Complete genome sequence and genetic organization of a Taiwan isolate of Zucchini yellow mosaic virus

Abstract

The complete nucleotide sequence of the RNA genome of a Taiwan isolate of Zucchini yellow mosaic virus (ZYMV TW-TN3) was determined from five overlapping cDNA clones 9591 nucleotides in length excluding the poly (A) tail. Computer analysis of the sequence revealed a large open reading frame (ORF) that encodes a polyprotein of 3080 amino acids. Comparison of the gene products of TW-TN3 with those of the reported California (CA), Reunion Island (RU), and Singapore (S) isolates of ZYMV revealed that P1 protein is most variable, with amino acid identities of 59.0-93.2%. The 5′untranslated region (UTR) of TW-TN3 shares 61.6-83.3% nucleotide identities, and the 3′UTR shares 90.4-95.7% nucleotide identities, with those of the other isolates. A phylogenetic tree derived from the sequences of P1 proteins of TW-TN3 and the other six reported ZYMV isolates revealed four major genotypes. TW-TN3 was classified in genotype I, and US isolates were in genotype II. The Reunion Island and Singapore isolates were separated into genotypes III and IV, respectively. The distance relationships of P1 protein of genotype I were closer to genotype II, indicating that the Taiwan and US isolates may evolve from the same ancestor. Analyses on the cleavage sites of the C-terminal halves of the polyproteins of TW-TN3, CA, RU, and S isolates revealed that NIa protease cleaves at Q-S, and E-S dipeptide sequences, with a consensus sequence of V-x-x-(Q, E)/(S, A, G). The genetic organization of TW-TN3 was concluded as Vpg/5′ leader/P1 (36kDa)/HC Pro (52kDa)/P3 (40kDa)/6Kl (6kDa)/CIP (71kDa)/6K2 (6kDa)/NIa-Vpg (22kDa)/NIa-Pro (27kDa)/NIb (60kDa)/CP (31kDa)/3′ UTR-poly(A) tract.