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

	Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
	Meadows, JRS; Kidd, JM; Wang, GD; Parker, HG; Schall, PZ; Bianchi, M; Christmas, MJ; Bougiouri, K; Buckley, RM; Hitte, C; Nguyen, AK; Wang, C; Jagannathan, V; Niskanen, JE; Frantz, LAF; Arumilli, M; Hundi, S; Lindblad-Toh, K; Ginja, C; Agustina, KK; André, C; Boyko, AR; Davis, BW; Drögemüller, M; Feng, XY; Gkagkavouzis, K; Iliopoulos, G; Harris, AC; Hytönen, M; Kalthoff, DC; Liu, YH; Lymberakis, P; Poulakakis, N; Pires, AE; Racimo, F; Ramos-Almodovar, F; Savolainen, P; Venetsani, S; Tammen, I; Triantafyllidis, A; vonHoldt, B; Wayne, RK; Larson, G; Nicholas, FW; Lohi, H; Leeb, T; Zhang, YP; Ostrander, EA
	2023
发表期刊	GENOME BIOLOGY
ISSN	1474-760X
卷号	24 期号:1
摘要	BackgroundThe international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 x 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.ResultsWe 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.ConclusionsWe 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.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14078
专题	科研部门_行为遗传与进化（王国栋）
推荐引用方式 GB/T 7714	Meadows, JRS,Kidd, JM,Wang, GD,et al. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture[J]. GENOME BIOLOGY,2023,24(1).
APA	Meadows, JRS.,Kidd, JM.,Wang, GD.,Parker, HG.,Schall, PZ.,...&Ostrander, EA.(2023).Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.GENOME BIOLOGY,24(1).
MLA	Meadows, JRS,et al."Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture".GENOME BIOLOGY 24.1(2023).

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20240531104.pdf（4795KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	请求全文