The Genome Sequences of Baculoviruses from the Tufted Apple Bud Moth, Platynota idaeusalis, Reveal Recombination Between an Alphabaculovirus and a Betabaculovirus from the Same Host

Abstract

The USDA-ARS collection of insect viruses at Beltsville, MD, USA, contains samples of an alphabaculovirus from larvae of the tufted apple bud moth, Platynota idaeusalis Walker, as well as a presumptive betabaculovirus from the same host species. The viruses in these samples-Platynota idaeusalis nucleopolyhedrovirus isolate 2680 (PlidNPV-2680) and Platynota idaeusalis granulovirus isolate 2683 (PlidGV-2683)-were characterized by electron microscopy of their occlusion bodies (OBs) and determination and analysis of their genome sequences. Scanning and transmission electron microscopy of the OBs revealed morphologies typical for alphabaculoviruses and betabaculoviruses. Sequencing viral DNA resulted in circular genomes of 121,881 bp and 106,633 bp for PlidNPV-2680 and PlidGV-2683, respectively. Similar numbers of ORFs (128 for PlidNPV-2680, 125 for PlidGV-2683) were annotated, along with ten homologous regions (hrs) in the PlidNPV-2680 genome and five intergenic regions of tandem direct repeats (drs) in the PlidGV genome. Phylogenetic inference from core gene alignments suggested that PlidMNPV-2680 represents a unique lineage within the genus Alphabaculovirus, while PlidGV-2683 was grouped with clade b betabaculoviruses. A comparison of the PlidNPV-2680 and PlidGV-2683 genomes revealed a 1516 bp region in PlidNPV-2680 that exhibited 97.5% sequence identity to a region of the PlidGV-2683 genome, suggesting that recombination had occurred recently between viruses from these lineages.

Keywords: Alphabaculovirus; Betabaculovirus; Platynota idaeusalis; baculovirus; genome; granulovirus; nucleopolyhedrovirus; occlusion bodies; recombination.

Figure 1

OBs of an alphabaculovirus and betabaculovirus isolate from the tufted apple bud moth, P. idaeusalis. (a,b) Scanning electron micrographs of OBs from alphabaculovirus PlidNPV-2680. (c,d) Scanning electron micrographs of OBs from betabaculovirus PlidGV-2683. (e,f) Micrographs of ultrathin sections through PlidGV-2683 OBs. Scale bars: (a) 2 μm; (b,c) 1 μm; (d) 0.5 μm; and (e,f) 0.2 μm.

Figure 2

Consensus sequences of unit repeats in the direct repeat (dr) regions of PlidGV-2683. The consensus sequences for each repeat region (labeled dr#) are shown, unaligned, with nucleotide-specific color shading.

Figure 3

Maps of the open reading frames (ORFs) and other features of (a) PlidNPV-2680 and (b) PlidGV-2683. ORFs are represented by arrows, with the position and direction of the arrow indicating the ORFs’ position and orientation. Each ORF is color-coded to indicate whether it corresponds to a baculovirus core gene conserved in all four genera of Baculoviridae (yellow; [10,11]), an ORF conserved only among alphabaculoviruses or betabaculoviruses (green, [10]), an ORF with homologs in a more limited subset of other baculoviruses (blue), or an ORF with no baculovirus homologs (red). Homologous regions (hrs) or direct repeat regions (drs) are represented by black rectangles. ORFs are designated by either the names by which they are referred to in the literature or a number corresponding to their annotation in the genome.

Figure 4

Betabaculovirus homologs present in the alphabaculovirus PlidNPV-2680 genome. (a) Representation of the region in PlidNPV from nucleotide positions 87,700 to 92,260 showing betabaculovirus homologs of p35/p49 and orf603 (ac7). (b) Representation of the acquisition of PlidGV sequences containing three ORFs by PlidNPV. Genome segments and ORFs of PlidNPV-2680 are in dark blue, while segments and ORFs of betabaculovirus origin are in red. Dashed lines and light blue vertical lines denote the regions of PlidGV that are present in the PlidNPV-2680 genome, and the nucleotide sequence identities with the acquired PlidGV sequences are indicated (% ID).

Figure 5

Phylogeny showing the relationship of PlidGV-2683 to other viruses of the genus Betabaculovirus. The betabaculovirus subtree of a phylogram inferred from concatenated MUSCLE alignments of baculovirus core gene amino acid sequences by maximum likelihood is shown. Taxon names and genome sequence GenBank accession numbers are indicated for each branch, with PlidGV-2683 in red bold type. Betabaculovirus clades (a,b) [51] are indicated with brackets. The levels of bootstrap support for each node are shown, with 100% bootstrap support denoted by stars.

Figure 6

Phylogeny showing the relationship of PlidNPV-2680 to other viruses of the genus Alphabaculovirus. The alphabaculovirus subtree of a core gene phylogram, which was inferred as described for the betabaculovirus subtree (Figure 5), is shown. Taxon names and genome sequence GenBank accession numbers are indicated for each branch, with PlidNPV-2680 in red bold type. Alphabaculovirus group II clades IIa and IIb are indicated with brackets. The branches for groups of related viruses are collapsed, with the number of taxa indicated for each collapsed set. The levels of bootstrap support for each node are shown, with 100% bootstrap support denoted by stars.

Figure 7

Gene-parity plots comparing the ORF content and order of PlidNPV-2680 (x-axis) with four other alphabaculoviruses (y-axis), including representatives of group I (Autographa californica multiple nucleopolyhedrovirus, AcMNPV-C6), clade IIa (Peridroma sp. nucleopolyhedrovirus GR167 and PespNPV-GR167), clade IIb (Clanis bilineata nucleopolyhedrovirus DZ1 and ClbiNPV-DZ1), and clade IIc (Cryptophlebia peltastica nucleopolyhedrovirus SA and CrpeNPV-SA). Points correspond to individual ORFs. ORFs occurred only in one of the two genomes being compared and are plotted directly on the axis corresponding to the virus containing the ORF. Red points denote baculovirus core genes.