[Organization and transcription strategy of genome of Bombyx mori bidensovirus (China isolate) VD1]

To better understand the genomic structure and function of Bombyx mori bidensovirus (China isolate) VD1, the VD1 was purified and cloned into the pUC119 vector, and the complete nucleotide sequence of VD1 was determined. Sequence analysis showed that VD1 genome consisted of 6543 nts including inverted terminal repeats (ITRs) of 224 nts. In the viral genome, three major open reading frames (ORF1, ORF2 and ORF3) in the plus strand and one major ORF (ORF4) in the complementary strand were identified. Comparison of the complete genome sequence between Bombyx mori bidensovirus (China isolate) and BmDNV-2 (Yamanashi isolate) showed an identity of 98.4% in VD1, with a total number of 104 bp substitutions and 1 bp insertions found in Bombyx mori bidensovirus (China isolate), the highly variable regions were mainly located in VD1 ORF3 and VD1 ORF4. Northern blotting revealed that VD1 contained 1.1 kb and 1.5 kb transcript in the left-half 'plus' strand, and one transcript about 3.3 kb of 'minus' strand in the right-half. Sequencing of 3' and 5' ends of transcript products showed the 1.1 kb transcript started at nt 290 and ended at nt 1437, the 1.5 kb transcript was found to start nt 1423 and ended at 2931, and the 3.3 kb transcript was found to start nt 6287 and ended at nt 2922. Therefore, the 1.5 kb transcript in the left-half plus' strand and 3.3 kb transcripts of minus' strand in the right-half overlapped for 10 nts at the 3' ends. These results indicate that this virus employs a transcription strategy that is radically different from that of the other reported DNVs.