A Putative Defective Interfering RNA from Bean pod mottle virus

A putative defective interfering (DI) RNA from the Bean pod mottle virus (BPMV) was discovered by screening of random cDNA clones in a soybean cDNA library. This was unexpected because the library was constructed from mRNA of visually healthy soybean pods. The insert in the cDNA clone, VS-16, is not present in the soybean genome but showed strong mRNA expression in pod tissue of soybean and in bean leaf beetles collected in the field. Analysis of the VS-16 sequence reveals that it has significant homology to the 3.66-kb BPMV RNA-2. A 2-kb region has been deleted in VS-16, and other regions of the viral RNA genome have been rearranged to yield a putative defective interfering RNA (DI RNA) of 1.35 kb. The three regions of VS-16 are 95.8, 77.8, and 85.6% identical at the nucleotide level to the corresponding regions of BPMV RNA-2. This is the first report of a DI RNA from the comovirus group of plant viruses. It may be helpful in antivirus efforts for soybean, especially since there are increasing numbers of reports of BPMV in soybeans in the midwestern United States.