ABSTRACT
Zucchini yellow mosaic virus (ZYMV) is a destructive cucurbit virus that causes extensive losses in the yield and quality of cucurbits (e.g., zucchini). At present, the analysis of genetic evolution of ZYMV is mainly based on CP sequence, and there has been little progress in addressing its phylogenetic relationships and evolution at the whole genome level. In this study, the whole genome sequences of ZYMV isolated from Shanxi Wenshui (ZYMV-WS) and 109 other reported ZYMV isolates were used to explore their phylogenetic relationships. The results showed that ZYMV-WS had the highest level of nucleotide homology (94.35%) to ZYMV-SXSG, and the amino acid sequences of ZYMV-BR3 were identical (97.37%) to those of ZYMV-WS. In addition, the phylogenetic analysis of ZYMV revealed that all the isolates were clustered into two major branches, and its population structure assessment demonstrated a marked genetic differentiation between A4 and B. Furthermore, we also discovered the sites of specific amino-acid alteration, and their possible association with functional changes. These results will help to better understand the genetic diversity and phylogenetic process of ZYMV, and lay a theoretical foundation for the effective prevention and control of ZYMV infection in the near future.