TY - JOUR

T1 - Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

AU - Meadows, Jennifer R. S.

AU - Kidd, Jeffrey M.

AU - Wang, Guo Dong

AU - Parker, Heidi G.

AU - Schall, Peter Z.

AU - Bianchi, Matteo

AU - Christmas, Matthew J.

AU - Bougiouri, Katia

AU - Buckley, Reuben M.

AU - Hitte, Christophe

AU - Nguyen, Anthony K.

AU - Wang, Chao

AU - Jagannathan, Vidhya

AU - Niskanen, Julia E.

AU - Frantz, Laurent A. F.

AU - Arumilli, Meharji

AU - Hundi, Sruthi

AU - Lindblad-Toh, Kerstin

AU - Ginja, Catarina

AU - Agustina, Kadek Karang

AU - André, Catherine

AU - Boyko, Adam R.

AU - Davis, Brian W.

AU - Drögemüller, Michaela

AU - Feng, Xin-Yao

AU - Gkagkavouzis, Konstantinos

AU - Iliopoulos, Giorgos

AU - Harris, Alexander C.

AU - Hytönen, Marjo K.

AU - Kalthoff, Daniela C.

AU - Liu, Yan-Hu

AU - Lymberakis, Petros

AU - Poulakakis, Nikolaos

AU - Pires, Ana Elisabete

AU - Racimo, Fernando

AU - Ramos-Almodovar, Fabian

AU - Savolainen, Peter

AU - Venetsani, Semina

AU - Tammen, Imke

AU - Triantafyllidis, Alexandros

AU - vonHoldt, Bridgett

AU - Wayne, Robert K.

AU - Larson, Greger

AU - Nicholas, Frank W.

AU - Lohi, Hannes

AU - Leeb, Tosso

AU - Zhang, Ya-Ping

AU - Ostrander, Elaine A.

N1 - Publisher Copyright: © 2023. BioMed Central Ltd., part of Springer Nature.

PY - 2023

Y1 - 2023

N2 - 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.

AB - 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.

KW - Canine

KW - Demographic history

KW - Dog

KW - Genetic diversity

KW - Genomics

KW - Mitochondrial DNA

KW - Variation

U2 - 10.1186/s13059-023-03023-7

DO - 10.1186/s13059-023-03023-7

M3 - Journal article

C2 - 37582787

AN - SCOPUS:85168060188

VL - 24

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

SN - 1474-7596

M1 - 187

ER -