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.
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DOI：
10.1186/s13059-023-03023-7
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发表时间：
2023-08-15
期刊：
影响因子：
12.3
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中科院分区：
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--
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国际Dog 10 K项目旨在测序和分析数千只犬的基因组。通过对1987个个体的20 ×数据进行分析，包括1611只狗（321个品种），309只乡村狗，63只狼和4只郊狼，我们确定了犬科动物的基因组变异，为详细研究驯化，行为，形态，疾病易感性以及基因组结构和功能奠定了基础。我们报告了跨越常染色体、X染色体和线粒体的> 48 M单核苷酸、插入缺失和结构变体的分析。我们发现超过75%的239个样本品种的变化。等位基因共享分析表明，94.9%的品种形成单系簇和25个主要分支。德国牧羊犬及其相关品种与来自多个分支的独立品种具有最高的等位基因共享。平均而言，每个品种的狗与UU_Cfam_GSD_1.0参考的差异在于26，960个大于50 bp的缺失和14，034个大于50 bp的插入，而狼的变异多14%。发现的变异包括来自926个亲本基因的逆转录基因插入。为了帮助功能优先化，单核苷酸变体用SnpEff和Zoonomia CNOMP约束分数注释。限制位置与等位基因频率呈负相关。最后，评估了Dog 10 K数据作为插补参考组的效用，在不同的基因分型平台密度（包括Dog 10 K集合中未包含的品种）中生成高置信度调用。我们已经开发了一个密集的数据集1987测序犬科动物，揭示了等位基因共享模式，确定可能的功能变异，告知品种结构，并实现准确的插补。Dog 10 K数据是公开的。在线版本包含补充材料，可通过10.1186/s13059-023-03023-7获得。
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. 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. 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. The online version contains supplementary material available at 10.1186/s13059-023-03023-7.
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影响因子：
16.6
作者：
Botigué LR;Song S;Scheu A;Gopalan S;Pendleton AL;Oetjens M;Taravella AM;Seregély T;Zeeb-Lanz A;Arbogast RM;Bobo D;Daly K;Unterländer M;Burger J;Kidd JM;Veeramah KR
通讯作者：
Veeramah KR
影响因子：
7.3
作者：
通讯作者：
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来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
7
作者：
Batcher, Kevin;Varney, Scarlett;York, Daniel;Blacksmith, Matthew;Kidd, Jeffrey M;Rebhun, Robert;Dickinson, Peter;Bannasch, Danika
通讯作者：
Bannasch, Danika