School of Life Sciences, Yunnan University, Kunming 650500, China.
Yunnan International Joint Laboratory of Virology and Immunology, Kunming 650500, China.
Viruses. 2024 Aug 16;16(8):1306. doi: 10.3390/v16081306.
Endogenous viral elements (EVEs) have been reported to exist widely in the genomes of eukaryotic organisms, and they are closely associated with the growth, development, genetics, adaptation, and evolution of their hosts. In this study, two methods-homologous sequence search and genome alignment-were used to explore the endogenous viral sequences in the genomes of species. Results revealed abundant endogenous pararetroviruses (EPRVs) in the genomes of species, including 786 sequences belonging to five known taxa such as and other unclassified taxa. Differences were observed in the detected EPRVs between the two methods, with the homologous sequence search having a greater number of EPRVs. On the contrary, genome alignment identified various types and sources of virus-like sequences. Furthermore, through genome alignment, a 267-bp sequence with 95% similarity to the gene encoding the aphid-transmitted protein of () was discovered in the genome, which was likely a recent insertion. In addition, the statistical analysis of the genome alignment results indicated a remarkably higher abundance of virus-like sequences in the genomes of polyploid strawberries compared with diploid ones. Moreover, the differences in virus-like sequences were observed between the genomes of species and those of their close relatives. This study enriched the diversity of viruses that infect strawberries, and laid a theoretical foundation for further research on the origin of endogenous viruses in the strawberry genome, host-virus interactions, adaptation, evolution, and their functions.
内源性病毒元件 (EVEs) 广泛存在于真核生物的基因组中，与宿主的生长、发育、遗传、适应和进化密切相关。本研究采用同源序列搜索和基因组比对两种方法，探索 物种基因组中的内源性病毒序列。结果表明， 物种的基因组中存在丰富的内源性逆转录病毒 (EPRVs)，包括属于 和其他未分类分类群等 5 个已知分类群的 786 个序列。两种方法检测到的 EPRVs 存在差异，同源序列搜索方法检测到的 EPRVs 数量更多。相反，基因组比对鉴定出各种类型和来源的病毒样序列。此外，通过基因组比对，在 基因组中发现了一段与 () 编码的蚜虫传播蛋白基因具有 95%相似性的 267bp 序列，可能是最近的插入。此外，基因组比对结果的统计分析表明，多倍体草莓基因组中病毒样序列的丰度明显高于二倍体。此外， 物种基因组与近亲基因组中的病毒样序列存在差异。本研究丰富了感染草莓的病毒多样性，为进一步研究草莓基因组内源性病毒的起源、宿主-病毒相互作用、适应、进化及其功能奠定了理论基础。
