Molecular identification and phylogeny of cucumber mosaic virus and zucchini yellow mosaic virus co-infecting Luffa cylindrica L. in Shanxi, China

To identify the viruses that induced Luffa cylindrica L. mosaic disease, the viral genomic double-strand RNA (dsRNA) was extracted, followed by sequence-independent amplification (SIA) and sequencing. Results showed that Luffa cylindrica L. was co-infected by cucumber mosaic virus (CMV) and zucchini yellow mosaic virus (ZYMV). To further characterize the Shanxi isolates of cucumber mosaic virus (CMV-SXSG) and zucchini yellow mosaic virus (ZYMV-SXSG), the MP gene sequence of CMV-SXSG and the complete genomic sequence of ZYMV-SXSG were cloned and analyzed. The genomic RNA of ZYMV-SXSG is 9474 nucleotides in length and contains one putative ORF which encodes a polyprotein of 3080 amino acids. Sequence alignments showed that CMV-SXSG shared MP nucleotide sequence identities with other CMV isolates of 78.15% to 99.4%. The nucleotide sequence similarity for the CDS region between ZYMV-SXSG and representative ZYMV strains ranged from 81.71% to 98.40%. Phylogenetic analysis suggested that CMV-SXSG and CMV-QZ shared the same origin, and that ZYMV-SXSG showed the highest sequence identity to isolate KR-PA and formed an independent branch, indicating that they have the most closely evolutionary relationship. Recombination analysis revealed that ZYMV-SXSG was a putative recombinant, and that the potential major and minor parents were the ZZ (China isolate) and KR-PA (Korean isolate), respectively. These results will provide valuable hints for more accurate analysis of CMV or ZYMV genetic diversity, and also provide an effective theoretical basis for designing better virus control strategies.