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

التفاصيل البيبلوغرافية
العنوان: Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
المؤلفون: Jennifer R. S. Meadows, Jeffrey M. Kidd, Guo-Dong Wang, Heidi G. Parker, Peter Z. Schall, Matteo Bianchi, Matthew J. Christmas, Katia Bougiouri, Reuben M. Buckley, Christophe Hitte, Anthony K. Nguyen, Chao Wang, Vidhya Jagannathan, Julia E. Niskanen, Laurent A. F. Frantz, Meharji Arumilli, Sruthi Hundi, Kerstin Lindblad-Toh, Catarina Ginja, Kadek Karang Agustina, Catherine André, Adam R. Boyko, Brian W. Davis, Michaela Drögemüller, Xin-Yao Feng, Konstantinos Gkagkavouzis, Giorgos Iliopoulos, Alexander C. Harris, Marjo K. Hytönen, Daniela C. Kalthoff, Yan-Hu Liu, Petros Lymberakis, Nikolaos Poulakakis, Ana Elisabete Pires, Fernando Racimo, Fabian Ramos-Almodovar, Peter Savolainen, Semina Venetsani, Imke Tammen, Alexandros Triantafyllidis, Bridgett vonHoldt, Robert K. Wayne, Greger Larson, Frank W. Nicholas, Hannes Lohi, Tosso Leeb, Ya-Ping Zhang, Elaine A. Ostrander
المصدر: Genome Biology, Vol 24, Iss 1, Pp 1-41 (2023)
بيانات النشر: BMC, 2023.
سنة النشر: 2023
المجموعة: LCC:Biology (General)
LCC:Genetics
مصطلحات موضوعية: Canine, Dog, Genomics, Variation, Demographic history, Mitochondrial DNA, Biology (General), QH301-705.5, Genetics, QH426-470
الوصف: 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.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1474-760X
Relation: https://doaj.org/toc/1474-760X
DOI: 10.1186/s13059-023-03023-7
URL الوصول: https://doaj.org/article/070c928591184511adb6d4a61799d1db
رقم الأكسشن: edsdoj.070c928591184511adb6d4a61799d1db
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:1474760X
DOI:10.1186/s13059-023-03023-7