Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 have been named bro-a to bro-n based on their order in the genome (Fig. 1; Additional file 2). Most BROs con- tain a core sequence of 41 aa at the N-terminal half and several different domains throughout the sequence. The bro gene family has been divided into four groups based on the similarity of those domains [14]. Six of the Lyx- yMNPV bro genes, including ly-bro-b (Lyxy29), -h (Lyxy108), -j (Lyxy142), -k (Lyxy145), -l (Lyxy146) and -n (Lyxy154) which are homologues of ld-bro-b, -j, -b, -p, -n and -p, respectively, belong to group I, while three bros [ly-bro-a (Lyxy28), -i (Lyxy109) and -m (Lyxy147) which are homologues of ld-bro-a, -a and -o, respec- tively] belong to group II. Four of them, including ly- bro-c (Lyxy67), -d (Lyxy68), -e (Lyxy69), and -f (Lyxy70) which are homologues of ld-bro-c, -c, -c and -d, respec- tively, belong to group III. Only one bro [ly-bro-g (Lyxy71) which is homologues of ld-bro-g] belongs to group IV. The homologues of ld-bro-f, -h, -i, -k, -l and -m are not presented in LyxyMNPV genome. However, in LyxyMNPV, all group III bro genes encode small fragments of truncated protein (154 aa, 330 aa, 196 aa and 249 aa). Ly-bro-c, ly-bro-d and ly-bro-e are homolo- gous to different regions of ld-bro-c, but ly-bro-f is homologous to the N-terminal portion of ld-bro-d. Page 8 of 14 Homologous regions (hrs) A novel feature of many baculovirus genomes is the pre- sence of homologous regions (hrs) located throughout the genome [61]. A single hr comprises a palindrome that is usually flanked by direct repeats and is closely related to counterparts located elsewhere in the genome. According to the transient replication assays, hrs may play a role in the replication origins of NPVs and GVs [62] and function as enhancers of RNA polymerase II- mediated transcription of baculovirus early promoters in NPVs [63]. It has been suggested that hrs can probably substitute for each other. However, it was recently shown that no single homologous repeat region is essen- tial for DNA replication of AcMNPV [64]. The LyxyMNPV genome contains thirteen homolo- gous repeat regions (hr1, hr2, hr3a, hr3b, hr3c, hr4, hr5, hr6, hr7, hr8a, hr8b, hr8c and hr9) that include two to seven palindrome repeats for a total of 48 repeats (Fig. 3a) and account for 7.3% of the genome. Of these hrs, hr4 and hr6 are in the reverse direction compared to other hrs in the LyxyMNPV genome (Fig. 3a). Similar to the LdMNPV palindrome sequence [14], the LyxyMNPV hr palindrome consensus GGCCGRCACGTAAAATTC- TACGCGTCCGCC shows 24/30 palindrome matches Figure 4 Comparison of the genomic context of the hrs and hr locations relative to homologous ORFs between LyxyMNPV, LdMNPV [14] and AcMNPV [25] in the linearised genomes. Black bars indicate the locations of hrs in the linearised genomes. ORFs flanking the hrs are indicated below the line. AcMNPV hr2a is shown as in Possee & Rohrmann [84]. For consistency, all linearised genomes start with polh, but hrs and ORF numbers remain as in the original papers. The numbers in brackets indicate the number of complete repeats in the hr palindromes. A scale in kb is provided in the bottom of the figure