A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation

文献类型： 外文期刊

第一作者： Bian, Peipei

作者： Bian, Peipei;Li, Jiaxin;Zhou, Shishuo;Wang, Xingquan;Gong, Mian;Guo, Xi;Cai, Yudong;Yang, Qimeng;Fu, Jiaqi;Li, Rongrong;Huang, Shuhong;Luo, Funong;Shah, Ali Mujtaba;Li, Ran;Ren, Gang;Wang, Xiaolong;Li, Cong;Jiang, Yu;Wang, Xihong;Gong, Mian;Lenstra, Johannes A.;Mwacharo, Joram M.;Mwacharo, Joram M.;Zheng, Wenxin

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关键词： graph-based pangenome; structural variations; de novo assembly; domestication; low-coverage sequencing

期刊名称：MOLECULAR BIOLOGY AND EVOLUTION （ 影响因子：5.3； 五年影响因子：11.9 ）

ISSN： 0737-4038

年卷期： 2024 年 41 卷 12 期

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收录情况： SCI

摘要： Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.

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