The complete nucleotide sequence and genome organization of bean common mosaic virus (NL3 strain)

The nucleotide sequences of 3 cDNA clones corresponding to entire RNA genome of bean common mosaic virus NL3 strain have been determined. The RNA is 9612 nucleotides long, excluding a 3′-terminal poly(A) tail. A putative start codon located at nucleotide positions 170–172 initiates one large open reading frame that is terminated with a UAA codon at position 9368–9370. The predicted polyprotein has 3066 amino acids and an Mr of 340.3 kDa. The positions of putative protein cleavage sites have been determined by analogy to consensus sequences in other potyviruses. The nucleotides sequences of the non-translated regions and the predicted amino acid sequences of BCMV NL3 were compared with those of other potyviruses. Comparison of the BCMV NL3 proteins with those of other potyviruses indicated a similar genomic organization, and high percentage of amino acid sequence identity in the cylindrical inclusion protein, nuclear inclusion ‘b’ protein and coat protein. BCMV NL3 displays the highest amino acid sequence identity with soybean mosaic virus.