1
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Prall TM, Karl JA, Varghese JM, Baker DA, Minor NR, Raveendran M, Harris RA, Rogers J, Wiseman RW, O’Connor DH. Complete Genomic Assembly of Mauritian Cynomolgus Macaque Killer Ig-like Receptor and Natural Killer Group 2 Haplotypes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1754-1765. [PMID: 38639635 PMCID: PMC11102026 DOI: 10.4049/jimmunol.2300856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/24/2024] [Indexed: 04/20/2024]
Abstract
Mauritian-origin cynomolgus macaques (MCMs) serve as a powerful nonhuman primate model in biomedical research due to their unique genetic homogeneity, which simplifies experimental designs. Despite their extensive use, a comprehensive understanding of crucial immune-regulating gene families, particularly killer Ig-like receptors (KIR) and NK group 2 (NKG2), has been hindered by the lack of detailed genomic reference assemblies. In this study, we employ advanced long-read sequencing techniques to completely assemble eight KIR and seven NKG2 genomic haplotypes, providing an extensive insight into the structural and allelic diversity of these immunoregulatory gene clusters. Leveraging these genomic resources, we prototype a strategy for genotyping KIR and NKG2 using short-read, whole-exome capture data, illustrating the potential for cost-effective multilocus genotyping at colony scale. These results mark a significant enhancement for biomedical research in MCMs and underscore the feasibility of broad-scale genetic investigations.
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Affiliation(s)
- Trent M. Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
| | - Julie A. Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
| | - Joshua M. Varghese
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
| | - David A. Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
| | - Nicholas R. Minor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Jeffery Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Roger W. Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin–Madison, Madison, WI
- Wisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI
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2
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Jang YJ, Park BY, Tae HJ, Sim J, Ahn D. Whole-exome sequencing analysis of patent ductus arteriosus in a Japanese macaque (Macaca fuscata). J Med Primatol 2024; 53:e12686. [PMID: 37990472 DOI: 10.1111/jmp.12686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023]
Abstract
We performed whole-exome sequencing using a human exome capture kit to analyze the potential genetic factors related to patent ductus arteriosus in Japanese macaques. Compared with the reference sequences of other primates, we identified potential missense variants in five genes: ADAM15, AZGP1, CSPG4, TNFRSF13B, and EPOR.
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Affiliation(s)
- Young-Jin Jang
- Department of Veterinary Medicine, College of Veterinary Medicine and Institute of Animal Transplantation, Jeonbuk National University, Iksan-si, Jeollabuk-do, South Korea
| | - Byung-Yong Park
- Department of Veterinary Medicine, College of Veterinary Medicine and Institute of Animal Transplantation, Jeonbuk National University, Iksan-si, Jeollabuk-do, South Korea
| | - Hyun-Jin Tae
- Department of Veterinary Medicine, College of Veterinary Medicine and Institute of Animal Transplantation, Jeonbuk National University, Iksan-si, Jeollabuk-do, South Korea
| | - Jeoungha Sim
- Department of Nursing, College of Medical Science, Jeonju University, Jeonju-si, Jeollabuk-do, South Korea
| | - Dongchoon Ahn
- Department of Veterinary Medicine, College of Veterinary Medicine and Institute of Animal Transplantation, Jeonbuk National University, Iksan-si, Jeollabuk-do, South Korea
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3
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Forthman M, Gordon ERL, Kimball RT. Low hybridization temperatures improve target capture success of invertebrate loci: a case study of leaf-footed bugs (Hemiptera: Coreoidea). ROYAL SOCIETY OPEN SCIENCE 2023; 10:230307. [PMID: 37388308 PMCID: PMC10300676 DOI: 10.1098/rsos.230307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023]
Abstract
Target capture is widely used in phylogenomic, ecological and functional genomic studies. Bait sets that allow capture from a diversity of species can be advantageous, but high-sequence divergence from baits can limit yields. Currently, only four experimental comparisons of a critical target capture parameter, hybridization temperature, have been published. These have been in vertebrates, where bait divergences are typically low, and none include invertebrates where bait-target divergences may be higher. Most invertebrate capture studies use a fixed, high hybridization temperature to maximize the proportion of on-target data, but many report low locus recovery. Using leaf-footed bugs (Hemiptera: Coreoidea), we investigate the effect of hybridization temperature on capture success of ultraconserved elements targeted by (i) baits developed from divergent hemipteran genomes and (ii) baits developed from less divergent coreoid transcriptomes. Lower temperatures generally resulted in more contigs and improved recovery of targets despite a lower proportion of on-target reads, lower read depth and more putative paralogues. Hybridization temperatures had less of an effect when using transcriptome-derived baits, which is probably due to lower bait-target divergences and greater bait tiling density. Thus, accommodating low hybridization temperatures during target capture can provide a cost-effective, widely applicable solution to improve invertebrate locus recovery.
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Affiliation(s)
- Michael Forthman
- California State Collection of Arthropods, Plant Pest Diagnostics Branch, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- Entomology and Nematology Department, University of Florida, 1881 Natural Area Drive, Gainesville, FL 32611, USA
| | - Eric R. L. Gordon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, 876 Newell Drive, Gainesville, FL 32611, USA
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4
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Pacheco C, Lobo D, Silva P, Álvares F, García EJ, Castro D, Layna JF, López-Bao JV, Godinho R. Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.970249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.
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5
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Ishengoma E, Rhode C. Using SPAdes, AUGUSTUS, and BLAST in an Automated Pipeline for Clustering Homologous Exome Sequences. Curr Protoc 2022; 2:e449. [PMID: 35612494 DOI: 10.1002/cpz1.449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cross-species exome sequencing approaches provide unprecedented avenues for obtaining genetic diversity, evolutionary relationships, and functional information from a variety of organisms including non-model species. These approaches offer cost-effective opportunities to study multiple individuals or species in parallel, but also create bioinformatics challenges in the application of multiple but powerful bioinformatics tools for the identification of homologous gene families across individual or species boundaries. Popular tools of this kind include SPAdes for sequence assembly, AUGUSTUS for ab initio gene prediction, and BLAST for building homologous sequence families. These tools can also be sophisticated in terms of installation and usage. Here, we present detailed steps on how to run these tools for the recovery and clustering of exon sequences from cross-species raw exome-capture data into homologous sequence families. We also present a utility pipeline, CODSEQCP, that automates these steps to cluster exon sequences, facilitating population genomics and evolutionary studies. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Reads assembly using SPAdes Basic Protocol 2: Coding sequence extraction using AUGUSTUS Basic Protocol 3: Sequence clustering using BLAST Alternate Protocol: How to run CODSEQCP.
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Affiliation(s)
- Edson Ishengoma
- Department of Biological Sciences, Mkwawa University College of Education, University of Dar es Salaam, Tanzania.,Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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6
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Gunady EF, Ware KE, Hoskinson Plumlee S, Devos N, Corcoran D, Prinz J, Misetic H, Ciccarelli FD, Harrison TM, Thorne JL, Schopler R, Everitt JI, Eward WC, Somarelli JA. Exome sequencing of hepatocellular carcinoma in lemurs identifies potential cancer drivers: A pilot study. Evol Med Public Health 2022; 10:221-230. [PMID: 35557512 PMCID: PMC9086584 DOI: 10.1093/emph/eoac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/17/2022] [Indexed: 11/24/2022] Open
Abstract
Background and objectives Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers in this group is unknown. Characterizing the genetic changes associated with hepatocellular carcinoma in prosimians may point to possible causes, treatments and methods of prevention, aiding conservation efforts that are particularly crucial to the survival of endangered lemurs. Although genomic studies of cancer in non-human primates have been hampered by a lack of tools, recent studies have demonstrated the efficacy of using human exome capture reagents across primates. Methodology In this proof-of-principle study, we applied human exome capture reagents to tumor-normal pairs from five lemurs with hepatocellular carcinoma to characterize the mutational landscape of this disease in lemurs. Results Several genes implicated in human hepatocellular carcinoma, including ARID1A, TP53 and CTNNB1, were mutated in multiple lemurs, and analysis of cancer driver genes mutated in these samples identified enrichment of genes involved with TP53 degradation and regulation. In addition to these similarities with human hepatocellular carcinoma, we also noted unique features, including six genes that contain mutations in all five lemurs. Interestingly, these genes are infrequently mutated in human hepatocellular carcinoma, suggesting potential differences in the etiology and/or progression of this cancer in lemurs and humans. Conclusions and implications Collectively, this pilot study suggests that human exome capture reagents are a promising tool for genomic studies of cancer in lemurs and other non-human primates. Lay Summary Hepatocellular carcinoma occurs frequently in prosimians, but the cause of these liver cancers is unknown. In this proof-of-principle study, we applied human DNA sequencing tools to tumor-normal pairs from five lemurs with hepatocellular carcinoma and compared the lemur mutation profiles to those of human hepatocellular carcinomas.
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Affiliation(s)
- Ella F Gunady
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kathryn E Ware
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Nicolas Devos
- Duke Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - David Corcoran
- Duke Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Prinz
- Duke Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hrvoje Misetic
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK
| | - Tara M Harrison
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC, USA
- Exotic Species Cancer Research Alliance, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey L Thorne
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | | | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Durham, NC 27710, USA
| | - William C Eward
- Department of Orthopaedics, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Durham, NC 27710, USA
| | - Jason A Somarelli
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Duke Cancer Institute, Durham, NC 27710, USA
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7
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Jackson T, Ishengoma E, Rhode C. Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:560-575. [PMID: 34241713 DOI: 10.1007/s10126-021-10046-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.
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Affiliation(s)
- T Jackson
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - E Ishengoma
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
- Department of Biological Sciences, Mkwawa University College of Education, University of Dar Es Salaam, P.O. Box 2329, Dar es Salaam, Tanzania
| | - C Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
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8
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Chan J, Yao W, Howard TD, Hawkins GA, Olivier M, Jorgensen MJ, Cheeseman IH, Cole SA, Cox LA. Efficiency of whole-exome sequencing in old world and new world primates using human capture reagents. J Med Primatol 2021; 50:176-181. [PMID: 33876458 DOI: 10.1111/jmp.12524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Whole-exome sequencing (WES) can expedite research on genetic variation in non-human primate (NHP) models of human diseases. However, NHP-specific reagents for exome capture are not available. This study reports the use of human-specific capture reagents in WES for olive baboons, marmosets, and vervet monkeys. METHODS Exome capture was carried out using the SureSelect Human All Exon V6 panel from Agilent Technologies, followed by high-throughput sequencing. Capture of protein-coding genes and detection of single nucleotide variants were evaluated. RESULTS Exome capture and sequencing results showed that more than 97% of old world and 93% of new world monkey protein coding genes were detected. Single nucleotide variants were detected across the genomes and missense variants were found in genes associated with human diseases. CONCLUSIONS A cost-effective approach based on commercial, human-specific reagents can be used to perform WES for the discovery of genetic variants in these NHP species.
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Affiliation(s)
- Jeannie Chan
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Wen Yao
- College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Timothy D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Michael Olivier
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Matthew J Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Laura A Cox
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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9
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Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Urine as a high-quality source of host genomic DNA from wild populations. Mol Ecol Resour 2021; 21:170-182. [PMID: 32985084 PMCID: PMC7746602 DOI: 10.1111/1755-0998.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
Abstract
The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
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Affiliation(s)
- Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University
- Center for Evolution and Medicine, Arizona State University
| | - Timothy H. Webster
- Department of Anthropology, University of Utah
- School of Life Sciences, Arizona State University
| | - Ian C. Gilby
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
| | - Melissa A. Wilson
- Center for Evolution and Medicine, Arizona State University
- School of Life Sciences, Arizona State University
| | | | - Michael L. Wilson
- Department of Anthropology, University of Minnesota
- Department of Ecology, Evolution and Behavior, University of Minnesota
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
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10
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Banes GL, Fountain ED, Karklus A, Huang HM, Jang-Liaw NH, Burgess DL, Wendt J, Moehlenkamp C, Mayhew GF. Genomic targets for high-resolution inference of kinship, ancestry and disease susceptibility in orang-utans (genus: Pongo). BMC Genomics 2020; 21:873. [PMID: 33287706 PMCID: PMC7720378 DOI: 10.1186/s12864-020-07278-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive. Capitalizing on a tri-fold locus discovery approach, combining data from published whole-genome sequences, novel whole-exome sequencing, and microarray-derived genotype data, we aimed to develop a highly informative gene-focused panel of targets that can be used to address a broad range of research questions. RESULTS We identified and present genomic co-ordinates for 175,186 SNPs and 2315 Y-chromosomal targets, plus 185 genes either known or presumed to be pathogenic in cardiovascular (N = 109) or respiratory (N = 43) diseases in humans - the primary and secondary causes of captive orang-utan mortality - or a majority of other human diseases (N = 33). As proof of concept, we designed and synthesized 'SeqCap' hybrid capture probes for these targets, demonstrating cost-effective target enrichment and reduced-representation sequencing. CONCLUSIONS Our targets are of broad utility in studies of orang-utan ancestry, admixture and disease susceptibility and aetiology, and thus are of value in addressing questions key to the survival of these species. To facilitate comparative analyses, these targets could now be standardized for future orang-utan population genomic studies. The targets are broadly compatible with commercial target enrichment platforms and can be utilized as published here to synthesize applicable probes.
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Affiliation(s)
- Graham L Banes
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA.
| | - Emily D Fountain
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1220 Capitol Court, Madison, WI, 53715, USA
| | - Alyssa Karklus
- School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Drive, Madison, WI, 53706, USA
| | - Hao-Ming Huang
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, No. 30, Section 2, Xinguang Road, Wenshan District, Taipei City, Taiwan, 11656
| | - Nian-Hong Jang-Liaw
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, No. 30, Section 2, Xinguang Road, Wenshan District, Taipei City, Taiwan, 11656
| | - Daniel L Burgess
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Polymer Forge, Inc., 504 S Rosa Rd Ste 200, Madison, WI, 53719, USA
| | - Jennifer Wendt
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Promega Corporation, 2800 Woods Hollow Rd, Fitchburg, WI, 53711, USA
| | - Cynthia Moehlenkamp
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA.,Exact Sciences, 441 Charmany Dr, Madison, WI, 53719, USA
| | - George F Mayhew
- Roche Sequencing Solutions, 500 S Rosa Road, Madison, WI, 53719, USA
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11
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Paijmans JLA, Barlow A, Henneberger K, Fickel J, Hofreiter M, Foerster DWG. Ancestral mitogenome capture of the Southeast Asian banded linsang. PLoS One 2020; 15:e0234385. [PMID: 32603327 PMCID: PMC7326216 DOI: 10.1371/journal.pone.0234385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/26/2020] [Indexed: 01/21/2023] Open
Abstract
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.
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Affiliation(s)
- Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Leibniz Institute for Zoo- and Wildlife Research, Berlin, Germany
- * E-mail: (JLAP); (AB); (DWGF)
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
- * E-mail: (JLAP); (AB); (DWGF)
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Joerns Fickel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Leibniz Institute for Zoo- and Wildlife Research, Berlin, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daniel W. G. Foerster
- Leibniz Institute for Zoo- and Wildlife Research, Berlin, Germany
- * E-mail: (JLAP); (AB); (DWGF)
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12
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Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
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13
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Gauthier M, Konecny‐Dupré L, Nguyen A, Elbrecht V, Datry T, Douady C, Lefébure T. Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol. Mol Ecol Resour 2019; 20:79-96. [DOI: 10.1111/1755-0998.13088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mailys Gauthier
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Lara Konecny‐Dupré
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | | | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph Ontario Canada
| | - Thibault Datry
- IRSTEA UR‐RiverLy Centre de Lyon‐Villeurbanne Villeurbanne Cedex France
| | - Christophe Douady
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
| | - Tristan Lefébure
- CNRS UMR 5023 ENTPE Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon Université Claude Bernard Lyon 1 Villeurbanne France
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14
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Caskey JR, Wiseman RW, Karl JA, Baker DA, Lee T, Maddox RJ, Raveendran M, Harris RA, Hu J, Muzny DM, Rogers J, O'Connor DH. MHC genotyping from rhesus macaque exome sequences. Immunogenetics 2019; 71:531-544. [PMID: 31321455 PMCID: PMC6790296 DOI: 10.1007/s00251-019-01125-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/02/2019] [Indexed: 02/03/2023]
Abstract
Indian rhesus macaque major histocompatibility complex (MHC) variation can influence the outcomes of transplantation and infectious disease studies. Frequently, rhesus macaques are MHC genotyped to identify variants that could account for unexpected results. Since the MHC is only one region in the genome where variation could impact experimental outcomes, strategies for simultaneously profiling variation in the macaque MHC and the remainder of the protein coding genome would be useful. Here we determine MHC class I and class II genotypes using target-capture probes enriched for MHC sequences, a method we term macaque exome sequence (MES) genotyping. For a cohort of 27 Indian rhesus macaques, we describe two methods for obtaining MHC genotypes from MES data and demonstrate that the MHC class I and class II genotyping results obtained with these methods are 98.1% and 98.7% concordant, respectively, with expected MHC genotypes. In contrast, conventional MHC genotyping results obtained by deep sequencing of short multiplex PCR amplicons were only 92.6% concordant with expectations for this cohort.
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Affiliation(s)
- John R Caskey
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Taylor Lee
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Robert J Maddox
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | | | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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15
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White LC, Fontsere C, Lizano E, Hughes DA, Angedakin S, Arandjelovic M, Granjon AC, Hans JB, Lester JD, Rabanus-Wallace MT, Rowney C, Städele V, Marques-Bonet T, Langergraber KE, Vigilant L. A roadmap for high-throughput sequencing studies of wild animal populations using noninvasive samples and hybridization capture. Mol Ecol Resour 2019; 19:609-622. [PMID: 30637963 DOI: 10.1111/1755-0998.12993] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 11/30/2022]
Abstract
Large-scale genomic studies of wild animal populations are often limited by access to high-quality DNA. Although noninvasive samples, such as faeces, can be readily collected, DNA from the sample producers is usually present in low quantities, fragmented, and contaminated by microorganism and dietary DNAs. Hybridization capture can help to overcome these impediments by increasing the proportion of subject DNA prior to high-throughput sequencing. Here we evaluate a key design variable for hybridization capture, the number of rounds of capture, by testing whether one or two rounds are most appropriate, given varying sample quality (as measured by the ratios of subject to total DNA). We used a set of 1,780 quality-assessed wild chimpanzee (Pan troglodytes schweinfurthii) faecal samples and chose 110 samples of varying quality for exome capture and sequencing. We used multiple regression to assess the effects of the ratio of subject to total DNA (sample quality), rounds of capture and sequencing effort on the number of unique exome reads sequenced. We not only show that one round of capture is preferable when the proportion of subject DNA in a sample is above ~2%-3%, but also explore various types of bias introduced by capture, and develop a model that predicts the sequencing effort necessary for a desired data yield from samples of a given quality. Thus, our results provide a useful guide and pave a methodological way forward for researchers wishing to plan similar hybridization capture studies.
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Affiliation(s)
- Lauren C White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anne-Céline Granjon
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jörg B Hans
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Carolyn Rowney
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Veronika Städele
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute of Human Origins, Arizona State University, Tempe, Arizona
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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16
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Choquet M, Smolina I, Dhanasiri AKS, Blanco-Bercial L, Kopp M, Jueterbock A, Sundaram AYM, Hoarau G. Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus. ROYAL SOCIETY OPEN SCIENCE 2019; 6:180608. [PMID: 30891252 PMCID: PMC6408391 DOI: 10.1098/rsos.180608] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/07/2019] [Indexed: 05/09/2023]
Abstract
Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod Calanus finmarchicus (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in C. finmarchicus including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric C. glacialis. Preliminary analyses of these markers revealed similar levels of genetic diversity between the two Calanus species, while populations of C. glacialis showed stronger genetic structure compared to C. finmarchicus. Using this powerful set of markers, we did not detect any evidence of hybridization between C. finmarchicus and C. glacialis. Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.
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Affiliation(s)
- Marvin Choquet
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Author for correspondence: Marvin Choquet e-mail:
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Arvind Y. M. Sundaram
- Norwegian Sequencing Centre, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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17
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Förster DW, Bull JK, Lenz D, Autenrieth M, Paijmans JLA, Kraus RHS, Nowak C, Bayerl H, Kuehn R, Saveljev AP, Sindičić M, Hofreiter M, Schmidt K, Fickel J. Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species. Mol Ecol Resour 2018; 18:1356-1373. [PMID: 29978939 DOI: 10.1111/1755-0998.12924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022]
Abstract
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.
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Affiliation(s)
- Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - James K Bull
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marijke Autenrieth
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Helmut Bayerl
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany
| | - Ralph Kuehn
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany.,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, New Mexico
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Magda Sindičić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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18
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Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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19
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Zhang Y, Song J, Day K, Absher D. dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization. BMC Genomics 2017; 18:811. [PMID: 29061109 PMCID: PMC5653981 DOI: 10.1186/s12864-017-4159-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Targeted sequencing is a powerful tool with broad application in both basic and translational sciences. Relatively low on-target rates for most current targeted sequencing studies influence the required coverage and data quality for subsequent applications. RESULTS We present an improved targeted sequencing method that uses two rounds of in solution hybridization with probes synthesized from genomic clone templates, termed dCATCH-Seq. Independent captures of two large continuous genomic regions across three cell types within the human major histocompatibility complex (MHC) that spans ~3.5 Mb and a ~250 kb region on chromosome 11 demonstrated that dCATCH-Seq was highly reproducible with ~95% capture specificity. Comprehensive analyses of sequencing data generated using the dCATCH-Seq approach also showed high accuracy in the detection of genetic variants and HLA typing. The double hybridization capture approach can also be coupled with bisulfite sequencing for DNA methylation profiling of both CpG and non-CpG sites. CONCLUSIONS Altogether, dCATCH-Seq is a powerful and scalable targeted sequencing approach to investigate both genetic and epigenetic features.
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Affiliation(s)
- Yanfeng Zhang
- HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Jun Song
- HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Kenneth Day
- HudsonAlpha Institute for Biotechnology, Huntsville, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, USA. .,Ubiquity Genomics Inc., Huntsville, USA.
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20
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Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus). Sci Rep 2017; 7:6781. [PMID: 28754989 PMCID: PMC5533801 DOI: 10.1038/s41598-017-06582-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/13/2017] [Indexed: 01/05/2023] Open
Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) and target capture sequencing methods are used to explore population and phylogenetic questions in non-model organisms. ddRADseq offers a simple and reliable protocol for population genomic studies, however it can result in a large amount of missing data due to allelic dropout. Target capture sequencing offers an opportunity to increase sequencing coverage with little missing data and consistent orthologous loci across samples, although this approach has generally been applied to conserved markers for deeper evolutionary questions. Here, we combine both methods to generate high quality sequencing data for population genomic studies of all marine lobster species from the genus Jasus. We designed probes based on ddRADseq libraries of two lobster species (Jasus edwardsii and Sagmariasus verreauxi) and evaluated the captured sequencing data in five other Jasus species. We validated 4,465 polymorphic loci amongst these species using a cost effective sequencing protocol, of which 1,730 were recovered from all species, and 4,026 were present in at least three species. The method was also successfully applied to DNA samples obtained from museum specimens. This data will be further used to assess spatial-temporal genetic variation in Jasus species found in the Southern Hemisphere.
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21
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Prall TM, Graham ME, Karl JA, Wiseman RW, Ericsen AJ, Raveendran M, Alan Harris R, Muzny DM, Gibbs RA, Rogers J, O'Connor DH. Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques. Immunogenetics 2017; 69:325-339. [PMID: 28343239 PMCID: PMC5856007 DOI: 10.1007/s00251-017-0977-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/08/2017] [Indexed: 12/25/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens, and so, considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lack the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing Pacific Biosciences circular consensus sequencing (CCS). We also describe a new approach to Macaque Exome Sequencing (MES) and the development of the Rhexome1.0, an adapted target capture reagent that includes macaque-specific capture probe sets. By using sequence reads generated by whole genome sequencing (WGS) and MES to inform primer design, we were able to increase the sensitivity of KIR allele discovery. We demonstrate this increased sensitivity by defining nine novel alleles within a cohort of Mauritian cynomolgus macaques (MCM), a geographically isolated population with restricted KIR genetics that was thought to be completely characterized. Finally, we describe an approach to genotyping KIRs directly from sequence reads generated using WGS/MES reads. The findings presented here expand our understanding of KIR genetics in MCM by associating new genes with all eight KIR haplotypes and demonstrating the existence of at least one KIR3DS gene associated with every haplotype.
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Affiliation(s)
- Trent M Prall
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
| | - Michael E Graham
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA
| | - Adam J Ericsen
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA
| | | | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI, 53711, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, 53711, USA.
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22
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Bimber BN, Ramakrishnan R, Cervera-Juanes R, Madhira R, Peterson SM, Norgren RB, Ferguson B. Whole genome sequencing predicts novel human disease models in rhesus macaques. Genomics 2017; 109:214-220. [PMID: 28438488 DOI: 10.1016/j.ygeno.2017.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/10/2017] [Accepted: 04/14/2017] [Indexed: 12/23/2022]
Abstract
Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model. We detected an average of 131 mutations predicted to severely alter protein coding per animal, and identified 45 such variants that coincide with known pathogenic human variants. These data suggest that expanded screening of existing breeding colonies will identify novel models of human disease, and that increased genomic characterization can help inform research studies in macaques.
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Affiliation(s)
- Benjamin N Bimber
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Ranjani Ramakrishnan
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Rita Cervera-Juanes
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Ravi Madhira
- Oregon Health & Sciences University, Portland, OR 97239, United States
| | - Samuel M Peterson
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States
| | - Robert B Norgren
- Dept. of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Betsy Ferguson
- Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR 97006, United States.
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23
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Sarver BA, Keeble S, Cosart T, Tucker PK, Dean MD, Good JM. Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach. Genome Biol Evol 2017; 9:726-739. [PMID: 28338821 PMCID: PMC5381554 DOI: 10.1093/gbe/evx034] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (ten species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa.
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Affiliation(s)
- Brice A.J. Sarver
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Ted Cosart
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Priscilla K. Tucker
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI
| | - Matthew D. Dean
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT
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24
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Schott RK, Panesar B, Card DC, Preston M, Castoe TA, Chang BS. Targeted Capture of Complete Coding Regions across Divergent Species. Genome Biol Evol 2017; 9:398-414. [PMID: 28137744 PMCID: PMC5381602 DOI: 10.1093/gbe/evx005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 02/06/2023] Open
Abstract
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here, we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.
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Affiliation(s)
- Ryan K. Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Bhawandeep Panesar
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Daren C. Card
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Matthew Preston
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Belinda S.W. Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
- Centre for the Analysis of Genomes and Function, University of Toronto, Canada
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25
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Gradnigo JS, Majumdar A, Norgren RB, Moriyama EN. Advantages of an Improved Rhesus Macaque Genome for Evolutionary Analyses. PLoS One 2016; 11:e0167376. [PMID: 27911958 PMCID: PMC5135103 DOI: 10.1371/journal.pone.0167376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 11/14/2016] [Indexed: 01/12/2023] Open
Abstract
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct. The rhesus macaque provides a unique opportunity to determine whether an improved genome (MacaM) yields better results than a draft genome (rheMac2) for evolutionary studies. We compared protein-coding genes annotated in the rheMac2 and MacaM genomes with their human orthologs. We found many genes annotated in rheMac2 had apparently spurious sequences not present in genes derived from MacaM. The rheMac2 annotations also appeared to inflate a frequently used evolutionary index, ω (the ratio of nonsynonymous to synonymous substitution rates). Genes with these spurious sequences must be filtered out from evolutionary analyses to obtain correct results. With the MacaM genome, improved sequence information means many more genes can be examined for indications of selection. These results indicate how upgrading genomes from draft status to a higher level of quality can improve interpretation of evolutionary patterns.
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Affiliation(s)
- Julien S. Gradnigo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Abhishek Majumdar
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert B. Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Etsuko N. Moriyama
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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26
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Su Z, Zhang J, Kumar C, Molony C, Lu H, Chen R, Stone DJ, Ling F, Liu X. Species specific exome probes reveal new insights in positively selected genes in nonhuman primates. Sci Rep 2016; 6:33876. [PMID: 27659771 PMCID: PMC5034232 DOI: 10.1038/srep33876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/05/2016] [Indexed: 01/20/2023] Open
Abstract
Nonhuman primates (NHP) are important biomedical animal models for the study of human disease. Of these, the most widely used models in biomedical research currently are from the genus Macaca. However, evolutionary genetic divergence between human and NHP species makes human-based probes inefficient for the capture of genomic regions of NHP for sequencing and study. Here we introduce a new method to resequence the exome of NHP species by a designed capture approach specifically targeted to the NHP, and demonstrate its superior performance on four NHP species or subspecies. Detailed investigation on biomedically relevant genes demonstrated superior capture by the new approach. We identified 28 genes that appeared to be pseudogenized and inactivated in macaque. Finally, we identified 187 genes showing strong evidence for positive selection across all branches of the primate phylogeny including many novel findings.
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Affiliation(s)
- Zheng Su
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Junjie Zhang
- Shool of bioscience &bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Chanchal Kumar
- Translational Medicine Research Centre, Merck Research Laboratories, MSD, 8 Biomedical Grove, Neuros #04-01, Singapore 138665, Singapore
| | - Cliona Molony
- Merck Research Laboratories, Merck &Co. Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hongchao Lu
- Informatics IT, MSD R&D (China) Co., Ltd., Beijing, China
| | - Ronghua Chen
- Informatics IT, MSD R&D (China) Co., Ltd., Beijing, China.,Informatics IT, Merck &Co., Inc., Boston, MA, USA
| | - David J Stone
- Merck Research Laboratories, Merck &Co. Inc., 770 Sumneytown Pike, WP53B-120 West Point, PA 19486, USA
| | - Fei Ling
- Shool of bioscience &bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China.,Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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27
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Powell JH, Amish SJ, Haynes GD, Luikart G, Latch EK. Candidate adaptive genes associated with lineage divergence: identifying SNPs via next-generation targeted resequencing in mule deer (Odocoileus hemionus). Mol Ecol Resour 2016; 16:1165-72. [PMID: 27438092 DOI: 10.1111/1755-0998.12572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/15/2016] [Accepted: 06/23/2016] [Indexed: 11/29/2022]
Abstract
Mule deer (Odocoileus hemionus) are an excellent nonmodel species for empirically testing hypotheses in landscape and population genomics due to their large population sizes (low genetic drift), relatively continuous distribution, diversity of occupied habitats and phenotypic variation. Because few genomic resources are currently available for this species, we used exon data from a cattle (Bos taurus) reference genome to direct targeted resequencing of 5935 genes in mule deer. We sequenced approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69 genes) with putatively fixed allele frequency differences between the two major lineages of mule deer (mule deer and black-tailed deer), and our estimate of mean genetic divergence (genome-wide FST = 0.123) between these lineages was consistent with previous findings using microsatellite loci. We detected an over-representation of gamete generation and amino acid transport genes among the genes with SNPs exhibiting potentially fixed allele frequency differences between lineages. This targeted resequencing approach using exon capture techniques has identified a suite of loci that can be used in future research to investigate the genomic basis of adaptation and differentiation between black-tailed deer and mule deer. This study also highlights techniques (and an exon capture array) that will facilitate population genomic research in other cervids and nonmodel organisms.
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Affiliation(s)
- John H Powell
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N Maryland Ave., Milwaukee, WI, 53211, USA.,Inland Fish and Wildlife Department, Sault Ste. Marie Tribe of Chippewa Indians, 523 Ashmun Street, Sault Ste. Marie, MI, 49783, USA
| | - Stephen J Amish
- Fish and Wildlife Genomics Group, University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Gwilym D Haynes
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, USA
| | - Gordon Luikart
- Flathead Lake Biological Station, Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Polson, MT, 59860, USA
| | - Emily K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N Maryland Ave., Milwaukee, WI, 53211, USA
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28
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Purifying selection shapes the coincident SNP distribution of primate coding sequences. Sci Rep 2016; 6:27272. [PMID: 27255481 PMCID: PMC4891680 DOI: 10.1038/srep27272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/17/2016] [Indexed: 12/13/2022] Open
Abstract
Genome-wide analysis has observed an excess of coincident single nucleotide polymorphisms (coSNPs) at human-chimpanzee orthologous positions, and suggested that this is due to cryptic variation in the mutation rate. While this phenomenon primarily corresponds with non-coding coSNPs, the situation in coding sequences remains unclear. Here we calculate the observed-to-expected ratio of coSNPs (coSNPO/E) to estimate the prevalence of human-chimpanzee coSNPs, and show that the excess of coSNPs is also present in coding regions. Intriguingly, coSNPO/E is much higher at zero-fold than at nonzero-fold degenerate sites; such a difference is due to an elevation of coSNPO/E at zero-fold degenerate sites, rather than a reduction at nonzero-fold degenerate ones. These trends are independent of chimpanzee subpopulation, population size, or sequencing techniques; and hold in broad generality across primates. We find that this discrepancy cannot fully explained by sequence contexts, shared ancestral polymorphisms, SNP density, and recombination rate, and that coSNPO/E in coding sequences is significantly influenced by purifying selection. We also show that selection and mutation rate affect coSNPO/E independently, and coSNPs tend to be less damaging and more correlated with human diseases than non-coSNPs. These suggest that coSNPs may represent a “signature” during primate protein evolution.
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29
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Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. Genetics 2016; 203:699-714. [PMID: 27098910 PMCID: PMC4896188 DOI: 10.1534/genetics.116.187492] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/18/2016] [Indexed: 12/31/2022] Open
Abstract
Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.
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Cornish AS, Gibbs RM, Norgren RB. Exome screening to identify loss-of-function mutations in the rhesus macaque for development of preclinical models of human disease. BMC Genomics 2016; 17:170. [PMID: 26935327 PMCID: PMC4776415 DOI: 10.1186/s12864-016-2509-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/22/2016] [Indexed: 02/02/2023] Open
Abstract
Background Exome sequencing has been utilized to identify genetic variants associated with disease in humans. Identification of loss-of-function mutations with exome sequencing in rhesus macaques (Macaca mulatta) could lead to valuable animal models of genetic disease. Attempts have been made to identify variants in rhesus macaques by aligning exome data against the rheMac2 draft genome. However, such efforts have been impaired due to the incompleteness and annotation errors associated with rheMac2. We wished to determine whether aligning exome reads against our new, improved rhesus genome, MacaM, could be used to identify high impact, loss-of-function mutations in rhesus macaques that would be relevant to human disease. Results We compared alignments of exome reads from four rhesus macaques, the reference animal and three unrelated animals, against rheMac2 and MacaM. Substantially more reads aligned against MacaM than rheMac2. We followed the Broad Institute’s Best Practice guidelines for variant discovery which utilizes the Genome Analysis Toolkit to identify high impact mutations. When rheMac2 was used as the reference genome, a large number of apparent false positives were identified. When MacaM was used as the reference genome, the number of false positives was greatly reduced. After examining the variant analyses conducted with MacaM as reference genome, we identified two putative loss-of-function mutations, in the heterozygous state, in genes related to human health. Sanger sequencing confirmed the presence of these mutations. We followed the transmission of one of these mutations (in the butyrylthiocholine gene) through three generations of rhesus macaques. Further, we demonstrated a functional decrease in butyrylthiocholinesterase activity similar to that observed in human heterozygotes with loss-of-function mutations in the same gene. Conclusions The new MacaM genome can be effectively utilized to identify loss-of-function mutations in rhesus macaques without generating a high level of false positives. In some cases, heterozygotes may be immediately useful as models of human disease. For diseases where homozygous mutants are needed, directed breeding of loss-of-function heterozygous animals could be used to create rhesus macaque models of human genetic disease. The approach we describe here could be applied to other mammals, but only if their genomes have been improved beyond draft status. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2509-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam S Cornish
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, 68198-5805, Nebraska.
| | - Robert M Gibbs
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, 68198-5805, Nebraska.
| | - Robert B Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, 68198-5805, Nebraska.
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31
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Bailey J, Taylor K. Non-human Primates in Neuroscience Research: The Case against its Scientific Necessity. Altern Lab Anim 2016; 44:43-69. [DOI: 10.1177/026119291604400101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Public opposition to non-human primate (NHP) experiments is significant, yet those who defend them cite minimal harm to NHPs and substantial human benefit. Here we review these claims of benefit, specifically in neuroscience, and show that: a) there is a default assumption of their human relevance and benefit, rather than robust evidence; b) their human relevance and essential contribution and necessity are wholly overstated; c) the contribution and capacity of non-animal investigative methods are greatly understated; and d) confounding issues, such as species differences and the effects of stress and anaesthesia, are usually overlooked. This is the case in NHP research generally, but here we specifically focus on the development and interpretation of functional magnetic resonance imaging (fMRI), deep brain stimulation (DBS), the understanding of neural oscillations and memory, and investigation of the neural control of movement and of vision/binocular rivalry. The increasing power of human-specific methods, including advances in fMRI and invasive techniques such as electrocorticography and single-unit recordings, is discussed. These methods serve to render NHP approaches redundant. We conclude that the defence of NHP use is groundless, and that neuroscience would be more relevant and successful for humans, if it were conducted with a direct human focus. We have confidence in opposing NHP neuroscience, both on scientific as well as on ethical grounds.
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32
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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Liu S, Wang X, Xie L, Tan M, Li Z, Su X, Zhang H, Misof B, Kjer KM, Tang M, Niehuis O, Jiang H, Zhou X. Mitochondrial capture enriches mito‐DNA 100 fold, enabling PCR‐free mitogenomics biodiversity analysis. Mol Ecol Resour 2015; 16:470-9. [DOI: 10.1111/1755-0998.12472] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 09/19/2015] [Accepted: 09/24/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Shanlin Liu
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- Centre for GeoGenetics Natural History Museum of Denmark University of Copenhagen Øster Voldgade 5–7 1350 Copenhagen Denmark
| | - Xin Wang
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Lin Xie
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Meihua Tan
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Zhenyu Li
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Xu Su
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- Guizhou provincial Center For Disease Control And Prevention Guiyang Guizhou province 550004 China
| | - Hao Zhang
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Bernhard Misof
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Karl M. Kjer
- Department of Entomology and Nematology UC Davis Davis CA 95616 USA
| | - Min Tang
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Oliver Niehuis
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB) Bonn Germany
| | - Hui Jiang
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
| | - Xin Zhou
- China National GeneBank‐Shenzhen BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
- BGI‐Shenzhen Shenzhen Guangdong Province 518083 China
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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36
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Widdig A, Kessler MJ, Bercovitch FB, Berard JD, Duggleby C, Nürnberg P, Rawlins RG, Sauermann U, Wang Q, Krawczak M, Schmidtke J. Genetic studies on the Cayo Santiago rhesus macaques: A review of 40 years of research. Am J Primatol 2015; 78:44-62. [PMID: 26031601 DOI: 10.1002/ajp.22424] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 04/17/2015] [Accepted: 04/19/2015] [Indexed: 01/17/2023]
Abstract
Genetic studies not only contribute substantially to our current understanding of the natural variation in behavior and health in many species, they also provide the basis of numerous in vivo models of human traits. Despite the many challenges posed by the high level of biological and social complexity, a long lifespan and difficult access in the field, genetic studies of primates are particularly rewarding because of the close evolutionary relatedness of these species to humans. The free-ranging rhesus macaque (Macaca mulatta) population on Cayo Santiago (CS), Puerto Rico, provides a unique resource in this respect because several of the abovementioned caveats are of either minor importance there, or lacking altogether, thereby allowing long-term genetic research in a primate population under constant surveillance since 1956. This review summarizes more than 40 years of genetic research carried out on CS, from early blood group typing and the genetic characterization of skeletal material via population-wide paternity testing with DNA fingerprints and short tandem repeats (STRs) to the analysis of the highly polymorphic DQB1 locus within the major histocompatibility complex (MHC). The results of the paternity studies also facilitated subsequent studies of male dominance and other factors influencing male reproductive success, of male reproductive skew, paternal kin bias, and mechanisms of paternal kin recognition. More recently, the CS macaques have been the subjects of functional genetic and gene expression analyses and have played an important role in behavioral and quantitative genetic studies. In addition, the CS colony has been used as a natural model for human adult-onset macular degeneration, glaucoma, and circadian rhythm disorder. Our review finishes off with a discussion of potential future directions of research on CS, including the transition from STRs to single nucleotide polymorphism (SNP) typing and whole genome sequencing.
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Affiliation(s)
- Anja Widdig
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Leipzig, Germany.,Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Puerto Rico
| | - Matthew J Kessler
- Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Puerto Rico.,Division of Laboratory Animal Resources, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia
| | - Fred B Bercovitch
- Primate Research Institute & Wildlife Research Center, Kyoto University, Inuyama, Aichi, Japan
| | - John D Berard
- Department of Veterans Affairs, Greater Los Angeles Health Care System, North Hills, California
| | - Christine Duggleby
- Department of Anthropology, State University of New York at Buffalo, Buffalo, New York
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Köln, Germany
| | - Richard G Rawlins
- Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Puerto Rico
| | - Ulrike Sauermann
- Unit of Infection Models, German Primate Center, Göttingen, Germany
| | - Qian Wang
- Department of Biomedical Sciences, Texas A&M University Baylor College of Dentistry, Texas
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Jörg Schmidtke
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
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37
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Paijmans JLA, Fickel J, Courtiol A, Hofreiter M, Förster DW. Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Mol Ecol Resour 2015; 16:42-55. [DOI: 10.1111/1755-0998.12420] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Johanna L. A. Paijmans
- Department of Biology; University of York; York YO10 5DD UK
- Institute for Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Str 24-25 14476 Potsdam Germany
| | - Joerns Fickel
- Institute for Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Str 24-25 14476 Potsdam Germany
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17; 10315 Berlin Germany
| | - Alexandre Courtiol
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17; 10315 Berlin Germany
| | - Michael Hofreiter
- Department of Biology; University of York; York YO10 5DD UK
- Institute for Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Str 24-25 14476 Potsdam Germany
| | - Daniel W. Förster
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17; 10315 Berlin Germany
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, Treangen T, Salzberg SL, Yorke JA, Norgren RB. A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biol Direct 2014; 9:20. [PMID: 25319552 PMCID: PMC4214606 DOI: 10.1186/1745-6150-9-20] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022] Open
Abstract
Background The rhesus macaque (Macaca mulatta) is a key species for advancing biomedical research. Like all draft mammalian genomes, the draft rhesus assembly (rheMac2) has gaps, sequencing errors and misassemblies that have prevented automated annotation pipelines from functioning correctly. Another rhesus macaque assembly, CR_1.0, is also available but is substantially more fragmented than rheMac2 with smaller contigs and scaffolds. Annotations for these two assemblies are limited in completeness and accuracy. High quality assembly and annotation files are required for a wide range of studies including expression, genetic and evolutionary analyses. Results We report a new de novo assembly of the rhesus macaque genome (MacaM) that incorporates both the original Sanger sequences used to assemble rheMac2 and new Illumina sequences from the same animal. MacaM has a weighted average (N50) contig size of 64 kilobases, more than twice the size of the rheMac2 assembly and almost five times the size of the CR_1.0 assembly. The MacaM chromosome assembly incorporates information from previously unutilized mapping data and preliminary annotation of scaffolds. Independent assessment of the assemblies using Ion Torrent read alignments indicates that MacaM is more complete and accurate than rheMac2 and CR_1.0. We assembled messenger RNA sequences from several rhesus tissues into transcripts which allowed us to identify a total of 11,712 complete proteins representing 9,524 distinct genes. Using a combination of our assembled rhesus macaque transcripts and human transcripts, we annotated 18,757 transcripts and 16,050 genes with complete coding sequences in the MacaM assembly. Further, we demonstrate that the new annotations provide greatly improved accuracy as compared to the current annotations of rheMac2. Finally, we show that the MacaM genome provides an accurate resource for alignment of reads produced by RNA sequence expression studies. Conclusions The MacaM assembly and annotation files provide a substantially more complete and accurate representation of the rhesus macaque genome than rheMac2 or CR_1.0 and will serve as an important resource for investigators conducting next-generation sequencing studies with nonhuman primates. Reviewers This article was reviewed by Dr. Lutz Walter, Dr. Soojin Yi and Dr. Kateryna Makova.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Robert B Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
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Improved variant calling accuracy by merging replicates in whole-exome sequencing studies. BIOMED RESEARCH INTERNATIONAL 2014; 2014:319534. [PMID: 25162009 PMCID: PMC4137624 DOI: 10.1155/2014/319534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 12/30/2022]
Abstract
In large scale population-based whole-exome sequencing (WES) studies, there are some samples occasionally sequenced two or more times due to a variety of reasons. To investigate how to efficiently utilize these duplicated sequencing data, we conducted comprehensive evaluation of variant calling strategies. 92 samples subjected to WES twice were selected from a large population study. These 92 duplicated samples were divided into two groups: group H consisting of the higher sequencing depth for each subject and group L consisting of the lower depth for each subject. The merged samples for each subject were put in a third group M. Using the GATK multisample toolkit, we compared variant calling accuracy among three strategies. Hierarchical clustering analysis indicated that the two replicates for each subject showed high homogeneity. The comparative analyses on the basis of heterozygous-homozygous ratio (Hete/Homo), transition-transversion ratio (Ti/Tv), and overlapping rate with the 1000 Genomes Project consistently showed that the data quality of the SNPs detected from the M group was more accurate than that of SNPs detected from the H and L groups. These results suggested that merging homogeneous duplicated exomes instead of using one of them could improve variant calling accuracy.
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Vinson A, Prongay K, Ferguson B. The value of extended pedigrees for next-generation analysis of complex disease in the rhesus macaque. ILAR J 2014; 54:91-105. [PMID: 24174435 DOI: 10.1093/ilar/ilt041] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Complex diseases (e.g., cardiovascular disease and type 2 diabetes, among many others) pose the biggest threat to human health worldwide and are among the most challenging to investigate. Susceptibility to complex disease may be caused by multiple genetic variants (GVs) and their interaction, by environmental factors, and by interaction between GVs and environment, and large study cohorts with substantial analytical power are typically required to elucidate these individual contributions. Here, we discuss the advantages of both power and feasibility afforded by the use of extended pedigrees of rhesus macaques (Macaca mulatta) for genetic studies of complex human disease based on next-generation sequence data. We present these advantages in the context of previous research conducted in rhesus macaques for several representative complex diseases. We also describe a single, multigeneration pedigree of Indian-origin rhesus macaques and a sample biobank we have developed for genetic analysis of complex disease, including power of this pedigree to detect causal GVs using either genetic linkage or association methods in a variance decomposition approach. Finally, we summarize findings of significant heritability for a number of quantitative traits that demonstrate that genetic contributions to risk factors for complex disease can be detected and measured in this pedigree. We conclude that the development and application of an extended pedigree to analysis of complex disease traits in the rhesus macaque have shown promising early success and that genome-wide genetic and higher order -omics studies in this pedigree are likely to yield useful insights into the architecture of complex human disease.
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Abstract
The field of nonhuman primate genomics is undergoing rapid change and making impressive progress. Exploiting new technologies for DNA sequencing, researchers have generated new whole-genome sequence assemblies for multiple primate species over the past 6 years. In addition, investigations of within-species genetic variation, gene expression and RNA sequences, conservation of non-protein-coding regions of the genome, and other aspects of comparative genomics are moving at an accelerating speed. This progress is opening a wide array of new research opportunities in the analysis of comparative primate genome content and evolution. It also creates new possibilities for the use of nonhuman primates as model organisms in biomedical research. This transition, based on both new technology and the new information being generated in regard to human genetics, provides an important justification for reevaluating the research goals, strategies, and study designs used in primate genetics and genomics.
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Genome typing of nonhuman primate models: implications for biomedical research. Trends Genet 2014; 30:482-7. [PMID: 24954183 DOI: 10.1016/j.tig.2014.05.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 12/18/2022]
Abstract
The success of personalized medicine rests on understanding the genetic variation between individuals. Thus, as medical practice evolves and variation among individuals becomes a fundamental aspect of clinical medicine, a thorough consideration of the genetic and genomic information concerning the animals used as models in biomedical research also becomes critical. In particular, nonhuman primates (NHPs) offer great promise as models for many aspects of human health and disease. These are outbred species exhibiting substantial levels of genetic variation; however, understanding of the contribution of this variation to phenotypes is lagging behind in NHP species. Thus, there is a pivotal need to address this gap and define strategies for characterizing both genomic content and variability within primate models of human disease. Here, we discuss the current state of genomics of NHP models and offer guidelines for future work to ensure continued improvement and utility of this line of biomedical research.
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Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Genet 2014; 15:347-59. [PMID: 24709753 DOI: 10.1038/nrg3707] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.
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Andrews KR, Luikart G. Recent novel approaches for population genomics data analysis. Mol Ecol 2014; 23:1661-7. [DOI: 10.1111/mec.12686] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/25/2014] [Accepted: 01/29/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Kimberly R. Andrews
- School of Biological & Biomedical Sciences; Durham University; South Road Durham DH1 3LE UK
| | - Gordon Luikart
- Flathead Lake Biological Station; Fish and Wildlife Genomics Group; University of Montana; Polson MT 59860 USA
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Schiessl S, Samans B, Hüttel B, Reinhard R, Snowdon RJ. Capturing sequence variation among flowering-time regulatory gene homologs in the allopolyploid crop species Brassica napus. FRONTIERS IN PLANT SCIENCE 2014; 5:404. [PMID: 25202314 PMCID: PMC4142343 DOI: 10.3389/fpls.2014.00404] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/29/2014] [Indexed: 05/18/2023]
Abstract
Flowering, the transition from the vegetative to the generative phase, is a decisive time point in the lifecycle of a plant. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes ranging from germination and seed development through to fundamental developmental and yield-related traits. In the allopolyploid crop species Brassica napus, (genome AACC), homoeologous copies of flowering time regulatory genes are implicated in major phenological variation within the species, however the extent and control of intraspecific and intergenomic variation among flowering-time regulators is still unclear. To investigate differences among B. napus morphotypes in relation to flowering-time gene variation, we performed targeted deep sequencing of 29 regulatory flowering-time genes in four genetically and phenologically diverse B. napus accessions. The genotype panel included a winter-type oilseed rape, a winter fodder rape, a spring-type oilseed rape (all B. napus ssp. napus) and a swede (B. napus ssp. napobrassica), which show extreme differences in winter-hardiness, vernalization requirement and flowering behavior. A broad range of genetic variation was detected in the targeted genes for the different morphotypes, including non-synonymous SNPs, copy number variation and presence-absence variation. The results suggest that this broad variation in vernalization, clock and signaling genes could be a key driver of morphological differentiation for flowering-related traits in this recent allopolyploid crop species.
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Affiliation(s)
- Sarah Schiessl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, GiessenGiessen, Germany
- *Correspondence: Sarah Schiessl, Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, Giessen 35392, Germany e-mail:
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, GiessenGiessen, Germany
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Breeding ResearchCologne, Germany
| | - Richard Reinhard
- Max Planck Genome Centre Cologne, Max Planck Institute for Breeding ResearchCologne, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, GiessenGiessen, Germany
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Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KFX, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:494-505. [PMID: 23889683 PMCID: PMC4241023 DOI: 10.1111/tpj.12294] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/19/2013] [Indexed: 05/18/2023]
Abstract
Advanced resources for genome-assisted research in barley (Hordeum vulgare) including a whole-genome shotgun assembly and an integrated physical map have recently become available. These have made possible studies that aim to assess genetic diversity or to isolate single genes by whole-genome resequencing and in silico variant detection. However such an approach remains expensive given the 5 Gb size of the barley genome. Targeted sequencing of the mRNA-coding exome reduces barley genomic complexity more than 50-fold, thus dramatically reducing this heavy sequencing and analysis load. We have developed and employed an in-solution hybridization-based sequence capture platform to selectively enrich for a 61.6 megabase coding sequence target that includes predicted genes from the genome assembly of the cultivar Morex as well as publicly available full-length cDNAs and de novo assembled RNA-Seq consensus sequence contigs. The platform provides a highly specific capture with substantial and reproducible enrichment of targeted exons, both for cultivated barley and related species. We show that this exome capture platform provides a clear path towards a broader and deeper understanding of the natural variation residing in the mRNA-coding part of the barley genome and will thus constitute a valuable resource for applications such as mapping-by-sequencing and genetic diversity analyzes.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Todd A Richmond
- Roche NimbleGen, Inc.500 South Rosa Road, Madison, WI, 53719, USA
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Leah Clissold
- The Genome Analysis Centre, Norwich Research ParkNorwich, NR4 7UH, UK
| | - Dharanya Sampath
- The Genome Analysis Centre, Norwich Research ParkNorwich, NR4 7UH, UK
| | - Sarah Ayling
- The Genome Analysis Centre, Norwich Research ParkNorwich, NR4 7UH, UK
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- † Present address:The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Matthias Pfeifer
- MIPS/IBIS, Helmholtz Zentrum MünchenD-85764, Neuherberg, Germany
| | - Mark D'Ascenzo
- Roche NimbleGen, Inc.500 South Rosa Road, Madison, WI, 53719, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State UniversityManhattan, KS, 66506, USA
| | - Pete E Hedley
- The James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
| | - Ana M Gonzales
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Klaus FX Mayer
- MIPS/IBIS, Helmholtz Zentrum MünchenD-85764, Neuherberg, Germany
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of MinnesotaSt. Paul, MN, 55108, USA
- Department of Plant Biology, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Robbie Waugh
- The James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
| | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mail )
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Goswami DB, Ogawa LM, Ward JM, Miller GM, Vallender EJ. Large-scale polymorphism discovery in macaque G-protein coupled receptors. BMC Genomics 2013; 14:703. [PMID: 24119066 PMCID: PMC3907043 DOI: 10.1186/1471-2164-14-703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/04/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis). RESULTS Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals. CONCLUSIONS In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease.
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Affiliation(s)
- Dharmendra B Goswami
- New England Primate Research Center, Harvard Medical School, One Pine Hill Drive, Southborough, MA 01772, USA.
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Runcie DE, Wiedmann RT, Archie EA, Altmann J, Wray GA, Alberts SC, Tung J. Social environment influences the relationship between genotype and gene expression in wild baboons. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120345. [PMID: 23569293 DOI: 10.1098/rstb.2012.0345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Variation in the social environment can have profound effects on survival and reproduction in wild social mammals. However, we know little about the degree to which these effects are influenced by genetic differences among individuals, and conversely, the degree to which social environmental variation mediates genetic reaction norms. To better understand these relationships, we investigated the potential for dominance rank, social connectedness and group size to modify the effects of genetic variation on gene expression in the wild baboons of the Amboseli basin. We found evidence for a number of gene-environment interactions (GEIs) associated with variation in the social environment, encompassing social environments experienced in adulthood as well as persistent effects of early life social environment. Social connectedness, maternal dominance rank and group size all interacted with genotype to influence gene expression in at least one sex, and either in early life or in adulthood. These results suggest that social and behavioural variation, akin to other factors such as age and sex, can impact the genotype-phenotype relationship. We conclude that GEIs mediated by the social environment are important in the evolution and maintenance of individual differences in wild social mammals, including individual differences in responses to social stressors.
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Affiliation(s)
- Daniel E Runcie
- Department of Biology, Duke University, Durham, NC 27708, USA
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Shen S, Pyo CW, Vu Q, Wang R, Geraghty DE. The Essential Detail: The Genetics and Genomics of the Primate Immune Response. ILAR J 2013; 54:181-95. [DOI: 10.1093/ilar/ilt043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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