ArticleGenome biology2023
Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.
Erratum issuedOpen access · goldAbstract read
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Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 94 papers.
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94citing papers in PubMed
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94 citing papers in PubMed, 117 citations in OpenAlex.
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- Deletion in CACNA1F gene causes X-linked progressive retinal atrophy in English Cocker Spaniel dogs.BMC veterinary research · 2026Article
- Blood biomarkers and breed genetics of aging in pet dogs.bioRxiv : the preprint server for biology · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
48 authors at 20 institutions in 14 countries.
Jennifer R S Meadows *Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden. jennifer.meadows@imbim.uu.se.ORCID http://orcid.org/0000-0002-0850-230X
Jeffrey M Kidd *Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA. jmkidd@umich.edu.ORCID http://orcid.org/0000-0002-9631-1465
Guo-Dong WangState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.ORCID http://orcid.org/0000-0002-9407-4363
Heidi G ParkerNational Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.ORCID http://orcid.org/0000-0002-9707-6380
Peter Z SchallDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.ORCID http://orcid.org/0000-0003-1016-6998
Matteo BianchiScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.ORCID http://orcid.org/0000-0003-3394-6495
Matthew J ChristmasScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.ORCID http://orcid.org/0000-0002-6355-7581
Katia BougiouriSection for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-7890-2755
Reuben M BuckleyNational Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.ORCID http://orcid.org/0000-0001-6334-3906
Christophe HitteUniversity of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France.ORCID http://orcid.org/0000-0003-1714-437X
Anthony K NguyenDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.ORCID http://orcid.org/0000-0002-9634-1904
Chao WangScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.ORCID http://orcid.org/0000-0003-3936-4023
Vidhya JagannathanInstitute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.ORCID http://orcid.org/0000-0002-8155-0041
Julia E NiskanenDepartment of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland.ORCID http://orcid.org/0000-0002-2871-6890
Laurent A F FrantzSchool 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.ORCID http://orcid.org/0000-0001-8030-3885
Meharji ArumilliDepartment of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland.
Sruthi HundiDepartment of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland.ORCID http://orcid.org/0000-0002-5803-1841
Kerstin Lindblad-TohScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75132, Uppsala, Sweden.ORCID http://orcid.org/0000-0001-8338-0253
Catarina GinjaBIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal.ORCID http://orcid.org/0000-0003-2278-7089
Kadek Karang AgustinaDepartment of Public Health, Udayana University, Bali, 80361, Indonesia.ORCID http://orcid.org/0000-0002-7128-0914
Catherine AndréUniversity of Rennes, CNRS, Institute Genetics and Development Rennes - UMR6290, 35000, Rennes, France.
Adam R BoykoDepartment of Biomedical Sciences, Cornell University, 930 Campus Road, Ithaca, NY, 14853, USA.ORCID http://orcid.org/0000-0002-9125-6874
Brian W DavisDepartment of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.ORCID http://orcid.org/0000-0002-6121-135X
Michaela DrögemüllerInstitute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.ORCID http://orcid.org/0000-0001-9378-7903
Xin-Yao FengState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.ORCID http://orcid.org/0000-0002-2603-3105
Konstantinos GkagkavouzisDepartment 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.
Giorgos IliopoulosNGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece.
Alexander C HarrisNational Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA.ORCID http://orcid.org/0000-0002-6868-5363
Marjo K HytönenDepartment of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland.ORCID http://orcid.org/0000-0003-1976-5874
Daniela C KalthoffNGO "Callisto", Wildlife and Nature Conservation Society, 54621, Thessaloniki, Greece.ORCID http://orcid.org/0000-0003-2439-5484
Yan-Hu LiuState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.ORCID http://orcid.org/0000-0001-9991-4571
Petros LymberakisNatural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece.
Nikolaos PoulakakisNatural History Museum of Crete & Department of Biology, University of Crete, 71202, Irakleio, Greece.
Ana Elisabete PiresBIOPOLIS-CIBIO-InBIO-Centro de Investigação Em Biodiversidade E Recursos Genéticos - ArchGen Group, Universidade Do Porto, 4485-661, Vairão, Portugal.ORCID http://orcid.org/0000-0002-1118-8569
Fernando RacimoSection for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-5025-2607
Fabian Ramos-AlmodovarDepartment of Human Genetics, University of Michigan, Ann Arbor, MI, 48107, USA.ORCID http://orcid.org/0000-0001-9094-7895
Peter SavolainenDepartment of Gene Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, 17121, Solna, Sweden.ORCID http://orcid.org/0000-0002-1495-8338
Semina VenetsaniDepartment of Genetics, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Macedonia, Greece.
Imke TammenSydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia.ORCID http://orcid.org/0000-0002-5520-6597
Alexandros TriantafyllidisDepartment 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.ORCID http://orcid.org/0000-0003-0469-011X
Bridgett vonHoldtDepartment of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.ORCID http://orcid.org/0000-0001-6908-1687
Robert K WayneDepartment of Ecology and Evolutionary Biology, Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-7246, USA.ORCID http://orcid.org/0000-0003-3537-2245
Greger LarsonPalaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK.ORCID http://orcid.org/0000-0002-4092-0392
Frank W NicholasSydney School of Veterinary Science, The University of Sydney, Sydney, NSW, 2570, Australia.ORCID http://orcid.org/0000-0002-9178-3965
Hannes LohiDepartment of Medical and Clinical Genetics, Department of Veterinary Biosciences, University of Helsinki and Folkhälsan Research Center, 02900, Helsinki, Finland.ORCID http://orcid.org/0000-0003-1087-5532
Tosso LeebInstitute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.ORCID http://orcid.org/0000-0003-0553-4880
Ya-Ping Zhang *State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.ORCID http://orcid.org/0000-0002-5401-1114
Elaine A Ostrander *National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA. eostrand@mail.nih.gov.ORCID http://orcid.org/0000-0001-6075-9738
University of Helsinki · FIKunming Institute of Zoology · CNNational Institutes of Health · USUniversity of Michigan · USUppsala University · SEAristotle University of Thessaloniki · GRUniversity of Bern · CHCentre National de la Recherche Scientifique · FRThe University of Sydney · AUUniversidade do Porto · PTUniversity of Copenhagen · DKUniversity of Crete · GRBroad Institute · USCornell University · USPrinceton University · USQueen Mary University of London · GBScience for Life Laboratory · SETexas A&M University · USUdayana University · IDUniversity of California, Los Angeles · US
Funding
University of Michigan Postbaccalaureate Research Education Program (UM PREP)R25GM086262 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALLEN, BENJAMIN · 2009 to 2024
$6.1MIdentification of Factors Critical for SINE RetrotranspositionR01GM140135 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI KIDD, JEFFREY M, MORAN, JOHN V. · 2021 to 2024
$1.9MTools for Genetic and Genomic Studies in the DogR24GM082910 · NIGMS · CORNELL UNIVERSITY · PI ACLAND, GREGORY M · 2008 to 2011
$1.5MNIGMS NIH HHS R01 GM140135NIGMS NIH HHS R24 GM082910NIGMS NIH HHS R25 GM086262
Abstract
backgroundThe 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.
resultsWe 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.
conclusionsWe 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.
Indexed as
WolvesAllelesAnimalsChromosome MappingDemographyDogsNucleotidesPolymorphism, Single NucleotideNucleotidesCanineDemographic historyDogGenetic diversityGenomicsMitochondrial DNAVariation
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