Center for Grapevine Biotechnology, W.H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711, USA.
Center for Grapevine Biotechnology, W.H. Darr College of Agriculture, Missouri State University, Mountain Grove, MO 65711, USA.
Virus Res. 2017 Feb 2;229:24-27. doi: 10.1016/j.virusres.2016.12.012. Epub 2016 Dec 21.
Viral small RNAs (vsRNAs) include viral small interfering RNAs (vsiRNAs) that are initiators and products of RNA silencing, and small RNAs that are derived from viral RNAs with function still unknown. Sequencing of vsRNAs allows assembling of viral genomes and revelation of viral population variations at genomic levels. Grapevine vein clearing virus (GVCV) is a new member of the family Caulimoviridae whose DNA genome is replicated by reverse transcription of pre-genomic RNA molecules. In this short report, three genomic sequences of GVCV were assembled from vsRNAs that were isolated and sequenced from three individual grapevines in commercial vineyards and compared to the GVCV-CHA reference genome. Profiles of single nucleotide polymorphism among three viral populations indicated a closer relatedness between two populations in different grape cultivars at the same location than those in the same grape cultivar at different locations, suggesting the spread of GVCV populations among vineyards of close proximity. Classic types of vsiRNAs (21-nt, 22-nt, and 24-nt) were found in the three GVCV vsiRNA populations, but these did not produce alignment hotspots on the GVCV-CHA reference genome. The number of 36-nt reads is the highest among vsRNAs, the role of these vsRNAs remains unclear. The analysis of vsRNAs provides a first holistic picture of genomic variations among GVCV viral quasispecies populations that help monitor epidemics and evolution of GVCV populations, an emerging virus that is becoming a threat to grape production in the Midwest region of the USA.
病毒小 RNA（vsRNA）包括病毒小干扰 RNA（vsiRNA），它是 RNA 沉默的启动子和产物，以及功能未知的源自病毒 RNA 的小 RNA。vsRNA 的测序允许组装病毒基因组，并在基因组水平上揭示病毒群体的变异。葡萄脉黄化病毒（GVCV）是 Caulimoviridae 科的一个新成员，其 DNA 基因组通过前基因组 RNA 分子的反转录复制。在这个简短的报告中，从商业葡萄园中三个单独的葡萄藤中分离和测序的 vsRNA 组装了三个 GVCV 基因组序列，并与 GVCV-CHA 参考基因组进行了比较。三个病毒群体中单核苷酸多态性的分析表明，同一地点不同葡萄品种的两个群体之间的亲缘关系比不同地点同一葡萄品种的群体之间更为密切，表明 GVCV 群体在临近的葡萄园之间传播。在三个 GVCV vsiRNA 群体中发现了经典类型的 vsiRNA（21-nt、22-nt 和 24-nt），但这些 vsiRNA 在 GVCV-CHA 参考基因组上没有产生对齐热点。36-nt 读长的数量在 vsRNA 中最高，这些 vsRNA 的作用尚不清楚。vsRNA 的分析提供了 GVCV 病毒准种群体基因组变异的整体图景，有助于监测 GVCV 群体的流行和进化，这是一种新兴病毒，正在成为美国中西部地区葡萄生产的威胁。
