We present here the first complete sequence of cucumber mosaic virus (CMV) from RNA sequencing of a dwarf periwinkle (Vinca minor) and a Wisteria sinensis in Iran by de novo assembly and annotation of contigs. The tripartite genome of CMV-Ir-VM and Ir-WS consists of a 3391-nucleotide (nt) RNA1, a 3038-nt RNA2, and a 2197-nt RNA3 segment. The sequence comparisons and phylogenetic analyses revealed that all three RNA segments of these two isolates belonged to the CMV subgroup II. RNA1, RNA2, and RNA3 of these two isolates, respectively shared 97.61–99.06%, 97.83–98.88%, and 97.19–98.86% nucleotide identities to those of CMV subgroup II isolates. In genetic analysis, the 2b gene revealed more genetic variability (π = 0.2614) compared with other regions. Our results indicated that purifying selection pressure was the major force acting upon the CMV genome, although some positively selected sites were identified for all encoded proteins.

中文翻译：

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伊朗小长春花和紫藤黄瓜花叶病毒全基因组序列分析

我们在此展示了第一个完整的黄瓜花叶病毒 (CMV) 序列，该序列来自伊朗的矮长春花（小长春花）和紫藤的 RNA 测序，通过从头组装和重叠群注释。CMV-Ir-VM 和 Ir-WS 的三方基因组由 3391 个核苷酸 (nt) RNA1、3038-nt RNA2 和 2197-nt RNA3 片段组成。序列比较和系统发育分析表明，这两个分离株的所有三个 RNA 片段都属于 CMV 亚组 II。这两个分离株的 RNA1、RNA2 和 RNA3 分别与 CMV 亚组 II 分离株的核苷酸同一性分别为 97.61–99.06%、97.83–98.88% 和 97.19–98.86%。在遗传分析中，与其他区域相比，2b 基因显示出更多的遗传变异性（π = 0.2614）。