Variability of P1 protein of zucchini yellow mosaic virus for strain differentiation and phylogenetic analysis with other potyviruses.

Abstract

The complete nucleotide sequence of a Singapore isolate of zucchini yellow mosaic potyvirus (ZYMV-S) was determined from viral cDNA clones. The complete genome is 9603 nucleotides in length excluding the poly (A) tail. Computer analysis of the sequence revealed a single large open reading frame (ORF) that presumably encodes a polyprotein of 3082 amino acids with a calculated molecular weight of 350 kDa. Analysis of the helper component (HC) protein showed that the highly conserved motif K-I-T-C which is involved in aphid transmission appeared as K-L-S-C. There is also a change of D-A-G to G-A-G triplet near the N-terminal of the coat protein (CP). Amino acid sequence identity comparison of ZYMV-S gene products with the California and Reunion Island isolates of ZYMV revealed a minimum range of 65-75% to a maximum range of 95-98%. Comparison with other distinct potyviruses showed a low degree of identity from 19-74%. The 5' untranslated region (UTR) of ZYMV-S showed 67% and 72% identity when compared with the California and Reunion Island isolates, respectively. The sequence variability in the 5' UTR of ZYMV can be exploited for strain differentiation and phylogenetic analysis. ZYMV-S shared 94% and 82% identity in the 3' UTR as compared to the California and Reunion Island isolates, respectively. The P1 protein of ZYMV-S shared moderate sequence variability among ZYMV isolates but high sequence variability among all potyviruses. In addition, phylogenetic analysis using the P1 protein indicated that highly variable proteins in the viral genome could also be employed in the study of potyvirus taxonomy and used for strain differentiation.