Identification And Sequence Analysis Of A Cucumber Mosaic Virus Isolate From Solanum Lycopersicum In Southwest China

Previous reports have shown the prevalence of Cucumber mosaic virus (CMV) subgroup I isolates in China. Here the complete genome of a new CMV isolate from tomato (Solanum lycopersicum) named CMV-SL was characterized and its comparative phylogenetic analysis with reference CMV isolates clustered it with subgroup II strains. CMV-SL showed high sequence identity with subgroup II isolates in RNA-1 (97-98%), RNA-2 (97-98%) and RNA-3 (95-97%). The corresponding regions were further compared. The results showed that the coding and non-coding regions of CMV-SL had high identity with other subgroup II strains. The 3'UTR of RNA-3 was the most variable region, and contained most of the observed variation. In addition, single nucleotide polymorphism (SNP) analysis of CMV is reported for the first time, showing that CMV has typical SNPs, which is a common form of genetic variation between isolates. We also estimated the. ratios of non-synonymous and synonymous substitutions of CMV subgroup II strains. We found that negative selection was the predominant evolutionary force operating upon coding regions. However, strong positive selection was identified in the coat protein (CP) of CMV subgroup II.