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 6 543 nt, including inverted terminal repeats (ITRs) of 224 nt. In the viral genome, three 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 insertion 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- and 1.5-kb transcripts in the left-half 'plus' strand, and one transcript of about 3.3 kb of 'minus' strand in the right-half. Sequencing of 3′ and 5′ ends of transcript products showed that the 1.1-kb transcript started at nt 290 and ended at nt 1437; the 1.5-kb transcript started at nt 1423 and ended at nt 2931; the 3.3-kb transcript started at 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 nt at the 3′ ends. These results indicate that this virus employs a transcription strategy that is radically different from that of other reported DNVs.