Watermelon mosaic virus (WMV) is one of the most important viruses infecting a wide range of plant species. Population genetic analysis of WMV was performed based on the virus coat protein (CP) gene sequences of ten isolates identified in this study and 89 additional isolates from five different countries (China, France, Iran, Spain and the USA) in three continents; Asia, Europe and North America. Phylogenetic analysis showed that WMV isolates clustered in three phylogroups; classical (CL), group 2 (G2) and emerging (EM) with significant FST values (> 0.43). Chinese, French, Iranian, Spanish and USA WMV populations were composed of multiple lineages. Genetic differentiation analysis of WMV populations showed that the Iranian and Spanish populations were statistically distinct from the other populations. The ratio of non-synonymous to synonymous nucleotide diversity (dN/dS= ω) was less than 1, indicating that the CP gene of WMV has been under negative selection. Most of the codons in the CP were under negative selection (ω < 1) except for codon 87, which were significantly under positive selection. This study suggests that host-adoption selection and founder effect were important evolutionary factors driving the genetic diversification of WMV.
