Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 orientation were also fused into a single ORF (Lyxy122) in LyxyMNPV. GeneParityPlot analysis Comparisons of the gene arrangement of the selected ORFs are shown in Fig. 2. The gene arrangement of the LyxyMNPV genome was highly colinear to that of LdMNPV. However, a large fragment flanked by Lyxy109 (bro-i) and Lyxy142 (bro-j) in the LyxyMNPV genome showed an inversion compared to LdMNPV (Fig. 2a). The gene arrangement of the LyxyMNPV gen- ome showed lower colinearity to AcMNPV, OpMNPV, MaviMNPV and SeMNPV. In contrast, the parity analy- sis of the LyxyMNPV and CpGV ORFs displayed a much more dispersed pattern. LyxyMNPV structural genes Compared to the 25 baculovirus structural genes listed by Hayakawa et al. (1999), Herniou et al., (2003) and Jehle et al. (2006)[2,26,33], only two genes were identi- fied to be absent in the LyxyMNPV genome. These genes included the protein tyrosine phosphatase gene (ptp) and group I NPV-specific gp64 (see Additional file 3), which is the major envelope fusion protein gene of AcMNPV [22], Bombyx mori MNPV (BmNPV) [34], OpMNPV [23] and Epiphyas postvittana NPV (EppoNPV) [35]. The GP64 protein appears to be unique to group I NPVs [36,37]. In LdMNPV, the F protein, an envelope fusion protein functionally analo- gous to the GP64 protein, is a product of the Ld130 gene. LyxyMNPV encodes an F protein homologue, Lyxy126, which shows 96% aa identity to Ld130. Ld130 homologues are present in all lepidopteran and dipteran baculoviruses that have been completely sequenced, including those that contain gp64. The role of the Ld130 homologue in the latter species is unclear, but it is likely that they have lost their envelope fusion proper- ties [37,38]. Of these structural proteins, the polyhedrin protein was the most conserved (100% identity). In con- trast, the products of genes pif-2, orf1629 and vp80 showed the lowest levels (75%, 71% and 69%, respec- tively) of sequence conservation between LyxyMNPV and LdMNPV (Additional file 2). A special characteristic of LyxyMNPV is that Lyxy15 and Lyxy155 are homolo- gous to odv-e27. Lyxy15 is flanked by homologues of Ld17 and Ld19, while Lyxy155 is close to LyxyMNPV hr9 and located between Lyxy154 and Lyxy156 which are homologues of Ld161 and Ld162, respectively. The identity between Lyxy15 and its LdMNPV homologue (Ld18) is up to 84%. However, the identity between the two LyxyMNPV odv-e27 genes is quite low (18%) which is not significantly higher than that to the AcMNPV, MaviMNPV or SeMNPV even AnpeNPV homologues (Additional file 2). The region of Lyxy155 has probably Page 4 of 14 undergone extensive rearrangement, because Ld18 homologue gene of other different baculoviruses is located in the similar site of Lyxy15. Therefore, it is pos- sible that Lyxy155 was acquired from other NPV species (AcMNPV, MaviMNPV, SeMNPV or AnpeNPV). In AcMNPV, the ODV-E27 protein was incorporated into both the envelope and capsid of the occluded virus [39]. However, only odv-e27 (Lyxy15) of LyxyMNPV has a late promoter motif. Therefore, it is possible that only one odv-e27 is transcribed in LyxyMNPV, and that it serves as a structural protein of the envelope and capsid of an occluded virus. It is notable that p10 (designated as Lyxy37’) of LyxyMNPV has a large N-terminal exten- sion. The identity between Lyxy37’ and its LdMNPV homologue (Ld41) is up to 87%, which is much higher than that of Lyxy37 and Ld41 (23%). Lyxy37 has early and late promoter motifs, but Lyxy37’ has only one late promoter motif. There may be two forms of p10 found in the early and late stages of LyxyMNPV-infected lar- vae or cells. The average identity of these structural pro- teins was generally 86.5% between LyxyMNPV and LdMNPV (Additional file 2), suggesting that the struc- ture of the viruses may be similar. Transcription-specific genes The genes involved in baculovirus late gene transcrip- tion that are present on other baculovirus genomes are also present in the LyxyMNPV genome, with no excep- tions, including lef 4-6, 8-11, 39K, p47 and vlf-1 [40]. These genes are found in LyxyMNPV as Lyxy89, Lyxy96, Lyxy34, Lyxy48, Lyxy61, Lyxy54, Lyxy41, Lyxy40, Lyxy44 and Lyxy82, respectively. Most of these genes were 80%-96% identical in amino acid sequences to those of LdMNPV. However, we noted that the amino acid identity of LdMNPV lef-6 and LyxyMNPV lef-6 aa was only 64%. DNA replication and repair genes A total of 19 lef genes in AcMNPV have been impli- cated in DNA replication and transcription [41]. Baculo- virus early genes are transcribed by the host cell RNA polymerase II, but this is often transactivated by genes such as ie-0, ie-1, ie-2 and pe38 [42]. Of these genes, ie- 0 and ie-1 are present in LyxyMNPV. Six baculovirus genes have previously been reported as essential DNA replication factors for baculoviruses, including lef-1, lef- 2, lef-3, DNApol, helicase and ie-1 [43], which are all present in LyxyMNPV. These genes are conserved with respect to those of LdMNPV (81%-91%), with the excep- tion of lef-3 (41%). Homologues of a single-stranded DNA-binding protein (dbp) [44] and an immediate-early gene, me53, both of which have been implicated in DNA replication, were also found in LyxyMNPV. Addi- tionally, similar to LdMNPV, LyxyMNPV also has two