Genomic sequence analysis of granulovirus isolated from the tobacco cutworm, Spodoptera litura

Abstract

Background: Spodoptera litura is a noctuid moth that is considered an agricultural pest. The larvae feed on a wide range of plants and have been recorded on plants from 40 plant families (mostly dicotyledons). It is a major pest of many crops. To better understand Spodoptera litura granulovirus (SpliGV), the nucleotide sequence of the SpliGV DNA genome was determined and analyzed.

Methodology/principal findings: The genome of the SpliGV was completely sequenced. The nucleotide sequence of the SpliGV genome was 124,121 bp long with 61.2% A+T content and contained 133 putative open reading frames (ORFs) of 150 or more nucleotides. The 133 putative ORFs covered 86.3% of the genome. Among these, 31 ORFs were conserved in most completely sequenced baculovirus genomes, 38 were granulovirus (GV)-specific, and 64 were present in some nucleopolyhedroviruses (NPVs) and/or GVs. We proved that 9 of the ORFs were SpliGV specific.

Conclusions/significance: The genome of SpliGV is 124,121 bp in size. One hundred thirty-three ORFs that putatively encode proteins of 50 or more amino acid residues with minimal overlap were determined. No chitinase or cathepsin genes, which are involved in the liquefaction of the infected host, were found in the SpliGV genome, explaining why SpliGV-infected insects do not degrade in a typical manner. The DNA photolyase gene was first found in the genus Granulovirus. When phylogenic relationships were analyzed, the SpliGV was most closely related to Trichoplusia ni granulovirus (TnGV) and Xestia c-nigrum granulovirus (XecnGV), which belong to the Type I-granuloviruses (Type I-GV).

Figure 1. Representation of the SpliGV genome.

ORFs and transcriptional direction are indicated by arrows. The ORFs present in most completely sequenced baculovirus genomes are colored gray; GV-specific ORFs are in blue; SpliGV unique ORFs are in red; and ORFs present in some NPVs and/or some GVs are in black.

Figure 2. RT-PCR of 9 SpliGV-specific ORFs using mRNAs from S. litura larvae infected with SpliGV as a template.

M1, 100-bp DNA ladder (Fermentas, USA); 1, Spli30; 2, Spli40; 3, Spli51; 4, Spli61; 5, Spli63; 6, Spli75; 7, Spli88; 8, Spli121; 9, Spli133; M2, 1-kb DNA ladder (Fermentas, USA).

Figure 3. Phylogenic relationship between 41 complete baculovirus genomes based on the nucleotide sequences of 24 genes.

The numbers on the branches represent bootstrap values for 1,000 replicates.

Figure 4. Nucleotide sequence comparison of the SpliGV genome and other GV genomes by matrix dot plot.

Figure 5. Gene order diagram of 24 genes from 45 complete baculovirus genomes.