Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
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Published:2023-08-15
Issue:1
Volume:24
Page:
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ISSN:1474-760X
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Container-title:Genome Biology
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language:en
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Short-container-title:Genome Biol
Author:
Meadows Jennifer R. S.ORCID, Kidd Jeffrey M.ORCID, Wang Guo-DongORCID, Parker Heidi G.ORCID, Schall Peter Z.ORCID, Bianchi MatteoORCID, Christmas Matthew J.ORCID, Bougiouri KatiaORCID, Buckley Reuben M.ORCID, Hitte ChristopheORCID, Nguyen Anthony K.ORCID, Wang ChaoORCID, Jagannathan VidhyaORCID, Niskanen Julia E.ORCID, Frantz Laurent A. F.ORCID, Arumilli Meharji, Hundi SruthiORCID, Lindblad-Toh KerstinORCID, Ginja CatarinaORCID, Agustina Kadek KarangORCID, André Catherine, Boyko Adam R.ORCID, Davis Brian W.ORCID, Drögemüller MichaelaORCID, Feng Xin-YaoORCID, Gkagkavouzis Konstantinos, Iliopoulos Giorgos, Harris Alexander C.ORCID, Hytönen Marjo K.ORCID, Kalthoff Daniela C.ORCID, Liu Yan-HuORCID, Lymberakis Petros, Poulakakis Nikolaos, Pires Ana ElisabeteORCID, Racimo FernandoORCID, Ramos-Almodovar FabianORCID, Savolainen PeterORCID, Venetsani Semina, Tammen ImkeORCID, Triantafyllidis AlexandrosORCID, vonHoldt BridgettORCID, Wayne Robert K.ORCID, Larson GregerORCID, Nicholas Frank W.ORCID, Lohi HannesORCID, Leeb TossoORCID, Zhang Ya-PingORCID, Ostrander Elaine A.ORCID
Abstract
Abstract
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.
Funder
National Institute of General Medical Sciences National Human Genome Research Institute Jane and Aatos Erkko Foundation European Research Council the Ronald Bruce Anstee Bequest INBS Infrastructure in Biology Health Swedish Research Council European Regional Development Fund Bali Animal Welfare Association National Science Foundation of China National Science and Technology Innovation 2030 Major Project of China National Key R&D Program of China Youth Innovation Promotion Association, Chinese Academy of Sciences Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences
Publisher
Springer Science and Business Media LLC
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