1/29/2024 0 Comments Coconut rhinoceros beetle![]() rhinoceros in Guam in 2007 was not controlled with OrNV, and the beetle’s subsequent expansion to other Pacific Islands including Papua New Guinea, Hawaii, Solomon Islands, and most recently Vanuatu and New Caledonia, suggests potential changes in this biological system that require new approaches to management, including the isolation and deployment of highly virulent OrNV strains for specific O. However, a highly damaging infestation by O. rhinoceros have been suppressed over the past 60 years through management approaches that included the release of a biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). Native to southeast Asia, this pest was accidentally introduced into Samoa in 1909, and it has since spread across the tropical Pacific, bringing a significant threat to the livelihoods of the peoples of Pacific island nations for whom the coconut palm (‘the tree of life’) is an important source of food, fibre and timber. This damages growing tissue and significantly reduces coconut yields and can lead to the death of trees. (Coleoptera: Scarabaeidae), feed by boring into the crown of coconut palms. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.Īdult coconut rhinoceros beetles, Oryctes rhinoceros L. The 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. 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. 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. The quality of our gene models was also confirmed with the correct placement of O. 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 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. These quality metrics place our assembly ahead of the published Coleopteran genomes, including that of an insect model, the red flour beetle ( Tribolium castaneum). 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%). High-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. 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. 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). Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. An 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.
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