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


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.

SUBMITTER: Meadows JRS 

PROVIDER: S-EPMC10426128 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Meadows Jennifer R S JRS   Kidd Jeffrey M JM   Wang Guo-Dong GD   Parker Heidi G HG   Schall Peter Z PZ   Bianchi Matteo M   Christmas Matthew J MJ   Bougiouri Katia K   Buckley Reuben M RM   Hitte Christophe C   Nguyen Anthony K AK   Wang Chao C   Jagannathan Vidhya V   Niskanen Julia E JE   Frantz Laurent A F LAF   Arumilli Meharji M   Hundi Sruthi S   Lindblad-Toh Kerstin K   Ginja Catarina C   Agustina Kadek Karang KK   André Catherine C   Boyko Adam R AR   Davis Brian W BW   Drögemüller Michaela M   Feng Xin-Yao XY   Gkagkavouzis Konstantinos K   Iliopoulos Giorgos G   Harris Alexander C AC   Hytönen Marjo K MK   Kalthoff Daniela C DC   Liu Yan-Hu YH   Lymberakis Petros P   Poulakakis Nikolaos N   Pires Ana Elisabete AE   Racimo Fernando F   Ramos-Almodovar Fabian F   Savolainen Peter P   Venetsani Semina S   Tammen Imke I   Triantafyllidis Alexandros A   vonHoldt Bridgett B   Wayne Robert K RK   Larson Greger G   Nicholas Frank W FW   Lohi Hannes H   Leeb Tosso T   Zhang Ya-Ping YP   Ostrander Elaine A EA  

Genome biology 20230815 1


<h4>Background</h4>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.<h4>Results</h4>We report the analysis of > 48 M single-nucleot  ...[more]

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