Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.

Autor: Meadows JRS; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden. jennifer.meadows@imbim.uu.se., Kidd JM; Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA. jmkidd@umich.edu., Wang GD; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China., Parker HG; National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA., Schall PZ; Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA., Bianchi M; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden., Christmas MJ; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden., Bougiouri K; Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark., Buckley RM; National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA., Hitte C; University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France., Nguyen AK; Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA., Wang C; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden., Jagannathan V; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland., Niskanen JE; Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland., Frantz LAF; School of Biological and Behavioural Sciences, Queen Mary University of London, London E14NS, UK and Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, D-80539, Munich, Germany., Arumilli M; Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland., Hundi S; Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland., Lindblad-Toh K; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA., Ginja C; BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal., Agustina KK; Department of Public Health, Udayana University, Bali, 80361, Indonesia., André C; University of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France., Boyko AR; Department of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA., Davis BW; Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA., Drögemüller M; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland., Feng XY; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China., Gkagkavouzis K; Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece., Iliopoulos G; NGO 'Callisto', Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece., Harris AC; National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA., Hytönen MK; Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland., Kalthoff DC; NGO 'Callisto', Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece., Liu YH; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China., Lymberakis P; Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece.; Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece.; Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece., Poulakakis N; Natural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece.; Biology Department, School of Sciences and Engineering, University of Crete, Heraklion, Greece.; Palaeogenomics and Evolutionary Genetics Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece., Pires AE; BIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal., Racimo F; Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark., Ramos-Almodovar F; Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA., Savolainen P; Department of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden., Venetsani S; Department of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece., Tammen I; Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia., Triantafyllidis A; Department of Genetics, School of Biology, ), Aristotle University of Thessaloniki, Thessaloniki, Macedonia 54124, Greece and Genomics and Epigenomics Translational Research (GENeTres), Center for Interdisciplinary Research and Innovation (CIRI-AUTH, Balkan Center, Thessaloniki, Greece., vonHoldt B; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA., Wayne RK; Department of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA., Larson G; Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK., Nicholas FW; Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia., Lohi H; Department of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland., Leeb T; Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland., Zhang YP; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China., Ostrander EA; National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA. eostrand@mail.nih.gov.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2023 Aug 15; Vol. 24 (1), pp. 187. Date of Electronic Publication: 2023 Aug 15.
DOI: 10.1186/s13059-023-03023-7
Abstrakt: Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.
Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.
Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
(© 2023. BioMed Central Ltd., part of Springer Nature.)
Databáze: MEDLINE
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