Molecular variability of five cucumber mosaic virus isolates from China

Abstract： Cucumber mosaic virus (CMV) is the type species of genus Cucumovirus and currently divided into three subgroups, IA, IB and II. Here we reported the genome encoding 1a, 2a, 2b, 3a and 3b of five CMV isolates from China and rechecked the subgrouping of CMV with sequences of more isolates. The phylogenetic results indicated that CMV could be divided into three groups genetically, and the group I could be further divided into at least three subgroups. Four of these five isolates belonged to subgroup IB, while isolate RZ was a natural intersubgroup reassortant. The 2b gene of CMV was under positive selection, while other genes were under negative selection. No evidence of selection associated with host adaptation and geographic distribution were found.