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

The complete nucleotide sequence of the RNA genome of a Taiwan isolate of Z ucchini yellow mosaic virus (ZYMV TW-TN3) was determined from five overlapp ing cDNA clones 9591 nucleotides in length excluding the poly (A) tail. Com puter analysis of the sequence revealed a large open reading frame (ORF) th at encodes a polyprotein of 3080 amino acids. Comparison of the gene produc ts 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 vari able, 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 sha res 90.4-95.7% nucleotide identities, with those of the other isolates. A p hylogenetic tree derived from the sequences of P1 proteins of TW-TN3 and th e other six reported ZYMV isolates revealed four major genotypes. TW-TN3 wa s classified in genotype I, and US isolates were in genotype II. The Reunio n Island and Singapore isolates were separated into genotypes III and IV, r espectively. The distance relationships of P1 protein of genotype I were cl oser 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 ha lves of the polyproteins of TW-TN3, CA, RU, and S isolates revealed that NI a protease cleaves at Q-S, and E-S dipeptide sequences, with a consensus se quence of V-x-x-(Q, E)/(S, A, G). The genetic organization of TW-TN3 was co ncluded as Vpg/5' leader/P1 (36 kDa)/HC Pro (52 kDa)/P3 (40 kDa)/6K1 (6 kDa )/CIP (71 kDa)/6K2 (6 kDa)/NIa-Vpg (22 kDa)/NIa-Pro (27 kDa)/NIb (60 kDa)/ CP (31 kDa)/3' UTR-poly(A) tract.