Volume 43 Issue 3
May  2022
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Jia-Qi Chen, Ming-Peng Zhang, Xin-Kai Tong, Jing-Quan Li, Zhou Zhang, Fei Huang, Hui-Peng Du, Meng Zhou, Hua-Shui Ai, Lu-Sheng Huang. Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds. Zoological Research, 2022, 43(3): 423-441. doi: 10.24272/j.issn.2095-8137.2021.379
Citation: Jia-Qi Chen, Ming-Peng Zhang, Xin-Kai Tong, Jing-Quan Li, Zhou Zhang, Fei Huang, Hui-Peng Du, Meng Zhou, Hua-Shui Ai, Lu-Sheng Huang. Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds. Zoological Research, 2022, 43(3): 423-441. doi: 10.24272/j.issn.2095-8137.2021.379

Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds

doi: 10.24272/j.issn.2095-8137.2021.379
Funds:  This study was supported by the National Swine Industry and Technology System of China (nycytx-009), and National Natural Science Foundation of China (31672383)
More Information
  • In pig-to-human xenotransplantation, the transmission risk of porcine endogenous retroviruses (PERVs) is of great concern. However, the distribution of PERVs in pig genomes, their genetic variation among Eurasian pigs, and their evolutionary history remain unclear. We scanned PERVs in the current pig reference genome (assembly Build 11.1), and identified 36 long complete or near-complete PERVs (lcPERVs) and 23 short incomplete PERVs (siPERVs). Besides three known PERVs (PERV-A, -B, and -C), four novel types (PERV-JX1, -JX2, -JX3, and -JX4) were detected in this study. According to evolutionary analyses, the newly discovered PERVs were more ancient, and PERV-Bs probably experienced a bottleneck ~0.5 million years ago (Ma). By analyzing 63 high-quality porcine whole-genome resequencing data, we found that the PERV copy numbers in Chinese pigs were lower (32.0±4.0) than in Western pigs (49.1±6.5). Additionally, the PERV sequence diversity was lower in Chinese pigs than in Western pigs. Regarding the lcPERV copy numbers, PERV-A and -JX2 in Western pigs were higher than in Chinese pigs. Notably, Bama Xiang (BMX) pigs had the lowest PERV copy number (27.8±5.1), and a BMX individual had no PERV-C and the lowest PERV copy number (23), suggesting that BMX pigs were more suitable for screening and/or modification as xenograft donors. Furthermore, we identified 451 PERV transposon insertion polymorphisms (TIPs), of which 86 were shared by all 10 Chinese and Western pig breeds. Our findings provide systematic insights into the genomic distribution, variation, evolution, and possible biological function of PERVs.
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