Complete nucleotide sequence and genetic organization of papaya ringspot virus RNA

The complete nucleotide sequence ofthe RNA genome of papaya ringspot virus (PRSV) was determined from four overlapping cDNA clones and by direct sequenc-ing of viral RNA. The genomic RNA is 10326 nucleotides in length, excluding the poly(A) tract, and contains one large open reading frame that starts at nucleotide positions 86 to 88 and ends at positions 10118 to 10120, encoding a polyprotein of 3344 amino acids. The highly conserved sequence AAAUAAAANANCUCAACACAACAUA at the 5' end of the RNA of PRSV and those of the other five reported potyviruses shows 80 % similarity, suggesting that this region may play a common important role for potyvirus replication. Two cleavage sites of the poly-protein were determined by amino acid sequencing of the N termini of helper component (HC-Pro, amor-phous inclusion) and cylindrical inclusion (CI) pro-teins. Other cleavage sites were predicted by analogy with the other potyviruses. The genetic organization of PRSV is similar to that of the other potyviruses xcept that the first protein processed from the N terminus of the polyprotein (NT protein) has an Mr of 63K, 18K to 34K larger than those of the other potyviruses. The cleavage site for liberating the N terminus of the HC-Pro protein was found at the same location down-stream from the consensus sequence FI(V)VRG as that reported for tobacco vein mottling virus. The NT protein of potyviruses i the most variable and may be considered important for identification of individual potyviruses. The most conserved protein ofpotyviruses appears to be the Nlb protein, the putative polymerase for the replication of the potyviral RNA. The genetic organization ofPRSV RNA is tentatively proposed to be VPg-5 ' leader-63K NT-52K HC-Pro-46K-72K CI-6K-48K NIa-59K NIb-35K coat protein-3 ' non-coding region-poly(A) tract