Zhengcao Li1, Xiaohong Liu1, Chen Wang1, Zhenyang Li1, Bo Jiang1, Ruifeng Zhang1, Lu Tong1, Youping Qu1, Sheng He1, Haifan Chen1, Yafei Mao2, Qingnan Li1, Torsten Pook3, Yu Wu1, Yanjun Zan4, Hui Zhang1, Lu Li1, Keying Wen1 and Yaosheng Chen1 1State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China; 2Bio-X Institutes, Shanghai Jiao Tong University, 200240 Shanghai, China; 3Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6700 AH, The Netherlands; 4Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China Corresponding authors: chyaoshmail.sysu.edu.cn, lizhc7mail.sysu.edu.cn Abstract

Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277638.122.

Freely available online through the Genome Research Open Access option.

Received December 31, 2022. Accepted September 12, 2023.