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
National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
iScience. 2023 Feb 2;26(3):106119. doi: 10.1016/j.isci.2023.106119. eCollection 2023 Mar 17.
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.
长读长测序（LRS）有助于基因组组装和结构变异（SV）的发现。在此，我们通过纳入11个LRS基因组构建了一个基于图的猪泛基因组，其平均BUSCO完整性评分为94.01%，揭示了206兆碱基的新序列。我们发现了183,352个非冗余SV（63%为新发现），占参考基因组的12.12%。通过对另外196个短读长测序样本中的SV进行基因分型，我们鉴定出数千个群体分层SV。特别地，我们检测到7568个西藏猪特有的SV，其中一些在西藏猪和低海拔猪之间表现出显著的群体分化，这可能与西藏猪对高海拔低氧的适应性有关。进一步整合功能基因组数据，发现了SV中可能有助于高海拔低氧适应的最有前景的候选基因。总体而言，我们的研究生成了一个基准泛基因组资源，用于阐明SV在猪的适应性进化、驯化和农艺性状遗传改良中的重要作用。
