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

TY - JOUR

T1 - Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs

AU - Jiang, Yi Fan

AU - Wang, Sheng

AU - Wang, Chong Long

AU - Xu, Ru Hai

AU - Wang, Wen Wen

AU - Jiang, Yao

AU - Wang, Ming Shan

AU - Jiang, Li

AU - Dai, Li He

AU - Wang, Jie Ru

AU - Chu, Xiao Hong

AU - Zeng, Yong Qing

AU - Fang, Ling Zhao

AU - Wu, Dong Dong

AU - Zhang, Qin

AU - Ding, Xiang Dong

N1 - Funding Information: This work was supported by grants for Key R&D Program of Shandong Province ( 2022LZGC003 ); China Agriculture Research System of MOF and MARA; the National Key Research and Development Project ( 2019YFE0106800 ); the 2020 Research Program of Sanya Yazhou Bay Science and Technology City ( SKJC-2020-02-007 ); the National Natural Science Foundation of China ( 32070568 , 31671327 and 31872327 ); Anhui Academy of Agricultural Sciences Key Laboratory Project ( 2019YL021 ); Hefei City Postdoctoral Science Foundation ( 2018PD22 ); China Postdoctoral Science Foundation ( 2020M681977 ); Key R&D Projects in Zhejiang Province ( 2021C02007 ) and Public Projects of Zhejiang Province ( LGN19C170005 ). Publisher Copyright: © 2023 The Authors

PY - 2023/3

Y1 - 2023/3

N2 - 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.

AB - 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.

KW - Animals

KW - Genomics

KW - Phylogenetics

UR - http://www.scopus.com/inward/record.url?scp=85148041417&partnerID=8YFLogxK

U2 - 10.1016/j.isci.2023.106119

DO - 10.1016/j.isci.2023.106119

M3 - Journal article

C2 - 36852268

AN - SCOPUS:85148041417

SN - 2589-0042

VL - 26

JO - iScience

JF - iScience

IS - 3

M1 - 106119

ER -