Complete nucleotide sequence of Sesbania mosaic virus: a new virus speciesof the genus Sobemovirus

The complete nucleotide sequence of the Sesbania mosaic virus (SeMV) genomi c RNA was determined by sequencing overlapping cDNA clones. The SeMV genome is 4149 nucleotides in length and encodes four potential overlapping open reading frames (ORFs). Comparison of the nucleotide sequence and the deduce d amino acid sequence of the four ORFs of SeMV with that of other sobemovir uses revealed that SeMV was closest to southern bean mosaic virus Arkansas isolate (SBMV-Ark, 73% identity). The 5' non-coding regions of SeMV, SBMV a nd southern cowpea mosaic virus (SCPMV) are nearly identical. However ORF1 of SeMV which encodes for a putative movement protein of M-r 18370 has only 34% identity with SBMV-Ark. ORF 2 encodes a polyprotein containing the ser ine protease, genome linked viral protein (VPg) and RNA dependent RNA polym erase domains and shows 78% identity with SBMV-Ark. The N-terminal amino ac id sequence of VPg was found to be TLPPELSIIEIP, which mapped to the region 326-337 of ORF2 product and the cleavage site between the protease domain and VPg was identified to be E-325-T-326. The cleavage site between VPg and RNA dependent RNA polymerase was predicted to be E-445-T-446 based on the amino acid sequence analysis of the polyprotein from different sobemoviruse s. ORF3 is nested within ORF2 in a -1 reading frame. The potential ribosoma l frame shift signal and the downstream stem-loop structure found in other sobemoviruses are also conserved in SeMV RNA sequence, indicating that ORF3 might be expressed via - 1 frame shifting mechanism. ORF4 encodes the coat protein of SeMV, which shows 76 and 66% identity with SBMV-Ark and SCPMV, respectively. Thus the comparison of the non-coding regions and the ORFs of SeMV with other sobemoviruses clearly revealed that it is not a strain of SBMV. Phylogenetic analysis of six different sobemoviruses, including SeMV, suggests that recombination event is not frequent in this group and that S eMV is a distinct member of the genus sobemovirus. The analysis also shows sobemoviruses infecting monocotyledons and dicotyledons fall into two disti nct clusters.