RT Journal
A1 Li, Zhengcao
A1 Liu, Xiaohong
A1 Wang, Chen
A1 Li, Zhenyang
A1 Jiang, Bo
A1 Zhang, Ruifeng
A1 Tong, Lu
A1 Qu, Youping
A1 He, Sheng
A1 Chen, Haifan
A1 Mao, Yafei
A1 Li, Qingnan
A1 Pook, Torsten
A1 Wu, Yu
A1 Zan, Yanjun
A1 Zhang, Hui
A1 Li, Lu
A1 Wen, Keying
A1 Chen, Yaosheng
T1 The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
JF Genome Research 
JO Genome Research 
YR 2023 
FD October 01 
VO 33 
IS 10 
SP 1833 
OP 1847 
DO 10.1101/gr.277638.122 
UL http://genome.cshlp.org/content/33/10/1833.abstract 
AB 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.