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

Meadows, Jennifer ; Kidd, Jeffrey M ; Wang, Guo-Dong ; Parker, Heidi G ; Schall, Peter Z ; Bianchi, Matteo ; Christmas, Matthew ; 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 ; Andre, Catherine ; Boyko, Adam R ; Davis, Brian W ; Drögemüller, Michaela ; Feng, Xin-Yao ; Gkagkavouzis, Konstantinos ; Iliopoulos, Giorgos ; Harris, Alexander C ; Hytonen, 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

Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA 2023

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Título:
Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
Autor: Meadows, Jennifer ; Kidd, Jeffrey M ; Wang, Guo-Dong ; Parker, Heidi G ; Schall, Peter Z ; Bianchi, Matteo ; Christmas, Matthew ; 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 ; Andre, Catherine ; Boyko, Adam R ; Davis, Brian W ; Drögemüller, Michaela ; Feng, Xin-Yao ; Gkagkavouzis, Konstantinos ; Iliopoulos, Giorgos ; Harris, Alexander C ; Hytonen, 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
Assuntos: Canine ; Demographic history ; Dog ; Genetic diversity ; Genetics ; Genetics and Breeding in Agricultural Sciences ; Genetik ; Genetik och förädling inom lantbruksvetenskap ; Genomics ; Mitochondrial DNA ; Variation
Notas: 0000-0003-1016-6998
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-510789
0000-0002-0850-230x
0000-0002-5025-2607
PMID 37582787
0000-0001-8338-0253
doi:10.1186/s13059-023-03023-7
0000-0002-6355-7581
ISI:001049571600001
Genome Biology, 1465-6906, 2023, 24
0000-0003-3394-6495
0000-0003-3936-4023
Descrição: Background: The 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. 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. Correction in: Genome Biology volume 24, Article number: 255 (2023)DOI: 10.1186/s13059-023-03101-w
Editor: Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA
Data de criação/publicação: 2023
Idioma: Inglês

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

Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA 2023

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