THE COMPLETE NUCLEOTIDE-SEQUENCE OF YAM MOSAIC-VIRUS (IVORY-COAST ISOLATE) GENOMIC RNA

The complete nucleotidic sequence of the yam mosaic virus (YMV) RNA wa s determined following the cloning of partial segments of the genome b y reverse transcription and polymerase chain reactions (RT-PCR) using degenerate and/or specific oligonucleotide primers. YMV genomic RNA is 9,608 nucleotides in length and contains one open reading frame (ORF) encoding a polyprotein of 3,103 amino acids (aa) with a calculated Mr of 350,915. The 5' leader sequence of YMV RNA preceding the ORF is 13 4 nucleotides (nt) long while the 3' untranslated region (UTR) is 165 nt excluding the poly(A) tail. A computer algorithm predicted that the 3'UTR forms four stem loop structures which form a cloverleaf-like se condary structure. These structures apparently share some homologies w ith those observed in the 3'UTR of the potato virus Y-NL1 strain. Seve n potential recognition sites for the NIa protease were found: one put ative cleavage site for the P1 proteinase and one for the HC proteinas e. The organization of the YMV genome is therefore similar to the othe r members of the genus Potyvirus based upon conserved sequence motifs common amongst members of this group. Despite its similarity with the other potyviruses in these conserved regions, YMV appears to be a dist inct potyvirus species based upon a comparison of its sequence with th ose of other potyviruses.