The Complete Genome Sequence of Plodia Interpunctella Granulovirus: Evidence for Horizontal Gene Transfer and Discovery of an Unusual Inhibitor-of-Apoptosis Gene

Abstract

The Indianmeal moth, Plodia interpunctella (Lepidoptera: Pyralidae), is a common pest of stored goods with a worldwide distribution. The complete genome sequence for a larval pathogen of this moth, the baculovirus Plodia interpunctella granulovirus (PiGV), was determined by next-generation sequencing. The PiGV genome was found to be 112, 536 bp in length with a 44.2% G+C nucleotide distribution. A total of 123 open reading frames (ORFs) and seven homologous regions (hrs) were identified and annotated. Phylogenetic inference using concatenated alignments of 36 baculovirus core genes placed PiGV in the "b" clade of viruses from genus Betabaculovirus with a branch length suggesting that PiGV represents a distinct betabaculovirus species. In addition to the baculovirus core genes and orthologues of other genes found in other betabaculovirus genomes, the PiGV genome sequence contained orthologues of the bidensovirus NS3 gene, as well as ORFs that occur in alphabaculoviruses but not betabaculoviruses. While PiGV contained an orthologue of inhibitor of apoptosis-5 (iap-5), an orthologue of inhibitor of apoptosis-3 (iap-3) was not present. Instead, the PiGV sequence contained an ORF (PiGV ORF81) encoding an IAP homologue with sequence similarity to insect cellular IAPs, but not to viral IAPs. Phylogenetic analysis of baculovirus and insect IAP amino acid sequences suggested that the baculovirus IAP-3 genes and the PiGV ORF81 IAP homologue represent different lineages arising from more than one acquisition event. The presence of genes from other sources in the PiGV genome highlights the extent to which baculovirus gene content is shaped by horizontal gene transfer.

Fig 1. Map of the ORFs and other features of the PiGV genome.

ORFs are represented by arrows, with the position and direction of the arrow indicating ORF position and orientation. Each ORF is designated by a number or, in the case of conserved or well-characterized baculovirus orthologues, a name. Categories of ORFs are indicated in the figure. Homologous repeat regions (hrs) are represented by red boxes.

Fig 2. Alignment of PiGV homologous region (hr) palindromic repeats.

Nucleotide positions of the repeats in the genome sequence are indicated. Identical nucleotides occupying >50% of aligned positions are shaded in black, and nucleotides of the same class as conserved nucleotides (containing either a purine or pyrimidine base) are shaded in gray. Nucleotides in the repeat consensus sequence are denoted by uppercase letters for positions in the alignment with completely identical residues, and lowercase letters for positions in the alignment with a majority of identical residues. The conserved 10-bp inverted terminal repeat sequence is indicated by boxes surrounding the aligned sequence at each end.

Fig 3. Relationships of PiGV and representative isolates of other baculovirus species, inferred from the predicted amino acid sequences of baculovirus core genes.

The phylogenetic tree was constructed from the concatenated alignments of 36 baculovirus core gene amino acid sequences using the minimum-evolution (ME) method. Taxon genera are indicated with colored text background. Both the group I and II clades of genus Alphabaculovirus and the a and b clades of Betabaculovirus are indicated with brackets. Bootstrap values >50% for both ME and maximum likelihood (ML) analysis are indicated for each interior branch (ME/ML). In addition to PiGV (indicated by a red arrow), virus taxa and accession numbers used in the analysis are as indicated in S1 Table.

Fig 4. Gene parity plots comparing PiGV with representative clade a and b granuloviruses.

Plots show the ORF content and order of the PiGV genome (x-axis) with that of (A) CpGV, (B) PiraGV, and (C) PlxyGV (y-axes). Each point in the plot represents an ORF. ORFs present in only one of the compared genomes appear on the axis corresponding to the virus in which they are present.

Fig 5. Phylogenetic analysis of baculovirus, bidensovirus, and densovirus NS3 homologues.

ME phylogram inferred from the alignment of NS3 homologue amino acid sequences are shown with bootstrap values (>50%) at interior branches for ME and ML analysis (ME/ML) where they occur. In addition to PiGV (indicated by a red arrow), virus taxa are as indicated in S1 Table. Family and/or genus of each taxon is indicated with a color-coded text background.

Fig 6. Phylogenetic analysis of baculovirus ac11 homologues.

ME phylogram inferred from the alignment of AcMNPV ac11 homologue amino acid sequences are shown with bootstrap values (>50%) at interior branches for ME and ML analysis (ME/ML) where they occur. Virus taxa and accession numbers used in the analysis are as indicated in S1 Table. The PiGV ac11 homologues are highlighted in yellow, and the group I alphabaculovirus sequences are indicated by a bracket.

Fig 7. Comparison of PiGV IAPs with representative IAPs from other baculoviruses and insects.

A schematic illustration of IAPs from PiGV, selected alphabaculoviruses (AcMNPV-C6, OpMNPV) and betabaculoviruses (CpGV), and insects. Lines representing the IAPs are drawn in proportion to the sizes of the proteins. The BIR domains are shown in green, the RING domain in orange, and the ubiquitin-association domain (UBA) of T. castaneum IAP-2 is shown in blue.

Fig 8. Phylogenetic analysis of viral and cellular IAPs.

ML phylogram inferred from the alignment of baculovirus and insect amino acid sequences are shown with bootstrap values (>50%) at interior branches for ME and ML analysis (ME/ML) where they occur. Branches for alphabaculovirus IAP-1, betabaculovirus IAP-5, and group I alphabaculovirus IAP-3 sequences are collapsed, and the nodes for these classes of IAPs are indicated in the tree. The baculovirus genus or insect order for each taxon is indicated with color-coded text background. The virus and insect taxa and their accession numbers are as listed in S1 Table.