Nai et al. BMC Genomics 2010, 11:116 http://www.biomedcentral.com/1471-2164/11/116 Page 9 of 14 Figure 5 Detailed hr locations and gene organisation in the LyxyMNPV genomic fragment ranging from Lyxy106 to the hr1 region relative to those of the LdMNPV genome. The number and transcriptional direction of each ORF are labelled by arrows indicating the direction of transcription. Each pair of LyxyMNPV and LdMNPV homologue genes is labelled in a different pattern. ORF numbers are shown below the arrows. The names of the putative genes are shown on the arrows. Grey rectangles indicate the locations and relative lengths of the hrs. (Fig. 3b) and the palindromic consensus sequence includes five highly variable positions (Fig. 3b). All nucleotides in the palindrome are >91.5% conserved, except for the eighteenth nucleotide (81.3% conserved), and with the variable nucleotides being 50%-77% con- served. In addition, the AcMNPV consensus hr palin- drome has 50% sequence identity with LyxyMNPV consensus hr sequence (Fig. 3b). The genomic positions of LyxyMNPV regions hr1 - hr5 are conserved with the genomic positions of LdMNPV hr1 - hr5 [14]. LyxyMNPV hr1, hr3a, hr3c, hr4 and hr5 are flanked by the same ORFs as those in the LdMNPV genome (Fig. 4) and LyxyMNPV hr7, hr8b and hr8c are flanked by the same ORFs as LdMNPV hr6, hr7d and hr8, respectively (Fig. 5). Major insertions and deletions were found near the LyxyMNPV hr2 and hr3b. Therefore, LyxyMNPV hr2 is flanked by Lyxy6 (Ld7) and Lyxy7 (Ld9) and hr3b is flanked by Lyxy27 (Ld30) and Lyxy28 (Ld32) (ld-bro-a) (Fig. 4). Conversely, LdMNPV hr7a, hr7b and hr7c are not present in the corresponding locations in the LyxyMNPV (Fig. 5). As reported in other comparisons of closely related viruses, ORF content tends to differ markedly between LdMNPV and LyxyMNPV around the hr6, hr8a and hr9. Lyx- yMNPV hr6 is located between Lyxy109 (Ld32) and Lyxy110 (Ld145), hr8a is located between Lyxy145 (Ld161) and Lyxy146 (Ld153) and hr9 is located between Lyxy154 (Ld161) and Lyxy155 (Ld18) (Fig. 5). It is notable that in the region from Lyxy110 to Lyxy142, between hr6 and hr7 showed a reverse gene arrangement compared to those of LdMNPV (Fig. 2a; Fig. 5). The positions of at least some hrs appear to be con- served relative to specific baculovirus genes. In particu- lar, it was found that an hr is conserved immediately downstream of Ac83 and the homologous genes in BmNPV [34], OpMNPV [23] and LdMNPV [14]. Lyx- yMNPV hr5 is located immediately downstream of Lyxy87 (vp91/p95), the LyxyMNPV homologue of Ac83 (Fig. 4). In addition, similar to LdMNPV, because no homologue of the AcMNPV ORFs (Ac84-Ac88) are pre- sent in the LyxyMNPV genome, Lyxy88 is located immediately downstream of this hr, which is the homo- logue of AcMNPV vp39 (Ac89). This indicates that the position of LyxyMNPV hr5 is conserved with regard to both the upstream and downstream genes. The ORF organisation downstream of this hr in OpMNPV, BmNPV [34] and LdMNPV is similar to LyxyMNPV. Homologues of Ac84-Ac86 are missing in BmNPV, while Ac84 and Ac86 are missing in OpMNPV. Given that hrs share higher similarity within a virus strain than any hrs between species, this evidence further indicates that hrs play a fundamental role in viral life cycle and replication process appears to be tightly linked to func- tional conservation. LyxyMNPV duplicate genes Two pairs of genes, Lyxy45/Lyxy46 and Lyxy50/Lyxy51, were identified as duplicated homologues of Ld49 and Ld53 in the LyxyMNPV genome. All of these duplicate