Evidence for the occurrence of two distinct subgroups of peanut stunt cucumovirus strains: molecular characterization of RNA3.

Strains of peanut stunt cucumovirus (PSV) were classified into two distinct subgroups, I and II, based on Western and Northern blot analyses using antisera and cloned cDNA probes to strains PSV-ER and PSV-W. These results were corroborated by nucleotide sequence analyses of full-length cDNA clones of RNA3 from representative strains of the two subgroups. Whereas the percentage nucleotide sequence identity between PSV-ER (or PSV-J) and PSV-W RNA3s was determined to be 80%, the corresponding value between strains ER and J was 91%, confirming that strains ER and J belong to the same subgroup (subgroup I) whereas strain W belongs to a separate subgroup (subgroup II). PSV-W and PSV-ER RNA3s are 2173 and 2188 nucleotides long, respectively. Each is dicistronic, encoding a putative movement protein (3a protein) and a coat protein (CP). The intercistronic and 5' untranslated region (UTR) sequences of PSV strains, unlike those of cucumber mosaic cucumovirus (CMV) strains, are highly conserved and thus not useful for distinguishing the two subgroups. However, the 3' UTR sequences of PSV strains, like those of CMV strains, can discriminate between the two subgroups since strains within the same subgroup are 95% identical in their 3' UTRs whereas those in different subgroups are only 74-78% identical. PSV-W and PSV-ER RNA4s were determined to be 994 and 1006 nucleotides long, respectively. PSV 3a and CP genes have higher percentage nucleotide sequence identities to those of tomato aspermy cucumovirus than to those of CMV.

Nucleotide sequence of the 3'-terminal region of the RNA of the El Amar strain of plum pox potyvirus.

The nucleotide sequence of the 3'-terminal 4773 nucleotides of the RNA of a widely divergent, aphid-transmissible strain of plum pox potyvirus isolated from Egypt (PPV-El Amar) was determined. The sequenced region covers the carboxy terminus of the cylindrical inclusion (CI) gene, and the putative 6K protein, the NIa protease, the NIb RNA polymerase and the coat protein genes, linked together as one large open reading frame (ORF) in a fashion similar to the canonical genomic organization of other potyviruses. The large ORF encoding the polyprotein is followed by a 217 nucleotide non-coding region and a poly(A) tail. However, whereas the three PPV strains previously sequenced show levels of identity in excess of 98%, PPV-El Amar shows levels of heterogeneity of 20% in the nucleotide sequence and 10% in the amino acid sequence, when compared with these previously sequenced strains. The N-terminal region of the capsid protein, postulated to be involved in the aphid transmission mechanism of the virus, was found to be the region which differed most between PPV-El Amar and the other strains.