Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs

文献类型： 外文期刊

第一作者： Jiang, Yi-Fan

作者： Jiang, Yi-Fan;Jiang, Yao;Jiang, Li;Ding, Xiang-Dong;Wang, Sheng;Wang, Ming-Shan;Wu, Dong-Dong;Wang, Chong-Long;Jiang, Yao;Wang, Jie-Ru;Xu, Ru-Hai;Dai, Li-He;Chu, Xiao-Hong;Wang, Wen-Wen;Zeng, Yong-Qing;Zhang, Qin;Fang, Ling-Zhao

作者机构：

期刊名称：ISCIENCE （ 影响因子：5.8； 五年影响因子：5.8 ）

ISSN：

年卷期： 2023 年 26 卷 3 期

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收录情况： SCI

摘要： Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.

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