Phylogenetic analysis of Iranian Cucumber mosaic virus isolates from Kerman and Yazd provinces

Cucumber mosaic virus (CMV) is one of the most important viruses of cucurbits worldwide. To study the phylogenetic relationships of several CMV isolates, a number of samples were collected from Kerman and Yazd provinces. The CMV infection of the samples was tested using DAS-ELISA method. Based on the host and geographical regions, six ELISA positive samples were chosen for molecular characterization. A 946 bp fragment comprising full-length of coat protein gene with its flankes was amplified by RT-PCR using specific primer pairs, cloned and sequenced. Sequence comparisons were done using DNAMAN software on CP gene of Iranian isolates and those of available in GenBank . Phylogenetic analysis showed that CMV isolates were divided into two subgroups I and II in which the subgroup I was further divided into two subgroups of IA and IB. Two Iranian isolates sequenced in the present study were placed in the subgroup IA and the rest of isolates in the subgroup IB . The higest nucleotide sequence identity of 99.1% was obtained for the isolates Ker.Ker.Pep and Ker.Ker.Mel.2 (subgroup IB) while the lowest for the isolates Ker.Jir.Cu isolate (subgroup IA) and the Yaz.Yaz.Tom of 92.1 %. Isolates of subgroup IB belong almost exclusively to East Asia. It is the first report of occurrence of subgroup IB of CMV isolates in Iran and Middle East.