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

The complete nucleotide sequence of a Singapore isolate of zucchini yellow mosaic potyvirus (ZYMV-S) was determined from viral cDNA clones. The comple te genome is 9603 nucleotides in length excluding the poly (A) tail. Comput er analysis of the sequence revealed a single large open reading frame (ORF ) that presumably encodes a polyprotein of 3082 amino acids with a calculat ed molecular weight of 350 kDa. Analysis of the helper component (HC) prote in showed that the highly conserved motif K-I-T-C which is involved in aphi d 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 Reunio n Island isolates of ZYMV revealed a minimum range of 65-75% to a maximum r ange of 95-98%. Comparison with other distinct potyviruses showed a low deg ree of identity from 19-74%. The 5' untranslated region (UTR) of ZYMV-S sho wed 67% and 72% identity when compared with the California and Reunion Isla nd isolates, respectively. The sequence variability in the 5' UTR of ZYMV c an be exploited for strain differentiation and phylogenetic analysis. ZYMV- S shared 94% and 82% identity in the 3' UTR as compared to the California a nd Reunion Island isolates, respectively. The P1 protein of ZYMV-S shared m oderate sequence variability among ZYMV isolates but high sequence variabil ity among all potyviruses. In addition, phylogenetic analysis using the PI protein indicated that highly variable proteins in the viral genome could a lso be employed in the study of potyvirus taxonomy and used for strain diff erentiation.