Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 Page 3 of 14 Figure 1 Circular map of the LyxyMNPV genome. The inner circles indicate the positions of cleavage sites for the following enzymes: outer circle, BamHI; middle circle, EcoRI; inner circle, EcoRV. LyxyMNPV ORFs are indicated outside these circles. Arrows indicate the direction of transcription. The locations of hrs are also shown. A scale in kb is provided in the centre of the figure. allow transcription of these genes during both the early and late stages of infection. This has also been reported for Ac128 (gp64) and Ac147 (ie-1) [28,29]. A total of 73 LyxyMNPV ORFs were shown to possess consensus late gene promoter motif. Additionally, the upstream 210 bp of 50 LyxyMNPV ORFs had an enhancer-like element consisting of a CGTGC motif (Additional file 2). A total of 48 LyxyMNPV ORFs did not possess consensus late or early promoter sequences. It seems likely that addi- tional, as-yet-unidentified, promoter sequences might exist within the LyxyMNPV genome, as in other Table 1 Six genes of LyxyMNPV with no homologue in LdMNPV genome. ORF* 11 19 49 123 130 131 Length (aa) 58 55 305 105 83 689 * LyxyMNPV unique genes are underlined. LyxyMNPV Homologue Clbi31 Agse52 Bombyx mori/gag-like Identity (%) 15 35 18 baculoviruses [28,29]. Unlike most baculoviruses, the p74 of LyxyMNPV lacks a late promoter [14]. Comparison of LyxyMNPV ORFs to other baculoviruses LyxyMNPV shares 109 ORFs with AcMNPV, 100 ORFs with OpMNPV, 93 ORFs with MaviMNPV, 151 with LdMNPV, 107 with SeMNPV and 76 with CpGV (Cydia pomonella GV). The average amino acid sequence iden- tity between LyxyMNPV and AcMNPV [22], OpMNPV [23], MaviMNPV [24], LdMNPV [14], SeMNPV [30] and CpGV [31,30] were 32.68%, 33.19%, 33.28%, 74.71%, 37.3% and 25.63%, respectively. Four ORFs (Lyxy11, Lyxy19, Lyxy130 and Lyxy131) were identified unique to LyxyMNPV (Additional file 2). Three pairs of adjacent AcMNPV ORFs (Ac58/Ac59, Ac106/Ac107, and Ac112/ Ac113) were fused together into single ORFs (Lyxy58, Lyxy115 and Lyxy105, respectively) in LyxyMNPV. As reported for Rachiplusia ou MNPV-R1, re-sequencing of these regions in AcMNPV-C6 had found that the ORF pairs occurred as a single ORF in the stock of AcMNPV-C6 [32]. The homologues of these ORFs were also found in other baculovirus genomes in which they are fused into a single ORF. Three adjacent LdMNPV ORFs (Ld133/Ld134/Ld135) that were in the same