Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

Abstract

AbstractOryctes rhinoceros nudivirus (OrNV) is a large circular double-stranded DNA virus which has been used as a biological control agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania in previously non-infested areas is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. In this study, chronically infected O. rhinoceros adults were field collected from the Philippines, Fiji, Papua New Guinea and the Solomon Islands. We extracted total RNA from these samples to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations between the four different populations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the Solomon Islands and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. The highest number of structural variants, including single nucleotide variants (SNV), insertion, deletion and non-synonymous mutations, were found in strains from Fiji and PNG when compared to complete recently sequenced Solomon Islands OrNV reference genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as OrNV_gp034 (DNA Helicase), lef-8, lef-4 and vp91. For examination of the global gene expression profile of OrNV in chronically infected populations, we found limited evidence of variation between geographic populations. Only a few genes such as OrNV_gp01 (DNA polymerase B), OrNV_gp022 and OrNV_gp107 (Pif-3) were differentially expressed among different strains. Additionally, small RNA sequencing from the Solomon Islands population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Additionally, we identified a highly abundant putative 22 nt miRNA from the 3’ of a pre-miRNA-like hairpin originating from OrNV-gp-098. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variation. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.