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

文献类型： 外文期刊

作者： Jiang, Yi-Fan 1 ; Wang, Sheng 2 ; Wang, Chong-Long 3 ; Xu, Ru-Hai 4 ; Wang, Wen-Wen 5 ; Jiang, Yao 1 ; Wang, Ming-Shan 2 ; Jiang, Li 1 ; Dai, Li-He 4 ; Wang, Jie-Ru 3 ; Chu, Xiao-Hong 4 ; Zeng, Yong-Qing 5 ; Fang, Ling-Zhao 6 ; Wu, Dong-Dong 2 ; Zhang, Qin 5 ; Ding, Xiang-Dong 1 ;

作者机构： 1.China Agr Univ, Coll Anim Sci & Technol, Natl Engn Lab Anim Breeding, Lab Anim Genet Breeding & Reprod,Minist Agr & Rur, Beijing 100193, Peoples R China

2.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Yunnan Lab Mol Biol Domest Anim, Kunming 650223, Yunnan, Peoples R China

3.Anhui Acad Agr Sci, Inst Anim Husb & Vet Med, Key Lab Pig Mol Quantitat Genet, Anhui Prov Key Lab Livestock & Poultry Prod Safet, Hefei 230031, Peoples R China

4.Zhejiang Acad Agr Sci, Inst Anim Husb & Vet Sci, Key Lab Anim Genet & Breeding Zhejiang Prov, Hangzhou 310021, Peoples R China

5.Shandong Agr Univ, Coll Anim Sci & Technol, Shandong Prov Key Lab Anim Biotechnol & Dis Contr, Tai An 271001, Shandong, Peoples R China

6.Aarhus Univ, Ctr Quantitat Genet & Genom, DK-8000 Aarhus, Denmark

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

页码：

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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