A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation
文献类型： 外文期刊
作者： Bian, Peipei 1 ; Li, Jiaxin 1 ; Zhou, Shishuo 1 ; Wang, Xingquan 1 ; Gong, Mian 1 ; Guo, Xi 1 ; Cai, Yudong 1 ; Yang, Qimeng 1 ; Fu, Jiaqi 1 ; Li, Rongrong 1 ; Huang, Shuhong 1 ; Luo, Funong 1 ; Shah, Ali Mujtaba 1 ; Lenstra, Johannes A. 3 ; Mwacharo, Joram M. 4 ; Li, Ran 1 ; Ren, Gang 1 ; Wang, Xiaolong 1 ; Li, Cong 1 ; Zheng, Wenxin 6 ; Jiang, Yu 1 ; Wang, Xihong 1 ;
作者机构： 1.Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712100, Shaanxi, Peoples R China
2.Chinese Acad Agr Sci CAAS, Inst Anim Sci, State Key Lab Anim Biotech Breeding, Beijing 100193, Peoples R China
3.Univ Utrecht, Fac Vet Med, NL-3508 TD Utrecht, Netherlands
4.Int Ctr Agr Res Dry Areas ICARDA, Dryland Livestock Genom, Addis Ababa, Ethiopia
5.Scotlands Rural Coll SRUC, Ctr Trop Livestock Genet & Hlth CTLGH, Anim & Vet Sci, Roslin Inst Bldg, Midlothian, England
6.Xinjiang Uyghur Autonomous Reg Acad Anim Sci, Urumqi 830011, Xinjiang, Peoples R China
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
页码：
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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