猪内源性逆转录病毒(ERVs)中由梭罗长末端重复序列(Solo-LTRs)诱导的多态性研究。

IF 3.8 3区 医学 Q2 VIROLOGY
Viruses-Basel Pub Date : 2024-11-20 DOI:10.3390/v16111801
Cai Chen, Zhanyu Du, Yao Zheng, Hong Chen, Ahmed A Saleh, Naisu Yang, Mengli Wang, Phiri Azele, Xiaoyan Wang, Chengyi Song
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引用次数: 0

摘要

ERV的5'和3'长末端重复序列(LTR)之间会发生同源重组事件,从而产生solo-LTR,这会导致不同基因组中与solo-LTR相关的多态性。在当前的研究中,建立了过滤solo-LTR的特定标准,结果在21个基因组中平均发现了5630个solo-LTR。随后,研究人员制定了检测猪基因组中单体-LTR 多态性的方案,结果发现了 927 个预测的单体-LTR 多态性位点。经过验证和过滤过程后,保留了 603 个高度可靠的单核-LTR 多态性位点,与参考基因组相比,涉及 446 个单核-LTR 存在位点(单核-LTR+)和 157 个单核-LTR 缺失位点(单核-LTR-)。与基因/功能区的交叉分析表明,有 248 个 solo-LTR- 位点和 23 个 solo-LTR+ 位点与基因重叠,或位于基因或功能区附近,对不同的基因结构产生了影响。此外,通过利用 156 个 solo-LTR 多态性位点进行群体遗传分析,观察到这些 solo-LTR 位点有效地将不同品种聚类在一起,符合预期并突出了其实用性。这项研究成功地建立了检测solo-LTR多态位点的方法。通过应用这些方法,共确定了603个高可靠性的solo-LTR多态性位点,其中近一半与基因或功能区相关。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Investigation of Polymorphisms Induced by the Solo Long Terminal Repeats (Solo-LTRs) in Porcine Endogenous Retroviruses (ERVs).

Homologous recombination events take place between the 5' and 3' long terminal repeats (LTRs) of ERVs, resulting in the generation of solo-LTR, which can cause solo-LTR-associated polymorphism across different genomes. In the current study, specific criteria were established for the filtration of solo-LTRs, resulting in an average of 5630 solo-LTRs being identified in 21 genomes. Subsequently, a protocol was developed for detecting solo-LTR polymorphisms in the pig genomes, resulting in the discovery of 927 predicted solo-LTR polymorphic sites. Following verification and filtration processes, 603 highly reliable solo-LTR polymorphic sites were retained, involving 446 solo-LTR presence sites (solo-LTR+) and 157 solo-LTR absence sites (solo-LTR-) relative to the reference genome. Intersection analysis with gene/functional regions revealed that 248 solo-LTR- sites and 23 solo-LTR+ sites overlapped with genes or were in the vicinity of genes or functional regions, impacting a diverse range of gene structures. Moreover, through the utilization of 156 solo-LTR polymorphic sites for population genetic analysis, it was observed that these solo-LTR loci effectively clustered various breeds together, aligning with expectations and underscoring their practical utility. This study successfully established a methodology for detecting solo-LTR polymorphic sites. By applying these methods, a total of 603 high-reliability solo-LTR polymorphic sites were pinpointed, with nearly half of them being linked to genes or functional regions.

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来源期刊
Viruses-Basel
Viruses-Basel VIROLOGY-
CiteScore
7.30
自引率
12.80%
发文量
2445
审稿时长
1 months
期刊介绍: Viruses (ISSN 1999-4915) is an open access journal which provides an advanced forum for studies of viruses. It publishes reviews, regular research papers, communications, conference reports and short notes. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. There is no restriction on the length of the papers. The full experimental details must be provided so that the results can be reproduced. We also encourage the publication of timely reviews and commentaries on topics of interest to the virology community and feature highlights from the virology literature in the ''News and Views'' section. Electronic files or software regarding the full details of the calculation and experimental procedure, if unable to be published in a normal way, can be deposited as supplementary material.
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