The complete genome of a baculovirus isolated from an insect of medical interest: Lonomia obliqua (Lepidoptera: Saturniidae)

Abstract

Lonomia obliqua (Lepidoptera: Saturniidae) is a species of medical importance due to the severity of reactions caused by accidental contact with the caterpillar bristles. Several natural pathogens have been identified in L. obliqua, and among them the baculovirus Lonomia obliqua multiple nucleopolyhedrovirus (LoobMNPV). The complete genome of LoobMNPV was sequenced and shown to have 120,022 bp long with 134 putative open reading frames (ORFs). Phylogenetic analysis of the LoobMNPV genome showed that it belongs to Alphabaculovirus group I (lepidopteran-infective NPV). A total of 12 unique ORFs were identified with no homologs in other sequenced baculovirus genomes. One of these, the predicted protein encoded by loob035, showed significant identity to an eukaryotic transcription terminator factor (TTF2) from the Lepidoptera Danaus plexippus, suggesting an independent acquisition through horizontal gene transfer. Homologs of cathepsin and chitinase genes, which are involved in host integument liquefaction and viral spread, were not found in this genome. As L. obliqua presents a gregarious behavior during the larvae stage the impact of this deletion might be neglectable.

Figure 1. Genome map and heat map of the LoobMNPV genome.

(a) Genome map showing all the 134 ORFs. The unique ORFs are represented in black. The outer track contains forward orientation ORFs, and the inner track contains reverse orientation ORFs. Hrs are shown on the line below the genome. (b) Heat map identity of the genomes of the species AcMNPV, ThorNPV, MaviMNPV, DekiNPV, and AnpeNPV (from the outside to the inside) compared to ortholog ORFs from LoobMNPV. The darker the blue, the higher is the correlated ORF identity.

Figure 2. LoobMNPV hr palindromes.

Alignment showing the position and the sequence of 38 hr-like imperfect palindromes found in the LoobMNPV genome, numbered sequentially, where letters designate palindromes within the same hr. The black shaded areas indicate residues that have strict identity, whereas grey shaded areas indicate conservation within the majority of the group (no strict identity). Dots represent gaps to achive a better alignment.

Figure 3. Phylogeny of baculoviruses.

Phylogenetic inference of 37 conserved proteins (core genes) present in 72 baculovirus genomes from different host species. The genera Gammabaculovirus, Betabaculovirus, and group II Alphaphabaculovirus are collapsed. CuniNPV was used to root the tree. LoobMNPV belongs to the genus Alphabaculovirus, on group I, and clustered with DekiNPV. Both species are a sister clade of AcMNPV-related species.

Figure 4. Genome sinteny of LoobMNPV.

(a) LoobMNPV sinteny comparison to the baculoviruses AnpeNPV (salmon), MaviMNPV (light pink), ThorNPV (blue), AcMNPV (green), and DekiNPV (orange). Each line represent an ortholog ORF to LoobMNPV based on the protein identity. LoobMNPV and DekiNPV are collinear, while the other genomes show an inversion when compared to LoobMNPV. (b) Zoom from (a) on the location where all baculoviruses compared overlap, showing hrs located closely to LoobMNPV unique ORFs (white gaps).

Figure 5. Phylogeny of GTAs and TTF2 genes.

Unrooted maximum likelihood phylogeny of the data set containing genes that correspond to TTF2 from Insecta (red), TTF2 from other eukaryote (orange), GTA from group I Alphabaculovirus (green), and loob035 (blue).

Figure 6. GTA genomic context in several alphabaculoviruses.

(a) The GTA gene is present in almost all group I Alphabaculovirus and is shown here aligned to the phylogeny previously showed on Fig. 3. In AcMNPV, AgMNPV, AnpeNPV, BmNPV, BomaNPV, CfMNPV, ChocNPV, ChmuNPV, ChroNPV, DekiNPV, EppoNPV, HycuMNPV, LoobMNPV, MaviMNPV, OpMNPV, PhcyNPV, PlxyMNPV, RoMNPV e ThorNPV, the GTA gene is always in between p-47 (followed by lef-12) and odv-e56. LoobMNPV, DekiNPV and MaviMNPV lack the GTA gene. Dotted lines represent absence of ORFs. (b) The position of loob035 in the genome of LoobMNPV is located between homologs of both ac110-like (loob034) and ac111-like (loob036). The position of two loob035 homologs (Table S1) from DekiNPV_Orf138 and ThorNPV_Orf117 are also represented in different genome contexts.