Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 Page 10 of 14 Figure 6 Phylogenetic analysis of concatenated amino acid sequence alignments, showing bootstrap values >50% for NJ and MP trees at each node (NJ/MP). The location of LyxyMNPV is printed in bold. genes show low identities to each other (20% and 6%). However, Ly45/Ly46 has higher identity (38%) from amino acid positions 51 to the 105, while Lyxy50/ Lyxy51 has higher identy (17%) from amino acid 60 to the 126. Of these duplicate genes, Lyxy45 and Lyxy50 have low identities to Ld49 (17%) and Ld53 (45%), respectively but Lyxy50 with the C-terminal portion consisting of 81 amino acids has over 75% identity to Ld53. However, both Lyxy46 and Lyxy51 are 13% identi- cal to the homologues of LdMNPV. Unique LyxyMNPV ORFs Four genes are unique in the LyxyMNPV genome, including Lyxy11, Lyxy19, Lyxy130 and Lyxy131 (Addi- tional file 2). Most of these ORFs are small in size (55-83 aa), with the exception of Lyxy131 (689 aa). Only Lyxy130 contain a recognisable promoter. Lyxy130 pos- sesses a late gene promoter motif and an enhancer-like element. Those ORFs with no recognisable promoter may not be transcribed, but Lyxy130 may be transcribed during the early or late stages of infection and could be contributing factor in host range expansion and some pathology of LyxyMNPV. Both Lyxy11 and Lyxy19 have no baculovirus homologue and no significant BLAST database hit. Lyxy130 and Lyxy131 however have at least one significant BLAST database hit. Lyxy130 had a 32% identity match to 20 aa of a hypothetical protein [Gen- Bank: XP_567060] of the fungal species Cryptococcus neoformans (the e-value is 25). Interestingly, Lyxy131 had a 31% identity match to 62 aa of Drosophila melanogaster GAG protein [GenBank: AAT12844] (the e-value is 5e- 25), which shows some homology, albeit low (10, 18 and 14%, respectively) to full length of D. melanogaster and B. mori [GenBank: BAB21762], and it has also been iden- tified in the highly repetitive elements (LDT1) of the gypsy moth (L. dispar) [GenBank: AAC72920] [65]. In retroviruses, the gag gene encodes structural proteins and will be primarily translated as Gag precursor that acts to generate structural proteins of the mature infec- tious virus. All retroviruses have at least three mature Gag proteins that are generically referred to as matrix (MA) protein, capsid (CA) protein, and nucleocapsid (NC) protein [66]. However, as mentioned above, the gag gene of LyxyMNPV has no recognizable promoter so it may not be transcribed and therefore may not contribute to the encapsidation of LyxyMNPV. Phylogenetic analysis of LyxyMNPV The neighbour-joining (NJ) and maximum parsimony (MP) trees generated similar results, but the NJ tree revealed higher bootstrap values. The results reflect the current systematic assignment of the viruses. As shown in Fig. 6, the family Baculoviridae consists of five major clades: the NPVs infecting Lepidoptera (including group I and group II), the GVs, the Hymenopteran-specific NPVs and CuniNPV. Two subclades within the lepidop- teran NPV group II resemble the LdMNPV and AdhoNPV lineages as reported by Oliveira et al. [67].