Molecular characterization and population evolution analysis of Watermelon mosaic virus isolates on cucurbits of Northwest Iran

Abstract

One of the destructive potyviruses which cause economic damage and serious yield losses to cucurbit crops around the world is Watermelon mosaic potyvirus. In 2016, 305 leaf samples from different cucurbit cultivars with deformation and reduction in leaf size, blistering, mild and severe mosaic symptoms were collected from different cucurbits-growing regions in Northwest of Iran. Total RNA and their cDNA were tested by RT-PCR assay using two sets of specific primers corresponding to the partial sequences of CP and P1 genomic regions, in which approximately 80 out of 305 samples were found to be infected by WMV. DNA fragments of about 780 bp and 545 bp in length were amplified that belonged to the CP and P1 genes, respectively. Phylogenetic trees of WMV isolates were clustered into three main independent groups with significant F_ST values (> 0.50 and > 0.55) for CP and P1 genes, respectively. dN/dS ratios obtained less than one (< 1) for CP gene that showed the WMV populations have been under the negative selection, whereas for P1 gene, the dN/dS values were calculated > 1 for EM clade containing; China, France, and Italy populations and < 1 for CL and G2 clades; South Korea and Iran populations. This results demonstrated that the WMV evolutionary selection pressure on the P1 gene is dependent on conditions such as the variety of cultivars and the type of cultivation.