Fig 1.
Occlusion bodies (OBs) of baculovirus isolate SpexNPV-244.1.
(A, B) Scanning electron micrographs of SpexNPV-244.1 OBs. (C, D) Transmission electron micrographs of ultrathin sections through SpexNPV-244.1 OBs. The red arrow in (C) indicates a longitudinal section through a virion containing a single nucleocapsid, while the red arrow in (D) indicates a cross-section through a virion containing four nucleocapsids. The lengths of scale bars are given beneath each scale bar.
Table 1.
Characteristics of genomes of Spodoptera spp. Alphabaculoviruses.
Fig 2.
Map of the ORFs and other features of the SpexNPV-244.1 genome.
ORFs are represented by arrows that indicate the orientation the ORF relative to the polyhedrin (polh) gene. The identity of each ORF is designated by a name (for conserved or well-characterized baculovirus homologs) or the number given to the ORF indicating its order in the annotation. A color key indicates different categories of ORFs in the figure, as well as homologous regions (hrs).
Fig 3.
SpexNPV-244.1 homologous region (hr) unit repeats.
An alignment of the individual repeats of the 5 SpexNPV-244.1 hrs are shown. The consensus sequence is located below the alignment. Shading corresponds to the degree of nucleotide conservation: black, 100%, dark grey, >85%, light grey, > 60%.
Fig 4.
Phylogenetic inference of the relationships among SpexNPV-244.1 and representative isolates of other baculovirus species.
Concatenated alignments of 38 baculovirus core gene amino acid sequences were used to construct ML and ME trees as described under Materials and Methods. Shown is the ML tree with bootstrap values ≥50% for branches in trees produced by both ME and ML methods (displayed as ME/ML). Stars indicate bootstrap values of 100%. Branches for the group I viruses of genus Alphabaculovirus and for the viruses of genera Betabaculovirus and Gammabaculovirus are collapsed. A red box with dashed lines indicates the cluster of viruses from subfamily Noctuinae (Lepidoptera: Noctuidae) into which SpexNPV-244.1 was placed.
Fig 5.
Gene parity plots comparing the ORF content and order of SpexNPV-244.1 and representative alpha- and betabaculoviruses.
Plots compare the ORF content and order of the SpexNPV-244.1 genome (y-axis) with that of AcMNPV-C6, SeMNPV-US1, SpltNPV-G2, and Cydia pomonella granulovirus M1 (CpGV-M1) (x-axes). Each point in the plot represents an ORF, and points corresponding to ORFs present in only one of the compared genomes appear on the axis for the virus in which they are present. ORFs corresponding to core genes of family Baculoviridae are represented by red triangles, and other ORFs are represented by blue triangles. A cluster of core genes with an order conserved in all five viruses are indicated with a bracket.
Fig 6.
Phylogenetic analysis of SpexNPV-244.1 ORF91 homologs.
An ML phylogram inferred from a MUSCLE alignment of amino acid sequences encoded by homologs of SpexNPV-244.1 ORF91 is shown. GenBank accession numbers for the homologs are listed next to the taxon abbreviations. Bootstrap values (≥50%) are indicated at interior branches for ME and ML analysis (presented as ME/ML) where they occur, with a dash (-) indicating when the branch was not supported in either the ME or ML tree. The baculovirus genus of each taxon in the tree is indicated with a color-coded text background.
Fig 7.
Phylogenetic analysis of mitochondrial sequences from group II alphabaculovirus host species.
An ML phylogram inferred from a MUSCLE alignment of mitochondrial nucleotide sequences from the 5′ end of the mitochondrial gene cytochrome c oxidase subunit I (COI-5P; [33]) is shown. Either GenBank abbreviation numbers or Barcode of Life Database BIN ID numbers are listed next to the species names. Bootstrap values (≥50%) are indicated as described for Fig 6. A vertical line delineates the clade of Spodoptera species. A COI-5P sequence from Apis mellifera (GenBank accession no. KR895607) was used as an outgroup.