Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture - Université de Rennes Accéder directement au contenu
Article Dans Une Revue Genome Biology Année : 2023

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

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

Résumé

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.
Fichier principal
Vignette du fichier
s13059-023-03023-7.pdf (4.68 Mo) Télécharger le fichier
13059_2023_3023_MOESM1_ESM.xlsx (3.27 Mo) Télécharger le fichier
13059_2023_3023_MOESM2_ESM.pdf (5.52 Mo) Télécharger le fichier
13059_2023_3023_MOESM3_ESM.pdf (1021.64 Ko) Télécharger le fichier
s13059-023-03101-w.pdf (1.24 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte
Commentaire : Updated version of record: An Author Correction to this article was published on 07 November 2023

Dates et versions

hal-04197751 , version 1 (06-09-2023)
hal-04197751 , version 2 (14-11-2023)

Licence

Paternité

Identifiants

Citer

Jennifer R S Meadows, Jeffrey M Kidd, Guo-Dong Wang, Heidi G Parker, Peter Z Schall, et al.. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biology, 2023, 24 (1), pp.187. ⟨10.1186/s13059-023-03023-7⟩. ⟨hal-04197751v2⟩
46 Consultations
377 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More