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Draft genome sequence, annotation and SSR mining data of Oryctes rhinoceros Linn. (Coleoptera: Scarabaeidae), the coconut rhinoceros beetle

ABSTRACT: The coconut rhinoceros beetle (CRB), Oryctes rhinoceros Linn. (Coleoptera: Scarabaeidae), is one of the major pests of coconut causing severe yield losses. The adult beetles feed on unopened spear leaf (resulting in the typical ‘V’-shaped cuts), spathes, inflorescence, and tender nut leading to stunted palm growth and yield reduction. Moreover, these damages serve as predisposing factors to the entry of other fatal enemies on palms, viz., red palm weevil and bud rot disease, causing yield loss as high as 10%. CRB attacks juvenile palms through the collar region, affecting the growth and initial establishment of the juvenile palms. While the immature stages of CRB sustain on organic debris, the adult beetles are ubiquitous pests on coconut and other palms. The discovery of a new invasive haplotype of CRB from Guam and other Pacific Islands, insensitive to Oryctes rhinoceros nudivirus (OrNV), a potent biocontrol agent, has raised serious concerns. The draft genome sequence and simple sequence repeat (SSR) marker data for this important pest of coconut are presented here. A total of 30 Gb of sequence data from an individual third instar larva was obtained on an Illumina HiSeq X Five platform. The draft genome assembly was found to be 372 Mb, with 97.6% completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment. Functional gene annotation predicted about 16,241 genes. In addition, a total of 21,999 putative simple sequence repeat (SSR) markers were identified. The obtained draft genome is a valuable resource for comprehending population genetics, dispersal patterns, phylogenetics, and species behavior.

SUBMITTER: K R

PROVIDER: S-EPMC8503585 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The coconut rhinoceros beetle, Oryctes rhinoceros L. (Insecta: Coleoptera: Scarabaeidae: Dynastinae) is one of the world's most important endemic and incessant pests of coconut (particularly in India and Southeast Asia), causing an estimated 10% yield loss in the crop. Various management strategies formulated and implemented to control this pest include bioagents, insecticide sprays, liquid formulations, pheromone traps, and botanical formulations. Also, potential microbial bioagents viz., Oryctes rhinoceros nudivirus (OrNV) and Metarhizium anisopliae have been implemented as biological control agents and this has led to a beneficial reduction of the pest population unless significant immigration occurs. To date, research and development activities are still on-going for the successful management of the pest; yet advances in understanding at the molecular level have been limited because basic genomic information is lacking for this cosmopolitan pest. Transcriptome approach has been proved extremely useful in finding potential genes for pest control. Transcriptome analysis aids in gaining insights into the transcriptional changes which occur during different developmental stages of an organism. We have performed RNA sequencing of certain different developmental stages of O. rhinoceros viz., early instar larva, late instar larva, pupa, and adult, in an Illumina HiSeq™ 2500 platform. Due to the unavailability of O. rhinoceros genome, the RNA-seq data generated were assembled de novo using Trinity and annotated following redundancy removal. A dataset of 87,451 transcripts, which resulted after redundancy removal, were annotated using the NCBI non-redundant (nr) protein and Uniprot databases. The data furnished could be used by others working in the development of pest management strategies, especially the identification of molecular targets for effective pest control. This information allows a better understanding of O. rhinoceros biology which would contribute to outlining a new generation of stage-specific, environmentally friendly pest management techniques.

Project description:Incursions of the coconut rhinoceros beetle (CRB), Oryctes rhinoceros, into different islands in the South Pacific have been detected in recent years. It has been suggested that this range expansion is related to an O. rhinoceros haplotype reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). Our understanding of the genetic characteristics which distinguish the population of O. rhinoceros that has recently established in Solomon Islands from other well-established populations across the region is very limited. Here, we hypothesized that the recently established O. rhinoceros population should have greater innate immune responses when challenged by OrNV than those of well-established and native O. rhinoceros populations. We used the RNA sequencing (RNA-Seq) approach to generate gene expression profiles of midgut tissue from OrNV-infected and noninfected individuals collected in the Solomon Islands (recent incursion), Papua New Guinea and Fiji (previously established), and the Philippines (within the native range). The collections included individuals from each of the three major mitochondrial lineages (CRB-G, CRB-PNG, and CRB-S) known to the region, allowing us to explore the specific responses of each haplotype to infection. Although insects from the Philippines and Solomon Islands that were tested belong to the same mitochondrial lineage (CRB-G), their overall responses to infection were different. The number of differentially expressed genes between OrNV-infected and noninfected wild-caught individuals from the four different locations varied from 148 to 252. Persistent OrNV infection caused a high level of induced antimicrobial activity and immune responses in O. rhinoceros, but the direction and magnitude of the responses were population specific. The insects tested from the Solomon Islands displayed extremely high expression of genes which are known to be involved in immune responses (e.g. coleoptericin, cecropin, and serpin). These variations in the host immune system among insects from different geographical regions might be driven by variations in the virulence of OrNV isolates, and this requires further investigation. Overall, our current findings support the importance of immunity in insect pest incursion and an expansion of the pest's geographic range. IMPORTANCE Oryctes rhinoceros nudivirus (OrNV) is a double-stranded DNA (dsDNA) virus which has been used as a biocontrol agent to suppress coconut rhinoceros beetle (CRB) in the Pacific Islands. Recently a new wave of CRB incursions in Oceania is thought to be related to the presence of low-virulence isolates of OrNV or virus-tolerant haplotypes of beetles (CRB-G). Our comparative analysis of OrNV-infected and noninfected CRBs revealed that specific sets of genes were induced by viral infection in the beetles. This induction was much stronger in beetles collected from the Solomon Islands, a newly invaded country, than in individuals collected from within the beetle's native range (the Philippines) or from longer-established populations in its exotic range (Fiji and Papua New Guinea [PNG]). Beetles from the Philippines and the Solomon Islands that were tested in this study all belonged to the CRB-G haplotype, but the country-specific responses of the beetles to OrNV infection were different.

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.

Project description:BackgroundThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.MethodsSequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.ResultsThe complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the O. rhinoceros mitogenome sequence and annotation.

Dataset Information

Draft genome sequence, annotation and SSR mining data of Oryctes rhinoceros Linn. (Coleoptera: Scarabaeidae), the coconut rhinoceros beetle

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