Complete nucleotide sequence of bean pod mottle virus RNA1: Sequence comparisons and evolutionary relationships to other comoviruses

The complete nucleotide sequence of bean pod mottle comovirus (BPMV) RNA1 w as determined. It is 5983 nucleotides long, excluding the poly(A) tail, and encodes a polyprotein of 1850 amino acid (aa) residues. Multiple alignment s of the deduced aa sequence of BPMV polyprotein with those of cowpea mosai c virus (CPMV), red clover mottle virus (RCMV) and cowpea severe mosaic vir us (CPSMV) indicated that BPMV RNA1 encodes the predicted set of five matur e proteins: the equivalent of CPMV 32K protease cofactor, 58K putative heli case, VPg, 24K protease and 87K putative RNA-dependent RNA polymerase. Of t he four proposed cleavage sites in BPMV RNA1 polyprotein, the one at the 32 K/58K site (Q/A) is distinct for BPMV polyprotein and those at the 58K/VPg and VPg/24K junctions (Q/S and Q/M, respectively) are identical in all four comovirus polyproteins. Sequence comparison and phylogenetic analysis reve aled that BPMV RNA1 is more closely related to CPSMV than to CPMV or to RCM V.