Zucchini yellow mosaic virus (ZYMV) is one of the most economically important viruses infecting cucurbits worldwide. Population genetic analysis of ZYMV was conducted based on the virus cylindrical inclusion (CI) gene sequences of 10 isolates identified in this study and 94 other isolates from different countries in six continents: Asia, Europe, Oceania, Africa, North and South America. The overall mean value of nucleotide sequence diversity among all isolates was 0.074±0.006. Phylogenetic analysis showed that ZYMV isolates fell into three main phylogroups with significant FST values (>0.55) and almost tended to cluster according to their geographical position. Group I was predominant and contained isolates originated from different parts of the world. Iranian isolates clustered into group I, sharing 87.7-99.7% and 92.5–100% nucleotide and amino acid identity, with other isolates of this group. Group II was a new group that included only Singapore isolates. Group III including East Timor, Reunion Island and AustraliaKununurra isolates which were genetically differentiated from other populations. ZYMV populations from different geographic origins were composed of multiple lineages. With exception of the Oceanian population which was strongly differentiated from the American population, most other geographical populations showed low to moderate genetic differentiation. There was moderate to high level of gene flow despite large separating geographic distances. Analysis of the synonymous-to-nonsynonymous ratio showed strong purifying selection in the CI gene. The analyses indicated that in addition to selection, random processes such as genetic drift and founder effects are important determinants for the genetic structure of populations of ZYMV.
