无PERV传染性“中畜”五指山小型猪近交系全基因组重测序分析

doi:10.16431/j.cnki.1671-7236.2025.06.001

摘要/Abstract

摘要： 【目的】自前期选育获得的无猪内源性反转录病毒(Porcine endogenous retrovirus，PERV)传染性“中畜”五指山小型猪近交系(Zhong Xu Wuzhishan Mini-pig Inbred line，ZXWIPIG)新品系中，选取1头雌性猪(ZXWIPIG505)进行全基因组重测序分析，以进一步从分子水平上阐释无PERV传染性猪新品系的序列特征。【方法】分离ZXWIPIG505外周血单个核细胞并提取其基因组DNA，利用Illumina HiSeq-4000测序平台进行全基因组重测序。分别使用BLAST和SAMtools 0.1.19软件，提取ZXWIPIG505基因组中整合的PERV长片段和PERV-pol基因序列片段，并使用DNAStar软件对整合的PERV结构基因序列进行分析。将ZXWIPIG505中整合的PERV-pol基因序列特征与前期鉴定的PERV-pol缺陷型ZXWIPIG452中PERV-pol基因序列进行比较研究。【结果】ZXWIPIG505全基因组重测序平均测序深度为14.32×，测序数据有效率为97.21%，Q20为94.37%，Q30为87.03%，GC含量为43.38%，表明本次测序数据质量较高。ZXWIPIG505基因组中共整合5条PERV长片段，其中仅scaffold5028含有PERV全部结构基因，但均为缺陷型。ZXWIPIG505基因组中共整合85条PERV-pol基因片段序列，比对发现所有PERV-pol基因片段均不完整，为缺陷型。ZXWIPIG505和ZXWIPIG452基因组中整合的PERV-pol基因序列存在高度相似性，60条序列长度相同，75条序列在猪基因组中的整合位点相同，42条序列的PERV-pol基因提前终止位点相同。【结论】前期选育的ZXWIPIG505为PERV-pol基因缺陷型猪，并且ZXWIPIG505和ZXWIPIG452中整合的PERV-pol基因序列具有高度相似性。

关键词: 猪内源性反转录病毒; “中畜”五指山小型猪近交系; 基因缺陷型; 全基因组重测序

Abstract: 【Objective】 One female pig (ZXWIPIG505) was selected for whole genome resequencing analysis from a new strain of Porcine endogenous retrovirus (PERV) non-transmitting Zhong Xu Wuzhishan Mini-pig Inbred line (ZXWIPIG),in order to further interpret sequence characteristics of the new PERV non-transmitting pig strain at molecular level.【Method】 Genomic DNA of ZXWIPIG505 peripheral blood mononuclear cells was extracted and whole genome resequencing was performed with Illumina hiseq-4000 sequencing platform.Blast and SAMtools-0.1.19 software were utilized to extract the PERV long fragment and PERV-pol gene sequence fragment integrated in ZXWIPIG505 genome,and DNAStar software was used to analyze the integrated PERV structural gene sequence.And then,the integrated PERV-pol gene sequence in ZXWIPIG505 were compared with the PERV-pol gene sequence in the previously identified PERV-pol deficient ZXWIPIG452.【Result】 The average sequencing depth of ZXWIPIG505 whole genome resequencing was 14.32×,and the effective rate of sequencing data was 97.21%.Q20,Q30 and GC content were respectively 94.37%,87.03%,and 43.38%.The above results indicated that the quality of this sequencing data was high.Five long PERV fragments were integrated in ZXWIPIG505 genome,of which only scaffold5028 contained all PERV structural genes but was defective.Eighty-five integrated PERV-pol gene fragments were detected in the ZXWIPIG505 genome,which were all found incomplete and defective by comparison.The PERV-pol gene sequences integrated into the genomes of ZXWIPIG505 and ZXWIPIG452 exhibited high similarity.There were 60 fragments of the same length,75 fragments with identical integration sites in the pig genome,and 42 fragments with the same PERV-pol gene premature termination sites.【Conclusion】 ZXWIPIG505 selected in the early stage was demonstrated to be a PERV-pol gene-deficient pig,and the integrated PERV-pol gene sequences in ZXWIPIG505 and ZXWIPIG452 had high similarity.

Key words: Porcine endogenous retrovirus; Zhong Xu Wuzhishan Mini-pig inbred line; gene deficient variant; whole genome resequencing

中图分类号:

S858.292

章冰艳, 范瑞, 冯书堂, 贾俊婷, 张建斌, 马玉媛. 无PERV传染性“中畜”五指山小型猪近交系全基因组重测序分析[J]. 中国畜牧兽医, 2025, 52(6): 2459-2467.

ZHANG Bingyan, FAN Rui, FENG Shutang, JIA Junting, ZHANG Jianbin, MA Yuyuan. Whole Genome Resequencing Analysis of PERV Non-transmitting Zhong Xu Wuzhishan Mini-pig Inbred Line[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(6): 2459-2467.

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