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

• Published in: iScience Vol. 26; no. 3; p. 106119
• Main Authors: Jiang, Yi-Fan, Wang, Sheng, Wang, Chong-Long, Xu, Ru-Hai, Wang, Wen-Wen, Jiang, Yao, Wang, Ming-Shan, Jiang, Li, Dai, Li-He, Wang, Jie-Ru, Chu, Xiao-Hong, Zeng, Yong-Qing, Fang, Ling-Zhao, Wu, Dong-Dong, Zhang, Qin, Ding, Xiang-Dong
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 17.03.2023; Elsevier
• Subjects: Animals; Genomics; Phylogenetics; Phylogenetics; Genomics; Animals
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2023.106119

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. [Display omitted] •De novo genome assemblies for 10 pigs using long-read sequencing•Built a graph-based pig pangenome revealing 206-mb novel sequences•Discovered 183,352 nonredundant structural variation with 63% novel•Tibetan specific structural variations associated with the high-altitude adaptation Animals; Genomics; Phylogenetics