Genomic sequencing and analysis of Sucra jujuba nucleopolyhedrovirus

Abstract

The complete nucleotide sequence of Sucra jujuba nucleopolyhedrovirus (SujuNPV) was determined by 454 pyrosequencing. The SujuNPV genome was 135,952 bp in length with an A+T content of 61.34%. It contained 131 putative open reading frames (ORFs) covering 87.9% of the genome. Among these ORFs, 37 were conserved in all baculovirus genomes that have been completely sequenced, 24 were conserved in lepidopteran baculoviruses, 65 were found in other baculoviruses, and 5 were unique to the SujuNPV genome. Seven homologous regions (hrs) were identified in the SujuNPV genome. SujuNPV contained several genes that were duplicated or copied multiple times: two copies of helicase, DNA binding protein gene (dbp), p26 and cg30, three copies of the inhibitor of the apoptosis gene (iap), and four copies of the baculovirus repeated ORF (bro). Phylogenetic analysis suggested that SujuNPV belongs to a subclade of group II alphabaculovirus, which differs from other baculoviruses in that all nine members of this subclade contain a second copy of dbp.

Figure 1. Circular map of the SujuNPV genome.

The arrows inside or outside the circle indicate the orientation of putative ORFs. Arrows, red represent the core genes, blue represent Lepidoptera baculovirus conserved genes, grey represent genes common to baculoviruses, open are genes unique to SujuNPV, and yellow rectangles indicate hrs. The collinear region conserved in Lepidoptera baculoviruses is also shown.

Figure 2. Phylogenic analysis of 62 complete baculovirus genomes.

The maximum likelihood (ML) tree was generated based on the concatenated protein sequences of 37 core genes with default parametes and 1000 randoms. The SujuNPV was labeled by a red point and the number on the branch means bootstrap values (only the values over 50 were shown). Pink branches indicate the unique subclade containing a second copy of dbp.

Figure 3. Gene-parity plot analysis.

Gene-parity plots of SujuNPV against three close viruses (EcobNPV, ApciNPV and OrleNPV) and five representative baculoviruses (AcMNPV, HearNPV, CpGV, NeleNPV and CuniNPV).

Figure 4. Analysis of SujuNPV hrs.

A. The location and distribution of hrs in the SujuNPV genome. Black bars indicate hrs in the SujuNPV linear map. The number in brackets refers to the number of palindrome repeats in the homologous region. B. The arrangement of palindrome repeats in each homologous region. The rectangle above or below the black line indicates the orientation of repeats and number in the bracket represent the corresponding size of each hr. Different colors means the different fragments within the repeats, and orange indicates the core palindrome region, which is conserved in all the hr repeats. One sequence of each orientation was displayed at the top as a sample. C. The second structure of the hr1–3 palindrome repeats. The background color is in line with the sequence displayed in Fig. 4B.

Figure 5. Analysis of the duplicated gene helicase and its conservative motifs.

A. The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms. B. Conservative motifs of E.coli UrvD, AcMNPV, SujuNPV Helicase (SujuNPV-1) and SujuNPV Helicase-2 (SujuNPV-2) were displayed. The blank line indicates the relevant protein with length in the bracket. The colored boxes on the line indicate motifs I-IV and the numbers above and below the box mean the start and end position of each motif in the protein, respectively.

Figure 6. Analysis of the duplicated gene dbp.

The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.

Figure 7. Analysis of the duplicated gene cg30.

The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.

Figure 8. Analysis of the duplicated gene p26.

The tree was reconstructed based on protein sequences by MEGA5. The second copy was colored by purple branches and pink background and the number on the branch indicates a bootstrap value of 1000 randoms.