Baculovirus: molecular insights on their diversity and conservation

Abstract

The Baculoviridae is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp. In this study, genome sequences from 57 baculoviruses were analyzed to reevaluate the number and identity of core genes and to understand the distribution of the remaining coding sequences. Thirty one core genes with orthologs in all genomes were identified along with other 895 genes differing in their degrees of representation among reported genomes. Many of these latter genes are common to well-defined lineages, whereas others are unique to one or a few of the viruses. Phylogenetic analyses based on core gene sequences and the gene composition of the genomes supported the current division of the Baculoviridae into 4 genera: Alphabaculovirus, Betabaculovirus, Gammabaculovirus, and Deltabaculovirus.

Figure 1

GC content in baculovirus genomes. The different histograms contain the distribution of baculovirus genomes according to their GC content and their genus classification. Black bars highlight genomes with a GC content higher than 50%.

Figure 2

Baculovirus core genes. The different circles represent the 4 baculovirus genera (in yellow Alphabaculovirus; in green Betabaculovirus; in red Gammabaculovirus; in blue Deltabaculovirus). The numbers contained within the overlapping regions indicate the amount of shared genes between all members of the genera. The numbers within the circles but outside the overlapping regions indicate the amount of genes shared by all members of that genus but with the absence of orthologous sequences in the remaining genera. These estimations were inferred by Blast P algorithm (http://www.ncbi.nlm.nih.gov/) considering E = 0.001 as cutoff value and comparing all reported baculovirus ORFs between them. The identity of common genes is provided in the Supplementary data available at doi:10.4061/2011/379424

Figure 3

Whole baculovirus gene content. The histogram shows the amount of different reported genes in each baculovirus genus or recognized lineage (bars in pink color), and the subset of shared genes for all members of the corresponding phylogenetic clade (bars in green color). This bar graph was performed using the information resulting from the comparison of all ORFs reported in the 57 baculovirus with known genomes, analyzing all against all by Blast P algorithm (http://www.ncbi.nlm.nih.gov/) considering E = 0.001 as cutoff value.

Figure 4

Baculovirus genome phylogeny. Cladogram based on amino acid sequence of core genes. The 31 identified core genes from Baculoviridae family were independently aligned using MEGA 4 [25] program with gap open penalty = 10, gap extension penalty = 1, and dayhoff matrix [26]. Then, a concatemer was generated and phylogeny inferred using the same software (UPGMA; bootstrap with 1000 replicates; gap/missing data = complete deletion; model = amino (dayhoff matrix); patterns among sites = same (homogeneous); rates among sites = different (gamma distributed); gamma parameter = 2.25). Baculoviruses are identified by the acronyms given in Table 1, and the accepted distribution in lineages and genera are also indicated. Gammabaculovirus and Deltabaculovirus are referenced by Greek letters. The proposed clades of Betabaculoviruses are shown in bold letters.

Figure 5

Baculovirus core gene variability. Histograms show the average PAM250 distances for each core gene with their corresponding standard deviations. These values were calculated using MEGA 4 program (UPGMA; bootstrap with 1000 replicates; gap/missing data = complete deletion; model = amino (dayhoff matrix); patterns among sites = same (homogeneous); rates among sites = different (gamma distributed; gamma parameter = 2.25)). PAM (point accepted mutation) matrices refers to the evolutionary distance between pairs of sequences. Given the weak similarity between several core proteins, PAM250 matrix was selected. The divergence considered in this matrix is 250 mutations per 100 amino acid sequence and was calculated to analyze more distantly related sequences. PAM250 is considered a good general matrix for protein similarity search.