The nucleotide sequence and genome organization of the whitefly transmitted sweetpotato mild mottle virus: a close relationship with members of the family Potyviridae

Primers corresponding to conserved regions in the RNA-dependent RNA polymerase and the RACE procedure led to the cloning of the complete sweetpotato mild mottle virus (SPMMV) RNA genome. The assembled SPMMV genomic sequence was 10 818 nucleotides in length with a polyadenylated tract at the 3′ terminus. The structure and organization of the SPMMV genome appear to be similar to those of potyviruses and rymoviruses. A 5′ untranslated region, rich in A and U residues, is present between nucleotides 1 and 139. A putative initiation codon, at nucleotides 140–142, marks the beginning of a large open reading frame (ORF) which ends in UAA at positions 10 508–10 510. A 308-nucleotide untranslated region is present between the termination codon of the ORF and the beginning of the 3′ polyadenylated region. Almost all known potyvirus motifs are present in the polyprotein of SPMMV. However, motifs in the putative helper-component and coat protein of SPMMV are incomplete or missing, which may account for its vector relations. Despite similarities with rymoviruses, potyviruses and, to a lesser extent, bymoviruses, comparative sequence analyses demonstrated that SPMMV belongs to a distinct genus of the family Potyviridae.