据报道,内源性病毒元件(EVE)广泛存在于真核生物的基因组中,它们与增长密切相关,发展,遗传学,适应,以及它们宿主的进化。在这项研究中,使用两种方法-同源序列搜索和基因组比对-来探索Fragaria物种基因组中的内源性病毒序列。结果表明,在Fragaria物种的基因组中存在丰富的内源性副逆转录病毒(EPRV),包括属于五个已知类群的786个序列,例如Caulimovirus和其他未分类类群。两种方法在检测到的EPRV中观察到差异,同源序列搜索具有更大数量的EPRV。相反,基因组比对鉴定了各种类型和来源的病毒样序列。此外,通过基因组比对,在黄蜂基因组中发现了一个267bp的序列,该序列与编码草莓脉带病毒(Caulimovirusvenafraagariae)的蚜虫传播蛋白的基因具有95%的相似性,这可能是最近的插入。此外,基因组比对结果的统计分析表明,与二倍体相比,多倍体草莓基因组中的病毒样序列丰度明显更高。此外,在Fragaria物种及其近亲的基因组之间观察到病毒样序列的差异。这项研究丰富了感染草莓的病毒的多样性,为进一步研究草莓基因组中内源性病毒的起源奠定了理论基础,宿主-病毒相互作用,适应,进化,以及它们的功能。
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 Fragaria species. Results revealed abundant endogenous pararetroviruses (EPRVs) in the genomes of Fragaria species, including 786 sequences belonging to five known taxa such as
Caulimovirus 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 Strawberry vein banding virus (
Caulimovirus venafragariae) was discovered in the F. chiloensis 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 Fragaria 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.