Abstract
We sequenced the Hyposidra talaca NPV (HytaNPV) double stranded circular DNA genome using PacBio single molecule sequencing technology. We found that the HytaNPV genome is 139,089 bp long with a GC content of 39.6%. It encodes 141 open reading frames (ORFs) including the 37 baculovirus core genes, 25 genes conserved among lepidopteran baculoviruses, 72 genes known in baculovirus, and 7 genes unique to the HytaNPV genome. It is a group II alphabaculovirus that codes for the F protein and lacks the gp64 gene found in group I alphabaculovirus viruses. Using RNA-seq, we confirmed the expression of the ORFs identified in the HytaNPV genome. Phylogenetic analysis showed HytaNPV to be closest to BusuNPV, SujuNPV and EcobNPV that infect other tea pests, Buzura suppressaria, Sucra jujuba, and Ectropis oblique, respectively. We identified repeat elements and a conserved non-coding baculovirus element in the genome. Analysis of the putative promoter sequences identified motif consistent with the temporal expression of the genes observed in the RNA-seq data.
Highlights
We sequenced the Hyposidra talaca Nuclear polyhedrosis viruses (NPVs) (HytaNPV) double stranded circular DNA genome using PacBio single molecule sequencing technology
It encodes 141 open reading frames (ORFs) including the 37 baculovirus core genes, 25 genes conserved among lepidopteran baculoviruses, 72 genes known in baculovirus, and 7 genes unique to the Hyposidra talaca NPV (HytaNPV) genome
We developed a pipeline (Supplementary Figure S1) that identified open reading frames (ORFs) coding for proteins 50 amino acids or longer in the HytaNPV genome and annotated the ORFs based on the homology to proteins they encode
Summary
We sequenced the Hyposidra talaca NPV (HytaNPV) double stranded circular DNA genome using PacBio single molecule sequencing technology. Using RNA-seq, we confirmed the expression of the ORFs identified in the HytaNPV genome. Phylogenetic analysis showed HytaNPV to be closest to BusuNPV, SujuNPV and EcobNPV that infect other tea pests, Buzura suppressaria, Sucra jujuba, and Ectropis oblique, respectively. Analysis of the putative promoter sequences identified motif consistent with the temporal expression of the genes observed in the RNA-seq data. Hyposidra talaca (Walk.) (Lepidoptera: Geometridae), typically found in forests of north-east India, has become a major defoliating pest of tea in these regions, surpassing Buzura suppressaria (Guen.) (Lepidoptera: Geometridae)[2,3,4]. Baculovirus double stranded circular DNA genomes range from 80 to 180 kb in size and encode between 90 and 180 genes[6]. Using an integrated analysis strategy, we have combined the genome and transcriptome data and performed a comparative analysis to annotate and understand the HytaNPV genome
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