Dataset Information

Complete Genome Sequences of Oryctes rhinoceros nudivirus Strains Detected in Haplotype-G Oryctes rhinoceros from Johor, Malaysia.

ABSTRACT: Two members of the species Oryctes rhinoceros nudivirus (OrNV) were detected in O. rhinoceros haplotype G beetles collected from an oil palm plantation in Kluang and a wild coconut tree in Batu Pahat (Johor, Malaysia). OrNV strain Kluang comprised 125,794 bp, encoding 125 open reading frames (ORFs), while OrNV strain Batu Pahat comprised 124,925 bp, encoding 126 ORFs.

SUBMITTER: Anggraini E

PROVIDER: S-EPMC10019304 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Complete Genome Sequences of Oryctes rhinoceros nudivirus Strains Detected in Haplotype-G Oryctes rhinoceros from Johor, Malaysia.

Anggraini Erise E Vadamalai Ganesan G Kong Lih Ling LL Mat Mazidah M Lau Wei Hong WH

Microbiology resource announcements 20230228 3

Two members of the species Oryctes rhinoceros nudivirus (OrNV) were detected in O. rhinoceros haplotype G beetles collected from an oil palm plantation in Kluang and a wild coconut tree in Batu Pahat (Johor, Malaysia). OrNV strain Kluang comprised 125,794 bp, encoding 125 open reading frames (ORFs), while OrNV strain Batu Pahat comprised 124,925 bp, encoding 126 ORFs. ...[more]

PMID: 36853043

Similar Datasets

Project description:Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress the coconut rhinoceros beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. A new wave of O. rhinoceros incursions in Oceania 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 beetles were collected from Philippines, Fiji, Papua New Guinea (PNG), and the Solomon Islands (SI). RNA sequencing (RNA-seq) was performed to investigate the global viral gene expression profiles and for comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and Philippines are closely related, 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. Nonsynonymous mutations were detected in several hypothetical proteins and 15 nudivirus core genes, such as gp034, lef-8, lef-4, and vp91 We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes, such as gp01, gp022, and gp107, were differentially expressed among different strains. Additionally, small RNA sequencing from the SI population suggested that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21-nucleotide small RNAs. Some of these genomic 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.IMPORTANCE Oryctes rhinoceros nudivirus has been an effective biocontrol agent against the coconut rhinoceros beetle in Southeast Asia and the Pacific Islands for decades. The recent outbreak of these beetles in many South Pacific islands has had a significant impact on livelihoods in the region. It has been suggested that the resurgence and spread of the pest are related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles. We examined viral genomic and transcriptional variations in chronically infected beetles from different geographical populations. A high number of polymorphic sites among several geographical strains of OrNV were identified, but potentially only a few of these variations in the genome are involved in functional changes and can potentially alter the typical function. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variations in different geographic regions and their potential link to virus pathogenicity.

Dataset Information

Complete Genome Sequences of Oryctes rhinoceros nudivirus Strains Detected in Haplotype-G Oryctes rhinoceros from Johor, Malaysia.

Publications

Complete Genome Sequences of Oryctes rhinoceros <i>nudivirus</i> Strains Detected in Haplotype-G Oryctes rhinoceros from Johor, Malaysia.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets