Analyses of the genetic variation and recombination of CymMV Guangdong isolates

Cymbidium mosaic virus (CymMV) is one of the most important viruses causing economic losses in orchids. The complete genomic sequences of three CymMV isolates collected from Guangdong Province, namely, CymMV-GDFS1, CymMV-GDFS2 and CymMV-GDFS3, were obtained via cloning, sequencing and assembling to clarify the variation and recombination of CymMVs. The mutation analyses of CymMV isolates demonstrated that the gene variation in CymMV followed the order of RdRp >TGBp1 > TGBp2 > TGBp3 > CP. Amongst them, RdRp had the most mutation sites, whereas TGBp3 had the least one. Moreover, the gene mutation of CymMV showed an obvious preference, the main type of mutation was the base transition of T→C or C→T. Notably, a recombinant event was detected in the RdRp gene of CymMV-GDFS1. The complete sequences of the three CymMV isolates shared more than 97% identities at nucleotide levels, phylogenetic relationship analyses revealed that the three CymMV Guangdong isolates belonged to subgroup A. This study provides a theoretical basis for the study of the evolution and pathogenicity of CymMV.