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

Jennifer R.S. Meadows, Jeffrey M. Kidd, Guo Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A.F. Frantz, Meharji Arumilli, Sruthi Hundi, Kerstin Lindblad-Toh, Catarina Ginja, Kadek Karang AgustinaCatherine André, Adam R. Boyko, Brian W. Davis, Michaela Drögemüller, Xin Yao Feng, Konstantinos Gkagkavouzis, Giorgos Iliopoulos, Alexander C. Harris, Marjo K. Hytönen, Daniela C. Kalthoff, Yan Hu Liu, Petros Lymberakis, Nikolaos Poulakakis, Ana Elisabete Pires, Fernando Racimo, Fabian Ramos-Almodovar, Peter Savolainen, Semina Venetsani, Imke Tammen, Alexandros Triantafyllidis, Bridgett vonHoldt, Robert K. Wayne, Greger Larson, Frank W. Nicholas, Hannes Lohi, Tosso Leeb, Ya Ping Zhang, Elaine A. Ostrander

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

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.

Original languageEnglish (US)
Article number187
JournalGenome biology
Volume24
Issue number1
DOIs
StatePublished - Dec 2023

All Science Journal Classification (ASJC) codes

  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Cell Biology

Keywords

  • Canine
  • Demographic history
  • Dog
  • Genetic diversity
  • Genomics
  • Mitochondrial DNA
  • Variation

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