | - Charles Suh
- Insect Control and Cotton Disease Research Unit, Southern Plains Agricultural Research Center, USDA, Agricultural Research Service, 2771 F and B Road, College Station, TX 77845, USA
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10
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Quinn L, Garcia-Erill G, Santander C, Brüniche-Olsen A, Liu X, Sinding MHS, Heaton MP, Smith TPL, Pečnerová P, Bertola LD, Hanghøj K, Rasmussen MS, de Jager D, Siegismund HR, Albrechtsen A, Heller R, Moltke I. Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo. Mol Ecol 2023; 32:1860-1874. [PMID: 36651275 DOI: 10.1111/mec.16851] [Citation(s) in RCA: 2] [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: 05/27/2022] [Revised: 12/23/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
The iconic Cape buffalo has experienced several documented population declines in recent history. These declines have been largely attributed to the late 19th century rinderpest pandemic. However, the effect of the rinderpest pandemic on their genetic diversity remains contentious, and other factors that have potentially affected this diversity include environmental changes during the Pleistocene, range expansions and recent human activity. Motivated by this, we present analyses of whole genome sequencing data from 59 individuals from across the Cape buffalo range to assess present-day levels of genome-wide genetic diversity and what factors have influenced these levels. We found that the Cape buffalo has high average heterozygosity overall (0.40%), with the two southernmost populations having significantly lower heterozygosity levels (0.33% and 0.29%) on par with that of the domesticated water buffalo (0.29%). Interestingly, we found that these lower levels are probably due to recent inbreeding (average fraction of runs of homozygosity 23.7% and 19.9%) rather than factors further back in time during the Pleistocene. Moreover, detailed investigations of recent demographic history show that events across the past three centuries were the main drivers of the exceptional loss of genetic diversity in the southernmost populations, coincident with the onset of colonialism in the southern extreme of the Cape buffalo range. Hence, our results add to the growing body of studies suggesting that multiple recent human-mediated impacts during the colonial period caused massive losses of large mammal abundance in southern Africa.
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Affiliation(s)
- Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Cindy Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, New Brunswick, USA
| | - Timothy P L Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, New Brunswick, USA
| | | | - Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Deon de Jager
- Section of Molecular Ecology and Evolution, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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11
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Murdoch BM, Davenport KM, Xie S, Salavati M, Clark E, Archibald A, White SN, Mousel MR, Worley K, Bhattarai S, McKay SD, Caulton A, Clarke S, Brauning R, Hadfield T, Rosen BD, Smith TPL, Cockett N. 378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome. J Anim Sci 2022. [DOI: 10.1093/jas/skac247.340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Characterizing the locations of genetic regulatory elements is critical for understanding the regulatory mechanisms of complex phenotypic traits related to production traits and health in livestock species. The Ovine Functional Annotation of Animal Genomes (FAANG) Project aims to characterize transcriptional regulatory elements across the sheep genome to facilitate a better understanding of the biological mechanisms influencing phenotypic traits in sheep. Assays including sequencing of messenger RNA (mRNA-seq), cap analysis of gene expression (CAGE), chromatin immunoprecipitation of histones (ChIP-seq), assay for transposase-accessible chromatin (ATAC-seq), whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) were performed on tissues collected from the Rambouillet ewe used to assemble the reference genome ARS-UI_Ramb_v2.0. Histone modifications were used to define nine chromatin states for tissues across the genome depicting promoters and enhancers (active, poised, and repressed) using ChromHMM. Chromatin states were overlayed with RNA-seq, ATAC-seq and DNA methylation. These data suggest that active promoter and enhancer states reside in open chromatin regions with a greater transcriptional activity and hypomethylated regions than other states. Further, poised and repressed enhancers did not primarily reside in open chromatin and had less transcriptional activity and more hypermethylated sites compared with active states. Collectively these data define transcriptional regulatory regions throughout the ovine genome which provides a valuable resource to better understand regulatory regions in the genome and how these influence economically important traits in sheep and other livestock species.
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Affiliation(s)
- Brenda M Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho
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12
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Zhou Y, Yang L, Han X, Han J, Hu Y, Li F, Xia H, Peng L, Boschiero C, Rosen BD, Bickhart DM, Zhang S, Guo A, Van Tassell CP, Smith TPL, Yang L, Liu GE. Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Res 2022; 32:gr.276550.122. [PMID: 35977842 PMCID: PMC9435747 DOI: 10.1101/gr.276550.122] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 07/21/2022] [Indexed: 02/03/2023]
Abstract
A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in the cattle reference genome, representing 3.1% novel sequence compared with the 2.71-Gb reference. A catalog of structural variants developed from this cattle population identified 3.3 million deletions, 0.12 million inversions, and 0.18 million duplications. Estimates of breed ancestry and hybridization between cattle breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism-based analysis. Hundreds of deletions were observed to have stratification based on subspecies and breed. For example, an insertion of a Bov-tA1 repeat element was identified in the first intron of the APPL2 gene and correlated with cattle breed geographic distribution. This insertion falls within a segment overlapping predicted enhancer and promoter regions of the gene, and could affect important traits such as immune response, olfactory functions, cell proliferation, and glucose metabolism in muscle. The results indicate that pangenomes are a valuable resource for studying diversity and evolutionary history, and help to delineate how domestication, trait-based breeding, and adaptive introgression have shaped the cattle genome.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaotao Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingwei Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, ARS USDA, Madison, Wisconsin 53706, USA
| | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, ARS USDA, Clay Center, Nebraska 68933, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, Maryland 20705, USA
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13
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Ault-Seay TB, Brandt KJ, Henniger MT, Payton RR, Mathew DJ, Moorey SE, Schrick FN, Pohler KG, Smith TPL, Rhinehart JD, Schneider LG, McLean KJ, Myer PR. Bacterial Communities of the Uterus and Rumen During Heifer Development With Protein Supplementation. Front Anim Sci 2022. [DOI: 10.3389/fanim.2022.903909] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities play major roles in rumen and uterine function toward optimal animal performance and may be affected by changes occurring during heifer development such as nutritional supplementation for optimal growth and the attainment of puberty. The effect of different levels of protein supplementation on ruminal and uterine bacterial communities following weaning was examined through first breeding of heifers. Angus heifers (n = 39) were blocked by initial body weight (BW) and randomly assigned to one of three 163-day (d) crude protein (CP) supplementation diets including control (10% CP, n = 14), 20% CP (n = 11), or 40% CP (n = 14) treatment groups. Growth and development were monitored by body weight, with blood progesterone concentration determined every 14 d to determine pubertal status. Uterine flush and rumen fluid were collected on d 56, 112, and 163 relative to the start of supplementation. Bacterial DNA was extracted from fluid samples, the V1–V3 hypervariable region of the 16S rRNA gene was amplified, and amplicons were sequenced then processed in R 4.1. Statistical analyses were performed in SAS 9.4 with a GLIMMIX procedure utilizing fixed effects of protein, month, pubertal status, and interactions, with random effects including BW, interaction of BW and protein, and heifer within the interaction, and repeated measures of day. In the uterus, pubertal status and day of supplementation affected the observed amplicon sequence variants (ASVs) and led to clustering of samples in a principal coordinate analysis (PCoA; P < 0.05), but no effect of protein supplementation was observed. Ruminal samples clustered in PCoA (P = 0.001), and observed ASVs were impacted over time (P < 0.0001), but no effect of protein supplementation was detected. In contrast, protein supplementation, pubertal status, and day of supplementation affected the abundance of multiple phyla and genera in the uterus and rumen (P < 0.05). Temporal and pubertal status effects on the heifer’s uterine bacterial communities potentially indicate a maturing uterine microbiome. Protein supplementation did not impact microbial diversity measures but did affect the abundance of individual bacterial phyla and genera that may provide future opportunities to manipulate bacterial community composition and maximize productivity.
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14
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Leonard AS, Crysnanto D, Fang ZH, Heaton MP, Vander Ley BL, Herrera C, Bollwein H, Bickhart DM, Kuhn KL, Smith TPL, Rosen BD, Pausch H. Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nat Commun 2022; 13:3012. [PMID: 35641504 PMCID: PMC9156671 DOI: 10.1038/s41467-022-30680-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/06/2021] [Accepted: 05/10/2022] [Indexed: 12/12/2022] Open
Abstract
Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.
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Affiliation(s)
- Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
| | - Danang Crysnanto
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland
| | - Michael P Heaton
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Carolina Herrera
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, Department for Farm Animals, University of Zurich, 8057, Zurich, Switzerland
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Kristen L Kuhn
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD, 20705, USA.
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, 8006, Zurich, Switzerland.
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15
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Low WY, Rosen BD, Ren Y, Bickhart DM, To TH, Martin FJ, Billis K, Sonstegard TS, Sullivan ST, Hiendleder S, Williams JL, Heaton MP, Smith TPL. Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. BMC Genomics 2022; 23:344. [PMID: 35508966 PMCID: PMC9069736 DOI: 10.1186/s12864-022-08561-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/13/2022] [Indexed: 02/08/2023] Open
Abstract
Background The gaur (Bos gaurus) is the largest extant wild bovine species, native to South and Southeast Asia, with unique traits, and is listed as vulnerable by the International Union for Conservation of Nature (IUCN). Results We report the first gaur reference genome and identify three biological pathways including lysozyme activity, proton transmembrane transporter activity, and oxygen transport with significant changes in gene copy number in gaur compared to other mammals. These may reflect adaptation to challenges related to climate and nutrition. Comparative analyses with domesticated indicine (Bos indicus) and taurine (Bos taurus) cattle revealed genomic signatures of artificial selection, including the expansion of sperm odorant receptor genes in domesticated cattle, which may have important implications for understanding selection for male fertility. Conclusions Apart from aiding dissection of economically important traits, the gaur genome will also provide the foundation to conserve the species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08561-1.
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Affiliation(s)
- Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
| | - Benjamin D Rosen
- Animal Genomics and Improvement LaboratoryARS USDA, Beltsville, MD, USA
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | | | - Thu-Hien To
- Norwegian University of Life Sciences: NMBU, Universitetstunet 3, 1430, Ås, Norway
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Shawn T Sullivan
- Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA, 98195, USA
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.,Department of Animal Science, Food and Nutrition, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | - Michael P Heaton
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Timothy P L Smith
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA.
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16
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Field MA, Yadav S, Dudchenko O, Esvaran M, Rosen BD, Skvortsova K, Edwards RJ, Keilwagen J, Cochran BJ, Manandhar B, Bustamante S, Rasmussen JA, Melvin RG, Chernoff B, Omer A, Colaric Z, Chan EKF, Minoche AE, Smith TPL, Gilbert MTP, Bogdanovic O, Zammit RA, Thomas T, Aiden EL, Ballard JWO. The Australian dingo is an early offshoot of modern breed dogs. Sci Adv 2022; 8:eabm5944. [PMID: 35452284 PMCID: PMC9032958 DOI: 10.1126/sciadv.abm5944] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/09/2022] [Indexed: 06/11/2023]
Abstract
Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.
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Affiliation(s)
- Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Cairns, QLD 4878, Australia
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Sonu Yadav
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Meera Esvaran
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Blake J. Cochran
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bikash Manandhar
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sonia Bustamante
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Agerbo Rasmussen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Center for Evolutionary Hologenomics, Faculty of Health and Medical Sciences, The GLOBE Institute University of Copenhagen, Copenhagen, Denmark
| | - Richard G. Melvin
- Department of Biomedical Sciences, University of Minnesota Medical School, 1035 University Drive, Duluth, MN 55812, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth and Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Arina Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eva K. F. Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle, NSW 2300, Australia
| | - Andre E. Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Timothy P. L. Smith
- U.S. Meat Animal Research Center, Agricultural Research Service, USDA, Rd 313, Clay Center, NE 68933, USA
| | - M. Thomas P. Gilbert
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Torsten Thomas
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Erez L. Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Pudong 201210, China
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - J. William O. Ballard
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, VIC 3086, Australia
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, VIC 3052, Australia
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17
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Safonova Y, Shin SB, Kramer L, Reecy J, Watson CT, Smith TPL, Pevzner PA. Variations in antibody repertoires correlate with vaccine responses. Genome Res 2022; 32:791-804. [PMID: 35361626 PMCID: PMC8997358 DOI: 10.1101/gr.276027.121] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 02/28/2022] [Indexed: 11/24/2022]
Abstract
An important challenge in vaccine development is to figure out why a vaccine succeeds in some individuals and fails in others. Although antibody repertoires hold the key to answering this question, there have been very few personalized immunogenomics studies so far aimed at revealing how variations in immunoglobulin genes affect a vaccine response. We conducted an immunosequencing study of 204 calves vaccinated against bovine respiratory disease (BRD) with the goal to reveal variations in immunoglobulin genes and somatic hypermutations that impact the efficacy of vaccine response. Our study represents the largest longitudinal personalized immunogenomics study reported to date across all species, including humans. To analyze the generated data set, we developed an algorithm for identifying variations of the immunoglobulin genes (as well as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study reveals that ultralong antibodies are a key component of the immune response against the costliest disease of beef cattle in North America. The detected variants of the cattle immunoglobulin genes, which are implicated in the success/failure of the BRD vaccine, have the potential to direct the selection of individual cattle for ongoing breeding programs.
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Affiliation(s)
- Yana Safonova
- Computer Science and Engineering Department, University of California at San Diego, San Diego, California 92093, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Sung Bong Shin
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Nebraska 68933, USA
| | - Luke Kramer
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - James Reecy
- Department of Animal Science, Iowa State University, Ames, Iowa 50011, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, Nebraska 68933, USA
| | - Pavel A Pevzner
- Computer Science and Engineering Department, University of California at San Diego, San Diego, California 92093, USA
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18
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Bickhart DM, Koch LM, Smith TPL, Riday H, Sullivan ML. Chromosome-scale assembly of the highly heterozygous genome of red clover ( Trifolium pratense L.), an allogamous forage crop species. GigaByte 2022; 2022:gigabyte42. [PMID: 36824517 PMCID: PMC9650271 DOI: 10.46471/gigabyte.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Relative to other crops, red clover (Trifolium pratense L.) has various favorable traits making it an ideal forage crop. Conventional breeding has improved varieties, but modern genomic methods could accelerate progress and facilitate gene discovery. Existing short-read-based genome assemblies of the ∼420 megabase pair (Mbp) genome are fragmented into >135,000 contigs, with numerous order and orientation errors within scaffolds, probably associated with the plant's biology, which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. Here, we present a high-quality long-read-based assembly of red clover with a more than 500-fold reduction in contigs, improved per-base quality, and increased contig N50 by three orders of magnitude. The 413.5 Mbp assembly is nearly 20% longer than the 350 Mbp short-read assembly, closer to the predicted genome size. We also present quality measures and full-length isoform RNA transcript sequences for assessing accuracy and future genome annotation. The assembly accurately represents the seven main linkage groups in an allogamous (outcrossing), highly heterozygous plant genome.
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Affiliation(s)
- Derek M. Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA, Corresponding authors. E-mail: ;
| | - Lisa M. Koch
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA
| | - Timothy P. L. Smith
- US Meat Animal Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Clay Center, NE, USA
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA
| | - Michael L. Sullivan
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA, Corresponding authors. E-mail: ;
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19
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Davenport KM, Bickhart DM, Worley K, Murali SC, Salavati M, Clark EL, Cockett NE, Heaton MP, Smith TPL, Murdoch BM, Rosen BD. An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome. Gigascience 2022; 11:giab096. [PMID: 35134925 PMCID: PMC8848310 DOI: 10.1093/gigascience/giab096] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 08/17/2021] [Revised: 10/28/2021] [Accepted: 12/25/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome. FINDINGS Short-read Illumina (55× coverage), long-read Pacific Biosciences (75× coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50× coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. CONCLUSIONS The ARS-UI_Ramb_v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep.
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Affiliation(s)
- Kimberly M Davenport
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, 875 Perimeter Dr, Moscow, ID 83843, USA
| | - Derek M Bickhart
- US Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA
| | - Kim Worley
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha C Murali
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Mazdak Salavati
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Emily L Clark
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | | | - Michael P Heaton
- US Meat Animal Research Center, USDA-ARS, State Spur 18D, Clay Center, NE 68933, USA
| | - Timothy P L Smith
- US Meat Animal Research Center, USDA-ARS, State Spur 18D, Clay Center, NE 68933, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, 875 Perimeter Dr, Moscow, ID 83843, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705, USA
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20
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Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan ST, Shin SB, Zorea A, Andreu VP, Panke-Buisse K, Medema MH, Mizrahi I, Pevzner PA, Smith TPL. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nat Biotechnol 2022; 40:711-719. [PMID: 34980911 DOI: 10.1038/s41587-021-01130-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/13/2021] [Indexed: 12/18/2022]
Abstract
Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.
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Affiliation(s)
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California - San Diego, La Jolla, CA, USA
| | | | | | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Ivan Tolstoganov
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | | | | | | | | | - Alvah Zorea
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheba, Israel
| | | | | | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheba, Israel
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California - San Diego, La Jolla, CA, USA.
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21
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Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT, Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Davenport KM, Kuhn KL, Green RE, Shapiro B, Rosen BD. Erratum to: A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. J Hered 2021; 112:565. [PMID: 34436588 DOI: 10.1093/jhered/esab039] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | | | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TX, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
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22
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Davenport KM, Bickhart DM, Worley K, Murali SC, Cockett N, Heaton MP, Smith TPL, Murdoch BM, Rosen BD. 42 An Improved, High-quality Ovine Reference Genome Assembly. J Anim Sci 2021. [DOI: 10.1093/jas/skab235.039] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Sheep are an important agricultural species used for both food and fiber in the United States and globally. A high-quality reference genome enhances the ability to discover genetic and biological mechanisms influencing important traits, such as meat and wool quality. The rapid advances in genome assembly algorithms and emergence of increasingly long sequence read length provide the opportunity for an improved de novo assembly of the sheep reference genome. Tissue was collected postmortem from an adult Rambouillet ewe selected by USDA-ARS for the Ovine Functional Annotation of Animal Genomes project. Short-read (55x coverage), long-read PacBio (75x coverage), and Hi-C data from this ewe were retrieved from public databases. We generated an additional 50x coverage of Oxford Nanopore data and assembled the combined long-read data with canu v1.9. The assembled contigs were polished with Nanopolish v0.12.5 and scaffolded using Hi-C data with Salsa v2.2. Gaps were filled with PBsuite v15.8.24 and polished with Nanopolish v0.12.5 followed by removal of duplicate contigs with PurgeDups v1.0.1. Chromosomes were oriented by identifying centromeres and telomeres with RepeatMasker v4.1.1, indicating a need to reverse the orientation of chromosome 11 relative to Oar_rambouillet_v1.0. Final polishing was performed with two rounds of a pipeline which consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly has improved continuity (contig N50 of 43.19 Mb) with a 19-fold and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. This significantly improved reference assembly, public at NCBI GenBank under accession number GCA_016772045, will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits relevant the sheep industry.
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23
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Ren Y, MacPhillamy C, To TH, Smith TPL, Williams JL, Low WY. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics 2021; 113:3599-3609. [PMID: 34455036 DOI: 10.1016/j.ygeno.2021.08.021] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.
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Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Thu-Hien To
- Norwegian University of Life Sciences: NMBU, Universitetstunet 3, 1430 Ås, Norway
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia; Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
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24
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Cushman RA, Bennett GL, Tait RG, McNeel AK, Casas E, Smith TPL, Freetly HC. Relationship of molecular breeding value for beef tenderness with heifer traits through weaning of their first calf. Theriogenology 2021; 173:128-132. [PMID: 34375939 DOI: 10.1016/j.theriogenology.2021.07.020] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 07/08/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Polymorphisms in μ-calpain (CAPN1) that beneficially associate with beef tenderness are reported to antagonistically associate with calving day in beef heifers and post-partum interval to estrus in beef cows. We, therefore, hypothesized that a molecular breeding value for slice shear force, calculated based on CAPN1 and calpastatin (CAST) genotypes, would demonstrate an antagonistic relationship between genomically predicted slice shear force and ordinal calving date in replacement beef heifers. A secondary objective of this study was to evaluate the association of a polymorphism in diacylglycerol O-acyltransferase (DGAT1) with reproductive traits in beef heifers. One hundred eighty-seven MARC III heifers (¼ Angus, ¼ Hereford, ¼ Red Poll, and ¼ Pinzgauer) that had been selectively bred to increase the frequency of these polymorphisms were submitted for monthly ultrasound exams beginning at 333 d of age and continuing until the start of breeding to determine pubertal status. At the last exam before breeding, all antral follicles were counted, and the length and height of each ovary was measured to determine if genomic selection for slice shear force associated with ovarian follicle number. Calving date, calf gender, and calf birth weight were recorded at parturition. Regression analysis of the molecular breeding value for slice shear force of the heifers on ordinal calving date indicated no association between genomic prediction of tenderness and calving date (P = 0.16); however, there was a tendency for age at puberty to be delayed in heifers as genetic merit for tenderness improved (P = 0.09). The results of the present study indicate that within experimental precision, selecting for tenderness using genomic predictions had minimal or no antagonistic association with reproductive performance in heifers. Further analysis of reproductive performance as cows is needed within this population but applying these genetic markers to select for tenderness in steers does not antagonize reproductive traits influencing conception or first calf birth date and birth weight in replacement beef heifers.
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Affiliation(s)
- Robert A Cushman
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States.
| | - Gary L Bennett
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Richard G Tait
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Anthony K McNeel
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Eduardo Casas
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Timothy P L Smith
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Harvey C Freetly
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
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25
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Dickey AM, Smith TPL, Clawson ML, Heaton MP, Workman AM. Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns. F1000Res 2021; 9:1449. [PMID: 35035904 PMCID: PMC8749911 DOI: 10.12688/f1000research.27898.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods: Sequence variation within and among full-length assemblies of SRLV subtype A2 subgroups 1 and 2 was analyzed to identify genome-scale recombination patterns and subgroup-specific variants. Results: Consensus viral genomes were assembled from 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined consensus genomes. After accounting for recombination, 413 subgroup diagnostic single nucleotide polymorphisms (SNPs) were identified. Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2.
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Affiliation(s)
- Aaron M. Dickey
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Timothy P. L. Smith
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael L. Clawson
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael P. Heaton
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Aspen M. Workman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
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26
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Herrera-Uribe J, Wiarda JE, Sivasankaran SK, Daharsh L, Liu H, Byrne KA, Smith TPL, Lunney JK, Loving CL, Tuggle CK. Reference Transcriptomes of Porcine Peripheral Immune Cells Created Through Bulk and Single-Cell RNA Sequencing. Front Genet 2021; 12:689406. [PMID: 34249103 PMCID: PMC8261551 DOI: 10.3389/fgene.2021.689406] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [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: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023] Open
Abstract
Pigs are a valuable human biomedical model and an important protein source supporting global food security. The transcriptomes of peripheral blood immune cells in pigs were defined at the bulk cell-type and single cell levels. First, eight cell types were isolated in bulk from peripheral blood mononuclear cells (PBMCs) by cell sorting, representing Myeloid, NK cells and specific populations of T and B-cells. Transcriptomes for each bulk population of cells were generated by RNA-seq with 10,974 expressed genes detected. Pairwise comparisons between cell types revealed specific expression, while enrichment analysis identified 1,885 to 3,591 significantly enriched genes across all 8 cell types. Gene Ontology analysis for the top 25% of significantly enriched genes (SEG) showed high enrichment of biological processes related to the nature of each cell type. Comparison of gene expression indicated highly significant correlations between pig cells and corresponding human PBMC bulk RNA-seq data available in Haemopedia. Second, higher resolution of distinct cell populations was obtained by single-cell RNA-sequencing (scRNA-seq) of PBMC. Seven PBMC samples were partitioned and sequenced that produced 28,810 single cell transcriptomes distributed across 36 clusters and classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, B-cell, conventional CD4 and CD8 αβ T-cells, NK cells, and γδ T-cells. Signature gene sets from the human Haemopedia data were assessed for relative enrichment in genes expressed in pig cells and integration of pig scRNA-seq with a public human scRNA-seq dataset provided further validation for similarity between human and pig data. The sorted porcine bulk RNAseq dataset informed classification of scRNA-seq PBMC populations; specifically, an integration of the datasets showed that the pig bulk RNAseq data helped define the CD4CD8 double-positive T-cell populations in the scRNA-seq data. Overall, the data provides deep and well-validated transcriptomic data from sorted PBMC populations and the first single-cell transcriptomic data for porcine PBMCs. This resource will be invaluable for annotation of pig genes controlling immunogenetic traits as part of the porcine Functional Annotation of Animal Genomes (FAANG) project, as well as further study of, and development of new reagents for, porcine immunology.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Jayne E. Wiarda
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
- Immunobiology Graduate Program, Iowa State University, Ames, IA, United States
- Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program, Oak Ridge, TN, United States
| | - Sathesh K. Sivasankaran
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
- Genome Informatics Facility, Iowa State University, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kristen A. Byrne
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | | | - Joan K. Lunney
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, United States
| | - Crystal L. Loving
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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27
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Liu R, Tearle R, Low WY, Chen T, Thomsen D, Smith TPL, Hiendleder S, Williams JL. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. BMC Genomics 2021; 22:410. [PMID: 34082698 PMCID: PMC8176687 DOI: 10.1186/s12864-021-07667-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses. Results In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. Conclusions These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07667-2.
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Affiliation(s)
- Ruijie Liu
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Tong Chen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Dana Thomsen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Timothy P L Smith
- USMARC, USDA-ARS-US Meat Animal Research Center, Clay Center, NE, USA
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Present address: Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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28
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Bakshy K, Heimeier D, Schwartz JC, Glass EJ, Wilkinson S, Skuce RA, Allen AR, Young J, McClure JC, Cole JB, Null DJ, Hammond JA, Smith TPL, Bickhart DM. Development of polymorphic markers in the immune gene complex loci of cattle. J Dairy Sci 2021; 104:6897-6908. [PMID: 33685702 DOI: 10.3168/jds.2020-19809] [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: 10/19/2020] [Accepted: 01/18/2021] [Indexed: 11/19/2022]
Abstract
The addition of cattle health and immunity traits to genomic selection indices holds promise to increase individual animal longevity and productivity, and decrease economic losses from disease. However, highly variable genomic loci that contain multiple immune-related genes were poorly assembled in the first iterations of the cattle reference genome assembly and underrepresented during the development of most commercial genotyping platforms. As a consequence, there is a paucity of genetic markers within these loci that may track haplotypes related to disease susceptibility. By using hierarchical assembly of bacterial artificial chromosome inserts spanning 3 of these immune-related gene regions, we were able to assemble multiple full-length haplotypes of the major histocompatibility complex, the leukocyte receptor complex, and the natural killer cell complex. Using these new assemblies and the recently released ARS-UCD1.2 reference, we aligned whole-genome shotgun reads from 125 sequenced Holstein bulls to discover candidate variants for genetic marker development. We selected 124 SNPs, using heuristic and statistical models to develop a custom genotyping panel. In a proof-of-principle study, we used this custom panel to genotype 1,797 Holstein cows exposed to bovine tuberculosis (bTB) that were the subject of a previous GWAS study using the Illumina BovineHD array. Although we did not identify any significant association of bTB phenotypes with these new genetic markers, 2 markers exhibited substantial effects on bTB phenotypic prediction. The models and parameters trained in this study serve as a guide for future marker discovery surveys particularly in previously unassembled regions of the cattle genome.
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Affiliation(s)
- K Bakshy
- Dairy Forage Research Center, USDA-ARS, Madison, WI 53706
| | - D Heimeier
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - J C Schwartz
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - E J Glass
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, Edinburgh, UK
| | - S Wilkinson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, Edinburgh, UK
| | - R A Skuce
- Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland BT4 3SD, UK
| | - A R Allen
- Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland BT4 3SD, UK
| | - J Young
- Dairy Forage Research Center, USDA-ARS, Madison, WI 53706
| | - J C McClure
- Dairy Forage Research Center, USDA-ARS, Madison, WI 53706
| | - J B Cole
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705
| | - D J Null
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705
| | - J A Hammond
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, UK
| | - T P L Smith
- Meat Animal Research Center, USDA-ARS, Clay Center, NE 68933
| | - D M Bickhart
- Dairy Forage Research Center, USDA-ARS, Madison, WI 53706.
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29
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Davenport KM, Massa AT, Bhattarai S, McKay SD, Mousel MR, Herndon MK, White SN, Cockett NE, Smith TPL, Murdoch BM. Characterizing Genetic Regulatory Elements in Ovine Tissues. Front Genet 2021; 12:628849. [PMID: 34093640 PMCID: PMC8173140 DOI: 10.3389/fgene.2021.628849] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/13/2020] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Nine chromatin states including active promoters, active enhancers, poised enhancers, repressed enhancers, and insulators were characterized in each tissue using ChromHMM. Whole-genome bisulfite sequencing (WGBS) was performed to determine the complement of whole-genome DNA methylation with the ChIP-seq data. Hypermethylated and hypomethylated regions were identified across tissues, and these locations were compared with chromatin states to better distinguish and validate regulatory elements in these tissues. Interestingly, chromatin states with the poised enhancer mark H3K4me1 in the spleen and cerebellum and CTCF in the liver displayed the greatest number of hypermethylated sites. Not surprisingly, active enhancers in the liver and spleen, and promoters in the cerebellum, displayed the greatest number of hypomethylated sites. Overall, chromatin states defined by histone marks and CTCF occupied approximately 22% of the genome in all three tissues. Furthermore, the liver and spleen displayed in common the greatest percent of active promoter (65%) and active enhancer (81%) states, and the liver and cerebellum displayed in common the greatest percent of poised enhancer (53%), repressed enhancer (68%), hypermethylated sites (75%), and hypomethylated sites (73%). In addition, both known and de novo CTCF-binding motifs were identified in all three tissues, with the highest number of unique motifs identified in the cerebellum. In summary, this study has identified the regulatory regions of genes in three tissues that play key roles in defining health and economically important traits and has set the precedent for the characterization of regulatory elements in ovine tissues using the Rambouillet reference genome.
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Affiliation(s)
- Kimberly M. Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, United States
| | - Alisha T. Massa
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | | | | | - Michelle R. Mousel
- USDA, ARS, Animal Disease Research Unit, Pullman, WA, United States
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States
| | - Maria K. Herndon
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Stephen N. White
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
- USDA, ARS, Animal Disease Research Unit, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | | | - Timothy P. L. Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, United States
| | - Brenda M. Murdoch
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
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30
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Kronenberg ZN, Rhie A, Koren S, Concepcion GT, Peluso P, Munson KM, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, Eichler EE, Williams JL, Smith TPL, Jarvis ED, Sullivan ST, Kingan SB. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nat Commun 2021; 12:1935. [PMID: 33911078 PMCID: PMC8081726 DOI: 10.1038/s41467-020-20536-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 05/13/2020] [Accepted: 11/12/2020] [Indexed: 01/27/2023] Open
Abstract
Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80-91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.
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Affiliation(s)
- Zev N Kronenberg
- Phase Genomics, Seattle, WA, USA.
- Pacific Biosciences, Menlo Park, CA, USA.
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kristen Kuhn
- US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA
| | | | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Olivier Fedrigo
- Vertebrate Genomes Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | | | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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31
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Trigo BB, Utsunomiya ATH, Fortunato AAAD, Milanesi M, Torrecilha RBP, Lamb H, Nguyen L, Ross EM, Hayes B, Padula RCM, Sussai TS, Zavarez LB, Cipriano RS, Caminhas MMT, Lopes FL, Pelle C, Leeb T, Bannasch D, Bickhart D, Smith TPL, Sonstegard TS, Garcia JF, Utsunomiya YT. Variants at the ASIP locus contribute to coat color darkening in Nellore cattle. Genet Sel Evol 2021; 53:40. [PMID: 33910501 PMCID: PMC8082809 DOI: 10.1186/s12711-021-00633-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 01/14/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. RESULTS We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. CONCLUSIONS Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.
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Affiliation(s)
- Beatriz B Trigo
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | - Adam T H Utsunomiya
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Alvaro A A D Fortunato
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,Personal-PEC, R. Sebastião Lima, 1336-Centro, Campo Grande, MS, 79004-600, Brazil
| | - Marco Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Rafaela B P Torrecilha
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil
| | - Harrison Lamb
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Loan Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Elizabeth M Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Ben Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | - Thayla S Sussai
- Centro Universitário Católico Salesiano, Araçatuba, SP, Brazil
| | - Ludmilla B Zavarez
- International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil
| | | | - Maria M T Caminhas
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | - Flavia L Lopes
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Dermfocus, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland
| | - Danika Bannasch
- Institute of Genetics, Vetsuisse-Faculty, University of Bern, Bremgartenstrasse 109A, 3012, Bern, Switzerland.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Derek Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Timothy P L Smith
- US. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE, 68933, USA
| | | | - José F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil.,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.,School of Agriculture and Veterinarian Sciences, Jaboticabal, Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University (Unesp), Jaboticabal, SP, Brazil
| | - Yuri T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, SP, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, SP, Brazil. .,AgroPartners Consulting, R. Floriano Peixoto, 120-Sala 43a-Centro, Araçatuba, SP, 16010-220, Brazil.
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32
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Perkin LC, Smith TPL, Oppert B. Variants in the Mitochondrial Genome Sequence of Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae). Insects 2021; 12:insects12050387. [PMID: 33925386 PMCID: PMC8146127 DOI: 10.3390/insects12050387] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 11/20/2022]
Abstract
Simple Summary The lesser grain borer damages grains in storage worldwide. The major control method for this beetle is phosphine fumigation, but the increase in resistant populations has led to a loss in phosphine efficacy. Insect mitochondria are the major source of energy, and some phosphine-resistant insects have reduced energy production. Therefore, we want to understand whether changes in the mitochondrial genome may promote phosphine resistance in insects, but we need an accurate mitogenome sequence and annotation. We extracted and sequenced genomic DNA from a laboratory colony of the lesser grain borer and assembled and annotated the mitochondrial genome. The mitochondrial genome sequence was similar in structure to other insect mitochondria and encoded typical mitochondrial genes. We compared our predicted mitochondrial genome sequence to that of another lesser grain borer strain from Jingziguan (China). While there was mostly agreement among the two sequences, the data will be used to determine if key differences may suggest mutations in the two populations related to phosphine control pressure. However, differences also could be the result in different genome sequences and interpretations. The data will be useful as a research tool to examine the expression of mitochondrial genes in phosphine susceptible and -resistant insect populations. Abstract The lesser grain borer, Rhyzopertha dominica, is a coleopteran pest of stored grains and is mainly controlled by phosphine fumigation, but the increase in phosphine-resistant populations threatens efficacy. Some phosphine-resistant insects have reduced respiration, and thus studying the mitochondrial genome may provide additional information regarding resistance. Genomic DNA from an inbred laboratory strain of R. dominica was extracted and sequenced with both short (Illumina) and long (Pacific Biosciences) read technologies for whole genome sequence assembly and annotation. Short read sequences were assembled and annotated by open software to identify mitochondrial sequences, and the assembled sequence was manually annotated and verified by long read sequences. The mitochondrial genome sequence for R. dominica had a total length of 15,724 bp and encoded 22 trna genes, 2 rRNA genes, 13 protein coding genes (7 nad subunits, 3 cox, 2 atp, and 1 cytB), flanked by a long control region. We compared our predicted mitochondrial genome to that of another from a R. dominica strain from Jingziguan (China). While there was mostly agreement between the two assemblies, key differences will be further examined to determine if mutations in populations are related to insecticide control pressure, mainly that of phosphine. Differences in sequence data, assembly, and annotation also may result in different genome interpretations.
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Affiliation(s)
- Lindsey C. Perkin
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX 77845, USA;
| | | | - Brenda Oppert
- USDA-ARS, Center for Grain and Animal Health Research, Manhattan, KS 66502, USA
- Correspondence: ; Tel.: +1-785-776-2780
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33
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Heaton MP, Smith TPL, Bickhart DM, Vander Ley BL, Kuehn LA, Oppenheimer J, Shafer WR, Schuetze FT, Stroud B, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Davenport KM, Kuhn KL, Green RE, Shapiro B, Rosen BD. A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus. J Hered 2021; 112:184-191. [PMID: 33438035 PMCID: PMC8006815 DOI: 10.1093/jhered/esab002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 11/20/2020] [Accepted: 01/11/2021] [Indexed: 12/22/2022] Open
Abstract
Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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Affiliation(s)
| | | | | | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TX
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD
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Dobson LK, Zimin A, Bayles D, Fritz-Waters E, Alt D, Olsen S, Blanchong J, Reecy J, Smith TPL, Derr JN. De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification. Anim Genet 2021; 52:263-274. [PMID: 33780561 DOI: 10.1111/age.13060] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 12/30/2022]
Abstract
Genomic tools have improved the ability to manage bison populations and enhanced efforts to conserve this iconic species. These tools have been particularly useful for detecting introgression of cattle genome within bison herds but are limited by the need to use the cattle genome as a surrogate for mapping reads. This complicates efforts to distinguish the species of origin of chromosomal segments in individual bison at the genomic level. An assembly (Bison_UMD1.0) based on 75X genome coverage by Illumina and 454 reads was generated using the MaSuRCA assembler, generating a 2.81 Gigbases de novo reference genome from American bison. Comparison of bison and domestic cattle references identified 28 443 364 single nucleotide variants and 2 627 645 insertions/deletions distinguishing the species. Sequence alignment of an additional 12 modern bison samples and two historic bison samples to domestic cattle and bison references provides a dataset of genomic variants defining the different species and within-species variation. This first annotated draft assembly represents a resource for the management and conservation of bison, as well as a means to study the effects on the genome of interspecies hybridization. The comparisons of historical bison sequences with the new bison reference identified genomic differences between modern and pre-population bottleneck bison. The results support the application of genomics to enhance future research on disease, the establishment of satellite conservation herds and insight into bison and cattle speciation. The first genome assembly for bison and dataset provides a foundation that can be built upon as genetic technologies improve over the years.
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Affiliation(s)
- L K Dobson
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, 77845, USA
| | - A Zimin
- Department of Biomedical Engineering, Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - D Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, 50010, USA
| | - E Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - D Alt
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, 50010, USA
| | - S Olsen
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, 50010, USA
| | - J Blanchong
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - J Reecy
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - T P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, Clay Center, NE, 68933, USA
| | - J N Derr
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, 77845, USA
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Oppenheimer J, Rosen BD, Heaton MP, Vander Ley BL, Shafer WR, Schuetze FT, Stroud B, Kuehn LA, McClure JC, Barfield JP, Blackburn HD, Kalbfleisch TS, Bickhart DM, Davenport KM, Kuhn KL, Green RE, Shapiro B, Smith TPL. A Reference Genome Assembly of American Bison, Bison bison bison. J Hered 2021; 112:174-183. [PMID: 33595645 PMCID: PMC8006816 DOI: 10.1093/jhered/esab003] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/13/2021] [Indexed: 11/14/2022] Open
Abstract
Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.
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Affiliation(s)
- Jonas Oppenheimer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Benjamin D Rosen
- USDA, ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Michael P Heaton
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Brian L Vander Ley
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | | | - Brad Stroud
- Stroud Veterinary Embryo Services, Weatherford, TE, USA
| | - Larry A Kuehn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | - Jennifer P Barfield
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Kimberly M Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, USA
| | - Kristen L Kuhn
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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36
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Dickey AM, Smith TPL, Clawson ML, Heaton MP, Workman AM. Classification of small ruminant lentivirus subtype A2, subgroups 1 and 2 based on whole genome comparisons and complex recombination patterns. F1000Res 2020; 9:1449. [PMID: 35035904 PMCID: PMC8749911 DOI: 10.12688/f1000research.27898.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/19/2021] [Indexed: 01/08/2024] Open
Abstract
Background: Small ruminant lentiviruses (SRLVs) cause a multisystemic chronic wasting disease in sheep across much of the world. SRLV subtype A2 is prevalent in North America and further classified into multiple subgroups based on variation in the group antigens gene (gag) and envelope (env) genes. In sheep, the ovine transmembrane protein 154 (TMEM154) gene is associated with SRLV susceptibility. Ewes with at least one copy of TMEM154 encoding a full-length protein with glutamate at position 35 (E35; haplotypes 2 and 3), are highly susceptible to SRLV infection while ewes with any combination of TMEM154 haplotypes which encodes lysine (K35; haplotype 1), or truncated proteins (haplotypes 4 and 6) are several times less so. A2 subgroups 1 and 2 are associated with host TMEM154 genotypes; subgroup 1 with the K35/K35 genotype and subgroup 2 with the E35/E35 genotype. Methods: Sequence variation within and among full-length assemblies of SRLV subtype A2 subgroups 1 and 2 was analyzed to identify genome-scale recombination patterns and subgroup-specific variants. Results: Consensus viral genomes were assembled from 23 infected sheep, including animals of assorted TMEM154 genotypes comprised of haplotypes 1, 2, or 3. Viral genome analysis identified viral subgroups 1 and 2 among the samples, and revealed additional sub-structure within subgroup 2 based on models predicting complex patterns of recombination between the two subgroups in several genomes. Animals with evidence of dual subgroup infection also possessed the most diverse quasi-species and the most highly recombined consensus genomes. After accounting for recombination, 413 subgroup diagnostic single nucleotide polymorphisms (SNPs) were identified. Conclusions: The viral subgroup framework developed to classify SRLV consensus genomes along a continuum of recombination suggests that animals with the TMEM154 E35/K35 genotype may represent a reservoir for producing viral genomes representing recombination between A2 subgroups 1 and 2.
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Affiliation(s)
- Aaron M. Dickey
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Timothy P. L. Smith
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael L. Clawson
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Michael P. Heaton
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Aspen M. Workman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE, 68933, USA
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Kolmogorov M, Bickhart DM, Behsaz B, Gurevich A, Rayko M, Shin SB, Kuhn K, Yuan J, Polevikov E, Smith TPL, Pevzner PA. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat Methods 2020; 17:1103-1110. [PMID: 33020656 PMCID: PMC10699202 DOI: 10.1038/s41592-020-00971-x] [Citation(s) in RCA: 286] [Impact Index Per Article: 71.5] [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: 07/16/2020] [Revised: 08/22/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
Abstract
Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.
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Affiliation(s)
- Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Derek M Bickhart
- Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, USA
| | - Bahar Behsaz
- Graduate Program in Bioinformatics and System Biology, University of California, San Diego, CA, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Mikhail Rayko
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - Sung Bong Shin
- USDA-ARS US Meat Animal Research Center, Clay Center, NE, USA
| | - Kristen Kuhn
- USDA-ARS US Meat Animal Research Center, Clay Center, NE, USA
| | - Jeffrey Yuan
- Graduate Program in Bioinformatics and System Biology, University of California, San Diego, CA, USA
| | - Evgeny Polevikov
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | | | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, CA, USA.
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38
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Salavati M, Caulton A, Clark R, Gazova I, Smith TPL, Worley KC, Cockett NE, Archibald AL, Clarke SM, Murdoch BM, Clark EL. Global Analysis of Transcription Start Sites in the New Ovine Reference Genome ( Oar rambouillet v1.0). Front Genet 2020; 11:580580. [PMID: 33193703 PMCID: PMC7645153 DOI: 10.3389/fgene.2020.580580] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/09/2020] [Indexed: 02/04/2023] Open
Abstract
The overall aim of the Ovine FAANG project is to provide a comprehensive annotation of the new highly contiguous sheep reference genome sequence (Oar rambouillet v1.0). Mapping of transcription start sites (TSS) is a key first step in understanding transcript regulation and diversity. Using 56 tissue samples collected from the reference ewe Benz2616, we have performed a global analysis of TSS and TSS-Enhancer clusters using Cap Analysis Gene Expression (CAGE) sequencing. CAGE measures RNA expression by 5' cap-trapping and has been specifically designed to allow the characterization of TSS within promoters to single-nucleotide resolution. We have adapted an analysis pipeline that uses TagDust2 for clean-up and trimming, Bowtie2 for mapping, CAGEfightR for clustering, and the Integrative Genomics Viewer (IGV) for visualization. Mapping of CAGE tags indicated that the expression levels of CAGE tag clusters varied across tissues. Expression profiles across tissues were validated using corresponding polyA+ mRNA-Seq data from the same samples. After removal of CAGE tags with <10 read counts, 39.3% of TSS overlapped with 5' ends of 31,113 transcripts that had been previously annotated by NCBI (out of a total of 56,308 from the NCBI annotation). For 25,195 of the transcripts, previously annotated by NCBI, no TSS meeting stringent criteria were identified. A further 14.7% of TSS mapped to within 50 bp of annotated promoter regions. Intersecting these predicted TSS regions with annotated promoter regions (±50 bp) revealed 46% of the predicted TSS were "novel" and previously un-annotated. Using whole-genome bisulfite sequencing data from the same tissues, we were able to determine that a proportion of these "novel" TSS were hypo-methylated (32.2%) indicating that they are likely to be reproducible rather than "noise". This global analysis of TSS in sheep will significantly enhance the annotation of gene models in the new ovine reference assembly. Our analyses provide one of the highest resolution annotations of transcript regulation and diversity in a livestock species to date.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Alex Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Richard Clark
- Genetics Core, Edinburgh Clinical Research Facility, The University of Edinburgh, Edinburgh, United Kingdom
| | - Iveta Gazova
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, The University of Edinburgh, Edinburgh, United Kingdom
| | - Timothy P. L. Smith
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Kim C. Worley
- Baylor College of Medicine, Houston, TX, United States
| | - Noelle E. Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, United States
| | - Alan L. Archibald
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Emily L. Clark
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
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39
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Clawson ML, Schuller G, Dickey AM, Bono JL, Murray RW, Sweeney MT, Apley MD, DeDonder KD, Capik SF, Larson RL, Lubbers BV, White BJ, Blom J, Chitko-McKown CG, Brichta-Harhay DM, Smith TPL. Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica. BMC Microbiol 2020; 20:250. [PMID: 32787780 PMCID: PMC7424683 DOI: 10.1186/s12866-020-01932-2] [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: 12/10/2019] [Accepted: 07/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Mannheimia haemolytica strains isolated from North American cattle have been classified into two genotypes (1 and 2). Although members of both genotypes have been isolated from the upper and lower respiratory tracts of cattle with or without bovine respiratory disease (BRD), genotype 2 strains are much more frequently isolated from diseased lungs than genotype 1 strains. The mechanisms behind the increased association of genotype 2 M. haemolytica with BRD are not fully understood. To address that, and to search for interventions against genotype 2 M. haemolytica, complete, closed chromosome assemblies for 35 genotype 1 and 34 genotype 2 strains were generated and compared. Searches were conducted for the pan genome, core genes shared between the genotypes, and for genes specific to either genotype. Additionally, genes encoding outer membrane proteins (OMPs) specific to genotype 2 M. haemolytica were identified, and the diversity of their protein isoforms was characterized with predominantly unassembled, short-read genomic sequences for up to 1075 additional strains. RESULTS The pan genome of the 69 sequenced M. haemolytica strains consisted of 3111 genes, of which 1880 comprised a shared core between the genotypes. A core of 112 and 179 genes or gene variants were specific to genotype 1 and 2, respectively. Seven genes encoding predicted OMPs; a peptidase S6, a ligand-gated channel, an autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BD-CP), a porin, and three different trimeric autotransporter adhesins were specific to genotype 2 as their genotype 1 homologs were either pseudogenes, or not detected. The AOMB-BD-CP gene, however, appeared to be truncated across all examined genotype 2 strains and to likely encode dysfunctional protein. Homologous gene sequences from additional M. haemolytica strains confirmed the specificity of the remaining six genotype 2 OMP genes and revealed they encoded low isoform diversity at the population level. CONCLUSION Genotype 2 M. haemolytica possess genes encoding conserved OMPs not found intact in more commensally prone genotype 1 strains. Some of the genotype 2 specific genes identified in this study are likely to have important biological roles in the pathogenicity of genotype 2 M. haemolytica, which is the primary bacterial cause of BRD.
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Affiliation(s)
- Michael L Clawson
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA.
| | - Gennie Schuller
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Aaron M Dickey
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - James L Bono
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | | | | | | | - Keith D DeDonder
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS, USA
| | - Sarah F Capik
- Texas A&M AgriLife Research, Texas A&M University System, Amarillo, TX, USA
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | | | | | | | - Jochen Blom
- Justus-Liebig-University Giessen, Giessen, Hesse, Germany
| | - Carol G Chitko-McKown
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Dayna M Brichta-Harhay
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Timothy P L Smith
- United States Department of Agriculture, Genetics, Breeding, and Animal Health Research Unit, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, USA
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40
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Myer PR, McDaneld TG, Kuehn LA, Dedonder KD, Apley MD, Capik SF, Lubbers BV, Harhay GP, Harhay DM, Keele JW, Henniger MT, Clemmons BA, Smith TPL. Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing. PLoS One 2020; 15:e0235498. [PMID: 32658916 PMCID: PMC7357769 DOI: 10.1371/journal.pone.0235498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Surveys of microbial populations in environmental niches of interest often utilize sequence variation in the gene encoding the ribosomal small subunit (the 16S rRNA gene). Generally, these surveys target the 16S genes using semi-degenerate primers to amplify portions of a subset of bacterial species, sequence the amplicons in bulk, and assign to putative taxonomic categories by comparison to databases purporting to connect specific sequences in the main variable regions of the gene to specific organisms. Due to sequence length constraints of the most popular bulk sequencing platforms, the primers selected amplify one to three of the nine variable regions, and taxonomic assignment is based on relatively short stretches of sequence (150-500 bases). We demonstrate that taxonomic assignment is improved through reduced unassigned reads by including a survey of near-full-length sequences specific to the target environment, using a niche of interest represented by the upper respiratory tract (URT) of cattle. We created a custom Bovine URT database from these longer sequences for assignment of shorter, less expensive reads in comparisons of the upper respiratory tract among individual animals. This process improves the ability to detect changes in the microbial populations of a given environment, and the accuracy of defining the content of that environment at increasingly higher taxonomic resolution.
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Affiliation(s)
- Phillip R. Myer
- Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Tara G. McDaneld
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Larry A. Kuehn
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Keith D. Dedonder
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Michael D. Apley
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Sarah F. Capik
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Brian V. Lubbers
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States of America
| | - Gregory P. Harhay
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Dayna M. Harhay
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - John W. Keele
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
| | - Madison T. Henniger
- Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Brooke A. Clemmons
- Department of Animal Science, University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States of America
| | - Timothy P. L. Smith
- USDA-ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States of America
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Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 2020; 9:5858065. [PMID: 32543654 PMCID: PMC7448572 DOI: 10.1093/gigascience/giaa051] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [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: 10/28/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 01/05/2023] Open
Abstract
Background The domestic pig (Sus scrofa) is important both as a food source and
as a biomedical model given its similarity in size, anatomy, physiology, metabolism,
pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a
purebred Duroc female pig established using older clone-based sequencing methods was
incomplete, and unresolved redundancies, short-range order and orientation errors, and
associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created
with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the
same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0).
Both assemblies are of substantially higher (>90-fold) continuity and accuracy than
Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read
assemblies provide an unprecedented view of the genetic make-up of this important
agricultural and biomedical model species. We propose that the improved Duroc assembly
(Sscrofa11.1) become the reference genome for genomic research in pigs.
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Affiliation(s)
- Amanda Warr
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Nabeel Affara
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamid Beiki
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lel Eory
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Heather A Finlayson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Carlos G Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Richard Hall
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | | | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane QLD 4104, Australia
| | - Osagie Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristi Kim
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Haibou Liu
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Nancy Manchanda
- Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Dan J Nonneman
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Gary A Rohrer
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Carole A Sargent
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | | | - Ben M Skinner
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Richard Talbot
- Edinburgh Genomics, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Christopher K Tuggle
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA.,Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AWC, Heaton MP, Phillippy AM, Hiendleder S, Smith TPL, Williams JL. Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nat Commun 2020; 11:2071. [PMID: 32350247 PMCID: PMC7190621 DOI: 10.1038/s41467-020-15848-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [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: 08/20/2019] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the two genomes. Here we report a haplotype-aware scaffolding and polishing pipeline which was used to create haplotype-resolved, chromosome-level genome assemblies of Angus (taurine) and Brahman (indicine) cattle subspecies from contigs generated by the trio binning method. These assemblies reveal structural and copy number variants that differentiate the subspecies and that variant detection is sensitive to the specific reference genome chosen. Six genes with immune related functions have additional copies in the indicine compared with taurine lineage and an indicus-specific extra copy of fatty acid desaturase is under positive selection. The haplotyped genomes also enable transcripts to be phased to detect allele-specific expression. This work exemplifies the value of haplotype-resolved genomes to better explore evolutionary and functional variations.
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Affiliation(s)
- Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Rick Tearle
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Ruijie Liu
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD, USA
| | - Zev N Kronenberg
- Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA, 98195, USA
| | | | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jay Ghurye
- Center for Bioinformatics and Computational Biology, Lab 3104A, Biomolecular Science Building, University of Maryland, College Park, MD, 20742, USA
| | | | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | | | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
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Bickhart DM, McClure JC, Schnabel RD, Rosen BD, Medrano JF, Smith TPL. Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection. J Dairy Sci 2020; 103:5278-5290. [PMID: 32331872 DOI: 10.3168/jds.2019-17693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/01/2019] [Accepted: 12/03/2019] [Indexed: 11/19/2022]
Abstract
The cattle reference genome assembly has underpinned major innovations in beef and dairy genetics through genome-enabled selection, including removal of deleterious recessive variants and selection for favorable alleles affecting quantitative production traits. The initial reference assemblies, up to and including UMD3.1 and Btau4.1, were based on a combination of clone-by-clone sequencing of bacterial artificial chromosome clones generated from blood DNA of a Hereford bull and whole-genome shotgun sequencing of blood DNA from his inbred daughter/granddaughter named L1 Dominette 01449 (Dominette). The approach introduced assembly gaps, misassemblies, and errors, and it limited the ability to assemble regions that undergo rearrangement in blood cells, such as immune gene clusters. Nonetheless, the reference supported the creation of genotyping tools and provided a basis for many studies of gene expression. Recently, long-read sequencing technologies have emerged that facilitated a re-assembly of the reference genome, using lung tissue from Dominette to resolve many of the problems and providing a bridge to place historical studies in common context. The new reference, ARS-UCD1.2, successfully assembled germline immune gene clusters and improved overall continuity (i.e., reduction of gaps and inversions) by over 250-fold. This reference properly places nearly all of the legacy genetic markers used for over a decade in the industry. In this review, we discuss the improvements made to the cattle reference; remaining issues present in the assembly; tools developed to support genome-based studies in beef and dairy cattle; and the emergence of newer genome assembly methods that are producing even higher-quality assemblies for other breeds of cattle at a fraction of the cost. The new frontier for cattle genomics research will likely include a transition from the individual Hereford reference genome, to a "pan-genome" reference, representing all the DNA segments existing in commonly used cattle breeds, bringing the cattle reference into line with the current direction of human genome research.
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Affiliation(s)
- D M Bickhart
- US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53705.
| | - J C McClure
- US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI 53705
| | - R D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211; MU Institute for Data Science and Informatics, University of Missouri, Columbia, 65211
| | - B D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - J F Medrano
- Department of Animal Science, University of California Davis, 95616
| | - T P L Smith
- Meat Animal Research Center, Agricultural Research Service, USDA, Clay Center, NE 68933
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Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D. Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO. Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. Gigascience 2020; 9:giaa027. [PMID: 32236524 PMCID: PMC7111595 DOI: 10.1093/gigascience/giaa027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 10/21/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties. FINDINGS Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy. CONCLUSIONS GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield Road, Cairns, QLD 4878, Australia
- John Curtin School of Medical Research, Australian National University, Garran Rd, Canberra, ACT 2600, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Baltimore Ave, Beltsville, MD 20705, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
| | - Eva K F Chan
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Andre E Minoche
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales Sydney, Victoria Street, Darlinghurst NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Kirston Barton
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Ruth J Lyons
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Vanessa M Hayes
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
- Central Clinical School, University of Sydney, Parramatta Road, Camperdown, NSW 2050, Australia
| | - Arina D. Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Zane Colaric
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany
| | - Ksenia Skvortsova
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Martin A Smith
- Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010, Australia
- Faculty of Medicine, UNSW Sydney, High St, Kensington, NSW 2052, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Plaza, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Main St, Houston, TX 77005, USA
- Center for Theoretical and Biological Physics, Rice University, Main St, Houston, TX 77005, USA
- Broad Institute of MIT and Harvard, Main St, Cambridge, MA 02142, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, ShanghaiTech University, Huaxia Middle Rd, Pudong 201210, China
| | - Timothy P L Smith
- US Meat Animal Research Center, Agricultural Research Service USDA, Rd 313, Clay Center, NE 68933, USA
| | - Robert A Zammit
- Vineyard Veterinary Hospital, Windsor Rd, Vineyard, NSW 2765, Australia
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, High St, Kensington, NSW 2052, Australia
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Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Ley BV, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TPL. Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle. Gigascience 2020; 9:giaa029. [PMID: 32242610 PMCID: PMC7118895 DOI: 10.1093/gigascience/giaa029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 10/01/2019] [Revised: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The development of trio binning as an approach for assembling diploid genomes has enabled the creation of fully haplotype-resolved reference genomes. Unlike other methods of assembly for diploid genomes, this approach is enhanced, rather than hindered, by the heterozygosity of the individual sequenced. To maximize heterozygosity and simultaneously assemble reference genomes for 2 species, we applied trio binning to an interspecies F1 hybrid of yak (Bos grunniens) and cattle (Bos taurus), 2 species that diverged nearly 5 million years ago. The genomes of both of these species are composed of acrocentric autosomes. RESULTS We produced the most continuous haplotype-resolved assemblies for a diploid animal yet reported. Both the maternal (yak) and paternal (cattle) assemblies have the largest 2 chromosomes in single haplotigs, and more than one-third of the autosomes similarly lack gaps. The maximum length haplotig produced was 153 Mb without any scaffolding or gap-filling steps and represents the longest haplotig reported for any species. The assemblies are also more complete and accurate than those reported for most other vertebrates, with 97% of mammalian universal single-copy orthologs present. CONCLUSIONS The high heterozygosity inherent to interspecies crosses maximizes the effectiveness of the trio binning method. The interspecies trio binning approach we describe is likely to provide the highest-quality assemblies for any pair of species that can interbreed to produce hybrid offspring that develop to sufficient cell numbers for DNA extraction.
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Affiliation(s)
- Edward S Rice
- Department of Animal Science, University of Nebraska–Lincoln, C203 ANSC, Lincoln, NE 68583, USA
- Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Michael P Heaton
- US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA
| | - Theodore S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, 1400 Nicholasville Rd., Lexington, KY 40546, USA
| | | | | | - Derek M Bickhart
- Dairy Forage Research Center, 1925 Linden Drive, ARS USDA, Madison, WI 53706, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, 10300 Baltimore Ave., ARS USDA, Beltsville, MD 20705, USA
| | - Brian Vander Ley
- Great Plains Veterinary Educational Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska–Lincoln, 820 Road 313, Clay Center, NE 68933, USA
| | - Nicholas W Maurer
- Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, 1156 High St., Santa Cruz, CA 95064, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska–Lincoln, C203 ANSC, Lincoln, NE 68583, USA
| | - Timothy P L Smith
- US Meat Animal Research Center, US Department of Agriculture, State Spur 18D, Clay Center, NE 68933, USA
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Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, Thibaud-Nissen F, Hoffman J, Murdoch BM, Snelling WM, McDaneld TG, Hammond JA, Schwartz JC, Nandolo W, Hagen DE, Dreischer C, Schultheiss SJ, Schroeder SG, Phillippy AM, Cole JB, Van Tassell CP, Liu G, Smith TPL, Medrano JF. De novo assembly of the cattle reference genome with single-molecule sequencing. Gigascience 2020; 9:5810242. [PMID: 32191811 PMCID: PMC7081964 DOI: 10.1093/gigascience/giaa021] [Citation(s) in RCA: 299] [Impact Index Per Article: 74.8] [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: 09/24/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. RESULTS We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. CONCLUSIONS We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.
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Affiliation(s)
- Benjamin D Rosen
- USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Troy N Rowan
- Division of Animal Sciences, University of Missouri, 162 Animal Science Research Center, Columbia, MO 65211, USA
| | - Wai Y Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Aleksey Zimin
- Johns Hopkins University, Welch Library of Medicine, Ste 105, 1900 E. Monument St., Baltimore, MD 21205, USA
| | - Christine Couldrey
- Livestock Improvement Corporation, Private Bag 3016, Hamilton 3240, New Zealand
| | - Richard Hall
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Wenli Li
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI, 53706, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jay Ghurye
- Department of Computer Science, University of Maryland, 8125 Paint Branch Drive, College Park, MD 20742 USA
| | - Stephanie D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Brenda M Murdoch
- Department of Animal and Veterinary Science, University of Idaho, 875 Perimeter Drive MS 2330, Moscow, ID 83844-2330, USA
| | - Warren M Snelling
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA
| | - Tara G McDaneld
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA
| | | | | | - Wilson Nandolo
- Division of Livestock Sciences, University of Natural Resources and Life Sciences, Gregor Mendel str. 33, A-1180, Vienna, Austria.,Animal Science Department, Lilongwe University of Agriculture and Natural Resources, P.O. Box 219, Lilongwe, Malawi
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, 101 Animal Science Building, Stillwater, OK 74078, USA
| | | | | | - Steven G Schroeder
- USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - John B Cole
- USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA
| | - Curtis P Van Tassell
- USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA
| | - George Liu
- USDA-ARS, Beltsville, MD, 20705-2350 , Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Ave, Beltsville, MD 20705-2350, USA
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, USDA-ARS, 844 Road 313, Clay Center, NE 68933, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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47
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Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes. BMC Genomics 2019; 20:1000. [PMID: 31856728 PMCID: PMC6923926 DOI: 10.1186/s12864-019-6364-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 07/26/2019] [Accepted: 12/02/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial evolutionary changes and accumulated male specific genes and genes involved in sex determination. The pseudoautosomal region (PAR) is conserved on the X and Y and pair during meiosis. The structure, evolution and function of mammalian sex chromosomes, particularly the Y chromsome, is still poorly understood because few species have high quality sex chromosome assemblies. RESULTS Here we report the first bovine sex chromosome assemblies that include the complete PAR spanning 6.84 Mb and three Y chromosome X-degenerate (X-d) regions. The PAR comprises 31 genes, including genes that are missing from the X chromosome in current cattle, sheep and goat reference genomes. Twenty-nine PAR genes are single-copy genes and two are multi-copy gene families, OBP, which has 3 copies and BDA20, which has 4 copies. The Y chromosome X-d1, 2a and 2b regions contain 11, 2 and 2 gametologs, respectively. CONCLUSIONS The ruminant PAR comprises 31 genes and is similar to the PAR of pig and dog but extends further than those of human and horse. Differences in the pseudoautosomal boundaries are consistent with evolutionary divergence times. A bovidae-specific expansion of members of the lipocalin gene family in the PAR reported here, may affect immune-modulation and anti-inflammatory responses in ruminants. Comparison of the X-d regions of Y chromosomes across species revealed that five of the X-Y gametologs, which are known to be global regulators of gene activity and candidate sexual dimorphism genes, are conserved.
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Affiliation(s)
- Ruijie Liu
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
| | - Rick Tearle
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jay Ghurye
- Center for Bioinformatics and Computational Biology, Lab 3104A, Biomolecular Science Building, University of Maryland, College Park, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, MD, USA
| | - Derek M Bickhart
- Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, WI, USA
| | | | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia
| | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia.
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48
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Harhay GP, Harhay DM, Bono JL, Capik SF, DeDonder KD, Apley MD, Lubbers BV, White BJ, Larson RL, Smith TPL. A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats. Sci Rep 2019; 9:18087. [PMID: 31792233 PMCID: PMC6889271 DOI: 10.1038/s41598-019-53866-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 01/31/2019] [Accepted: 11/04/2019] [Indexed: 01/17/2023] Open
Abstract
The virulence and pathogenicity of bacterial pathogens are related to their adaptability to changing environments. One process enabling adaptation is based on minor changes in genome sequence, as small as a few base pairs, within segments of genome called simple sequence repeats (SSRs) that consist of multiple copies of a short sequence (from one to several nucleotides), repeated in series. SSRs are found in eukaryotes as well as prokaryotes, and length variation in them occurs at frequencies up to a million-fold higher than bacterial point mutations through the process of slipped strand mispairing (SSM) by DNA polymerase during replication. The characterization of SSR length by standard sequencing methods is complicated by the appearance of length variation introduced during the sequencing process that obscures the lower abundance repeat number variants in a population. Here we report a computational approach to correct for sequencing process-induced artifacts, validated for tetranucleotide repeats by use of synthetic constructs of fixed, known length. We apply this method to a laboratory culture of Histophilus somni, prepared from a single colony, and demonstrate that the culture consists of populations of distinct sequence phase and length variants at individual tetranucleotide SSR loci.
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Affiliation(s)
- Gregory P Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States.
| | - Dayna M Harhay
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - James L Bono
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
| | - Sarah F Capik
- Texas A&M AgriLife Research, Amarillo, TX and the College of Veterinary Medicine & Biomedical Sciences, Texas A&M University System, College Station, TX, United States
| | - Keith D DeDonder
- Veterinary and Biomedical Research Center, Inc, Manhattan, KS, United States
| | - Michael D Apley
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Brian V Lubbers
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Bradley J White
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Robert L Larson
- Kansas State University, College of Veterinary Medicine, Manhattan, KS, United States
| | - Timothy P L Smith
- USDA ARS US Meat Animal Research Center, Clay Center, NE, United States
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49
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Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biol 2019; 20:153. [PMID: 31375138 PMCID: PMC6676630 DOI: 10.1186/s13059-019-1760-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 12/08/2018] [Accepted: 07/02/2019] [Indexed: 11/10/2022] Open
Abstract
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
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Affiliation(s)
- Derek M Bickhart
- Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA
| | - Mick Watson
- Division of Genetics and Genomics, The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Kevin Panke-Buisse
- Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA
| | - Laura M Cersosimo
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | | | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kiranmayee Bakshy
- Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA
| | | | | | - Phillip R Myer
- Department of Animal Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jay Ghurye
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Mihai Pop
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Paul J Weimer
- Cell Wall Biology and Utilization Laboratory, Dairy Forage Research Center, USDA, Madison, WI, 53706, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.
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50
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Henniger MT, Myer PR, Smith TPL, McDaneld TG, Kuehn LA, Keele JW. PSI-17 A 16S rDNA reference database of the deep-nasopharynx in steers for bacterial community analysis of cattle with bovine respiratory disease complex. J Anim Sci 2019. [DOI: 10.1093/jas/skz122.442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Bovine respiratory disease complex (BRDC) is caused by a variety of complex factors that involves host elements, environmental elements, inadequate management and housing, as well as viral and bacterial pathogens, such as Mannheimia haemolytica and Mycoplasma bovis. The objective of the study was to develop and evaluate a deep-nasopharyngeal bacterial community database to provide greater assignment of taxa within the bovine nasopharynx and as a site-specific tool for examining microbiome dysbioses involved in BRDC. A total of 180 cattle with an overall BW ranging from 164-269 kg were obtained from Athens, Tennessee (n = 60), Maryville, Missouri (n = 60), and Richmond, Kentucky (n = 60). Cattle were transported to a feeding facility in Kansas and housed in open air, dirt floor, group housing pens. At the first diagnosis of BRD, deep nasopharyngeal samples were collected. DNA library preparation of the bacterial 16S rRNA V1–V8 hypervariable regions was performed and sequenced on the Pacific Biosciences RSII instrument. Database construction and all sequencing data were curated using mothur (v1.39.5). For validation analyses using, a subset of cattle was sampled as described above, and three samples sequenced using the V1–V3 hypervariable 16SrRNA regions and the Illumina MiSeq. In the database, Mycoplasma accounted for over 57% of the reads and Mannheimia was present at 0.7%. When validating the database using short-reads, unassigned taxa in the Greengenes analysis was 4.22% contrasted to the 0.91% of the closed reference database analysis. The two taxonomic compositions were not correlated and the correlation was statistically significant (r = -0127; P = 0.001). All alpha diversity indices between the two analysis methods differed (P < 0.05). Development of this reference database provides researchers a tool with considerable improvements in performance for the analysis of bacterial communities in the nasopharynx relating to cattle diagnosed with BRDC.
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