Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 dbp (Lyxy33 and Lyxy43). The amino acid sequence identities of the two DBP to those of LdMNPV were 75% and 80% for Lyxy33 and Lyxy43, respectively. How- ever, the amino acid identity was very low between the two (19%). Genes for enzymatic functions in nucleotide metabolism, such as the large (rr1) and small (rr2) subu- nits of ribonucleotide reductase and deoxyuridyltripho- sphate (dutpase), which are found in several baculoviruses, were also present in LyxyMNPV, with the exception of rr1. Three genes that encode ribonucleotide reductase were found in LdMNPV. These include a homologue of the large subunit and two homologues of the small subunit of ribonucleotide reductase copies [14]. The rr2 of LyxyMNPV (Lyxy137) was more similar to Ld120 (rr2b, 86%) than to Ld147 (rr2a, 16%) homolo- gues. These enzymes are involved in nucleotide metabo- lism and catalyse the reduction of host cell rNTPs to dNTPs [45]. In addition, the homologues of non-essen- tial DNA replication stimulatory genes, ie-2, lef-7 and pe38 [46], which were unique in group I NPV, were not present in LyxyMNPV. Genes with auxiliary functions Auxiliary genes are not essential for viral replication, but provide a selective advantage to increase virus produc- tion/survival either at the cellular level or at the level of the organism [47]. A total of thirteen auxiliary genes have homologues in LyxyMNPV, including proteinki- nase-1 (pk-1), p10, ubiquitin (ubi), conotoxinlike peptide- 2 (ctl-2), chitinase, cathepsin L-like proteinase (v-cath), superoxide dismutases (sod), viral enhancing factor-1, (vef-1), vef-2, ecdysteroid UDP glucosyltransferase (egt), actin rearrangement-inducing factor-1 (arif-1), viral fibroblast growth factor (vfgf) and alkaline exonuclease (alk-exo). Almost all of these auxiliary genes in Lyx- yMNPV were 81%-95% identical in amino acid sequence to those of LdMNPV, except arif-1 and ctl-2. Lyx- yMNPV arif-1 was 64% identical to that of LdMNPV and its ctl-2 was 66% and 40% identical to OpMNPV and LdMNPV, respectively. Conotoxins are small disulfide-rich ion channel antagonists isolated from the gastropod genus Conus [48]. A single ctl gene is present in AcMNPV (Ac3). In contrast, the LdMNPV and OpMNPV genomes encode two ctl genes, called ctl-1 and ctl-2. However, there is only one ctl gene (ctl-2) found in LyxyMNPV, which has low amino acid identity to LdMNPV. This is because LdMNPV ctl-2 has a longer amino acid size (92 aa) than the other baculovirus ctls. The biological func- tion of CTL remains unclear, as no difference in mortal- ity, motility, or weight gain was observed when neonate or late instar Spodoptera frugiperda larvae were infected with the AcMNPV ctl-1 deletion mutant compared to infection with wild-type virus [49]. Page 6 of 14 The large VEF protein is metalloprotease that appears to degrade mucin and is thought to facilitate the approach of baculoviral virions to the surface of gut cells by disrupting the peritrophic membrane [50]. This protein forms ~5% of the mass of OBs of the Trichoplu- sia GV [51]. The vef gene does not exist in the AcMNPV [22] or OpMNPV [23] genomes, but LdMNPV has two vef genes, vef-1 and vef-2. Previous studies have revealed that both LdMNPV enhancins contributed to viral infectivity [52,53]. Two copies of vef (vef-1 and vef-2) have been identified in the LyxyMNPV genome (Lyxy62 and Lyxy153). The two gene products show low amino acid identity to each other (29%). Aux- iliary genes that are present in other lepidopteran NPVs but are not in LyxyMNPV include pcna, pk-2, ptp-1 and ctl-1. Anti-apoptosis genes Apoptosis or cell death can be a mechanism to defend against the establishment of infections and is usually triggered in the early period of virus infection. Baculo- viruses possess two families of genes that suppress apop- tosis: the p35/p49 family and the inhibitor of apoptosis (IAP) family. It has been shown that p35 blocks diverse pathways of apoptosis and plays a role in blocking AcMNPV-induced apoptosis in Sf21 cell [54]. This gene has been reported in a number of baculoviruses, such as AcMNPV, BmNPV, RoMNPV, S. litura MNPV (SpltMNPV) and MaviMNPV [22,24,32,34,55]. The iap family of genes have been found in all family members of the Baculoviridae sequenced to date. IAP homologues generally contain two baculovirus IAP repeats (BIR), which are associated with binding to apoptosis-inducing proteins, and a C-terminal zinc fin- ger-like (RING) Cys/His motif [56]. These features have enabled the iap genes to be divided into five groups from iap-1 to iap-5 [31]. Apoptotic inhibition has been recovered in AcMNPV p35 deletion mutants with a variety of baculovirus iap homologues [57]. In the Lyx- yMNPV genome, two iaps were observed, iap-2 (Lyxy75) and iap-3 (Lyxy116). Both iaps only have one BIR domain and one RING domain in the predicted amino acid sequences. Baculovirus repeated ORFs (bro genes) A striking feature of most lepidopteran and dipteran NPVs sequenced to date and in some of the GVs is the presence of one to 16 copies of bro genes. Typically bro genes are highly conserved, repetitive and widely distrib- uted amongst insect DNA viruses [58]. The function of these genes is unclear, but they have been shown to bind to DNA [59]. These genes have also been found to be associated with the regions of viral genome rearran- gement [60]. LyxyMNPV contains 14 bro genes, which