Although Watermelon mosaic virus (WMV) is one of the main cucurbit pathogens and has a worldwide distribution, reliable data on its molecular variability is still limited to some geographical regions. The genetic diversity of 36 WMV isolates from Slovakia and Iran were studied by sequence analysis targeting two opposite genomic regions (P1 and NIb-CP). Phylogenetic analysis using partial sequences of the P1 gene showed that Slovak WMV isolates had greater diversity, representing two groups (group 1 and group 2), whereas all Iranian isolates belonged to a single group (group 2), with relatively low divergeance. Interestingly, in the NIb-CP region, all analyzed Slovak and Iranian isolates clustered within the group 1, thereby illustrating the phylogenetic discrepancies between the two analyzed genomic regions. Based on these data, one-half of analyzed Slovak isolates and all Iranian WMV isolates showed a switch in affiliation based on considered genomic region, clearly indicating their recombinant nature. This work provides further evidence of the significant contribution of recombination to the evolutionary history of WMV and outlines the necessity to target more than a single genome fragment for accurate typing of WMV isolates.
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