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

	Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs
	Jiang, YF; Wang, S; Wang, CL; Xu, RH; Wang, WW; Jiang, Y; Wang, MS; Jiang, L; Dai, LH; Wang, JR; Chu, XH; Zeng, YQ; Fang, LZ; Wu, DD; Zhang, Q; Ding, XD
	2023
发表期刊	ISCIENCE
卷号	26 期号:3
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.
收录类别	SCI
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/14073
专题	科研部门_进化与发育转录组学（吴东东）
推荐引用方式 GB/T 7714	Jiang, YF,Wang, S,Wang, CL,et al. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs[J]. ISCIENCE,2023,26(3).
APA	Jiang, YF.,Wang, S.,Wang, CL.,Xu, RH.,Wang, WW.,...&Ding, XD.(2023).Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.ISCIENCE,26(3).
MLA	Jiang, YF,et al."Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs".ISCIENCE 26.3(2023).

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