Identification and phylogenetic analysis of sequences of Bean pod mottle virus, Soybean mosaic virus, and Cowpea chlorotic mottle virus in expressed sequence tag data from soybean

Field- or greenhouse-grown plants are naturally exposed to microbes. Sequence data derived from these plants can therefore inadvertently include microbe sequences. We have examined the extent of viral sequences in public soybean (Glycine max and Glycine soja) sequence data. A collection of 303 149 soybean expressed sequence tags (ESTs) was computationally analyzed for sequences from 12 viruses infecting soybean: Alfalfa mosaic virus (AMV), Bean pod mottle virus (BPMV), Bean yellow mosaic virus (BYMV), Cowpea chlorotic mottle virus (CCMV), Cowpea mosaic virus (CPMV), Cowpea severe mosaic virus (CPSMV), Cucumber mosaic virus (CMV), Peanut mottle virus (PeMoV), Peanut stunt virus (PSV), Soybean mosaic virus (SMV), Tobacco ringspot virus (TRSV), and Tobacco streak virus (TSV). A total of 1652 sequences matching BPMV (1097 sequences), SMV (132 sequences), and CCMV (423 sequences) were discovered in the soybean EST collection. The viral sequences were assembled into contiguous sequences, and sequence tracts in common were used in a parsimony analysis of the phylogenetic relationship of putative viral genotypes. Our results include representative sequences from two BPMV subgroups and, surprisingly, many variants of BPMV nucleotide sequences. Furthermore, the results suggest that BPMV viral strains may be mixes of different BPMV RNA-1 and RNA-2 genotypes. This study presents the largest collection of sequence data available to date for the BPMV, SMV, and CCMV viruses and represents the first report of this magnitude of varieties of BPMV nucleotide sequences.