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

Authors :
Meadows, Jennifer R. S.
Kidd, Jeffrey M.
Wang, Guo-Dong
Parker, Heidi G.
Schall, Peter Z.
Bianchi, Matteo
Christmas, Matthew J.
Bougiouri, Katia
Buckley, Reuben M.
Hitte, Christophe
Nguyen, Anthony K.
Wang, Chao
Jagannathan, Vidhya
Niskanen, Julia E.
Frantz, Laurent A. F.
Arumilli, Meharji
Hundi, Sruthi
Lindblad-Toh, Kerstin
Ginja, Catarina
Agustina, Kadek Karang
André, Catherine
Boyko, Adam R.
Davis, Brian W.
Drögemüller, Michaela
Feng, Xin-Yao
Gkagkavouzis, Konstantinos
Iliopoulos, Giorgos
Harris, Alexander C.
Hytönen, Marjo K.
Kalthoff, Daniela C.
Liu, Yan-Hu
Lymberakis, Petros
Poulakakis, Nikolaos
Pires, Ana Elisabete
Racimo, Fernando
Ramos-Almodovar, Fabian
Savolainen, Peter
Venetsani, Semina
Tammen, Imke
Triantafyllidis, Alexandros
vonHoldt, Bridgett
Wayne, Robert K.
Larson, Greger
Nicholas, Frank W.
Lohi, Hannes
Leeb, Tosso
Zhang, Ya-Ping
Ostrander, Elaine A.
Meadows, Jennifer R. S.
Kidd, Jeffrey M.
Wang, Guo-Dong
Parker, Heidi G.
Schall, Peter Z.
Bianchi, Matteo
Christmas, Matthew J.
Bougiouri, Katia
Buckley, Reuben M.
Hitte, Christophe
Nguyen, Anthony K.
Wang, Chao
Jagannathan, Vidhya
Niskanen, Julia E.
Frantz, Laurent A. F.
Arumilli, Meharji
Hundi, Sruthi
Lindblad-Toh, Kerstin
Ginja, Catarina
Agustina, Kadek Karang
André, Catherine
Boyko, Adam R.
Davis, Brian W.
Drögemüller, Michaela
Feng, Xin-Yao
Gkagkavouzis, Konstantinos
Iliopoulos, Giorgos
Harris, Alexander C.
Hytönen, Marjo K.
Kalthoff, Daniela C.
Liu, Yan-Hu
Lymberakis, Petros
Poulakakis, Nikolaos
Pires, Ana Elisabete
Racimo, Fernando
Ramos-Almodovar, Fabian
Savolainen, Peter
Venetsani, Semina
Tammen, Imke
Triantafyllidis, Alexandros
vonHoldt, Bridgett
Wayne, Robert K.
Larson, Greger
Nicholas, Frank W.
Lohi, Hannes
Leeb, Tosso
Zhang, Ya-Ping
Ostrander, Elaine A.
Publication Year :
2023

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.

Details

Database :
OAIster
Notes :
application/pdf, English
Publication Type :
Electronic Resource
Accession number :
edsoai.on1428110769
Document Type :
Electronic Resource
Full Text :
https://doi.org/10.1186.s13059-023-03023-7