Molecular characterization and population dynamics of the P1 gene region in watermelon mosaic virus (WMV) isolates

Watermelon mosaic virus (Potyvirus citrulli; WMV) infects plants in the Cucurbitaceae family. This virus can cause significant yield losses, especially in economically important crops such as watermelon, melon, squash, and cucumber. In this study, WMV isolates were collected from 10 cucurbit plants infected with WMV, confirmed serologically from the provinces of Eskişehir, Ankara, and Nevşehir. Two different primer pairs, amplifying regions of 750 and 849 bp in size, were designed to amplify the approximately 1317-nucleotide-long P1 region of these WMV isolates. The amplified products were sequenced, and GenBank accession numbers were obtained. Nucleotide similarity indexes and basic phylogenetic analysis divided global WMV isolates into five phylogroups based on the P1 region. According to genetic diversity and polymorphism analysis, the average number of nucleotide differences between sequences was found to be highest within phylogroup 3. While phylogroups 1, 2, and 4 did not show strong selection pressure, as indicated by high ω (dN/dS) ratios (ω > 2), the low ω value observed in phylogroup 3 suggested strong selection pressure in this group. FST values, which measure genetic diversity between populations, were found to exceed the reference value of 0.33 only in phylogroup 2. Based on the results of this study, it is concluded that additional isolates are needed for a more comprehensive analysis of the population dynamics of the P1 region. The findings are believed to contribute significantly to the understanding of the population dynamics of the WMV P1 region and offer a new perspective on P1 phylogeny.