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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:Recently, incursions of the Coconut rhinoceros beetle (CRB), Oryctes rhinoceros, have been detected in south Pacific countries that were previously free of the pest. It has been suggested that this range expansion is related to an O. rhinoceros haplotype that is reported to show reduced susceptibility to the well-established classical biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). We investigated O. rhinoceros population genetics and the OrNV status of specimens collected in Fiji, New Caledonia, Papua New Guinea (PNG), Samoa, Solomon Islands, Tonga, Vanuatu and the Philippines. Based on the sequence of the mitochondrial CoxI gene, we found three major mitochondrial haplotype groups (CRB-G, CRB-PNG and CRB-S) across the region. Haplotype diversity varied between and within countries and a high incidence of OrNV infection was detected in all haplotypes wherever they occurred. The O. rhinoceros population in some countries was monotypic and all individuals tested belonged to a single haplotype group. However, in Samoa we detected CRB-S and CRB-PNG and in Solomon Islands we detected all three haplotype groups. Genotyping-by-Sequencing (GBS) showed genetic differentiation in the O. rhinoceros nuclear genome across populations on different islands and provided evidence for gene flow, resulting in a well-mixed population, despite the presence of different CoxI haplotypes in Solomon Islands. Evidence of admixture was also detected on both islands of Samoa. The current CoxI based method is not a reliable diagnostic marker for phenotypic traits, especially in countries such as Solomon Islands where the mitochondrial haplotypes have come back into sympatry and are mixed. To identify possible mechanisms of resistance to OrNV, further molecular analyses O. rhinoceros in response to virus infection is required. To improve biological control of O. rhinoceros, such analyses will need to be combined with an improved understanding of the population genetics of the pest and the evolutionary history of OrNV in the region.

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:BackgroundAn optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetle's mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation.ResultsHigh-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.1%). These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle (Tribolium castaneum). The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes, with only 2.8% missing BUSCOs, and the expected number of non-coding RNAs. The number and structure of paralogous genes in a gene family like Sigma GST is lower than in another scarab beetle (Onthophagus taurus), but higher than in the red flour beetle (Tribolium castaneum), which suggests expansion of this GST class in Scarabaeidae. The quality of our gene models was also confirmed with the correct placement of O. rhinoceros among other members of the rhinoceros beetles (subfamily Dynastinae) in a phylogeny based on the sequences of 95 protein-coding genes in 373 beetle species from all major lineages of Coleoptera. Finally, we provide a list of 30 candidate dsRNA targets whose orthologs have been experimentally validated as highly effective targets for RNAi-based control of several beetles.ConclusionsThe genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.

Dataset Information

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

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