Genetic diversity and Phylogenetic analyses of cucumber mosaic virus strains in Iran

Cucumber mosaic virus (CMV) belongs to the genus Cucumovirus of the family Bromoviridae. Compared to other plant viruses, it has the broadest host range, and is reported from different regions of Iran. In the present study, the genetic diversity of Iranian CMV isolates was estimated through the sequence analysis of all the CMV genes and compared to those in other countries. To this purpose we report the genome sequence of two CMV strains isolated from squash (SqSh) and melon (MeEs) in Shiraz and Esfahan. The two isolates were closely related based on the analysis of all gene sequences. Phylogenetic analysis revealed that most of the Iranian CMV isolates belonged to the subgroup IA, however, they did not share a most recent common ancestor based on RNAs 2 and 3. The reassortment type of IA-IA-IB was fount to have played a very important role in the evolution and genetic diversity of CMV population in Iran. 1a and CP ORFs had the lowest and highest genetic diversity among Iranian CMV population of the subgroup I, respectively. We suggested that migration in long and short distances have played a role in evolution and genetic structure of CMV strains in Iran.