The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

Evaluasi morfologi permukaan semen ionomer kaca dengan modifikasi penambahan nanokitosan kumbang tanduk Surface morphology evaluation of glass ionomer cement modified with nano chitosan of rhinoceros beetle

Pendahuluan: Penambahan nanokitosan pada modifikasi bahan restorasi kedokteran gigi bertujuan untuk memperbaiki sifat mekanik. Sifat mekanik dari suatu bahan dipengaruhi oleh struktur permukaannya. Bahan restorasi yang banyak dilakukan modifikasi yaitu Semen Ionomer Kaca (SIK), salah satunya dengan menambahkan nanokitosan. Sumber nanokitosan dapat berasal dari eksoskeleton serangga kumbang tanduk (Xylotrupes gideon). Xylotrupes gideon memiliki kandungan kitin sebesar 47%. Penelitian ini bertujuan untuk menganalisis morfologi permukaan semen ionomer kaca dengan modifikasi penambahan nanokitosan kumang tanduk. Metode: Jenis penelitian yaitu eksperimental laboratorium. Sampel berbentuk silindris dengan ukuran 6 mm (tinggi) × 4 mm (diameter). Pengambilan sampel menggunakan teknik purposive sampling. Jumlah sampel minimal sebanyak 1 sampel untuk setiap kelompok yaitu kelompok (A) SIK konvensional (kontrol), (B) SIK modifikasi 10% vol/vol larutan nanokitosan, (C) SIK modifikasi 5% vol/vol larutan nanokitosan, (D) SIK modifikasi 10% weight/weight bubuk nanokitosan, dan (E) SIK modifikasi 5% weight/weight bubuk nanokitosan. Sampel yang telah dibuat disimpan dalam inkubator dengan suhu 37°C. Karakterisasi morfologi permukaan sampel menggunakan Scanning Electron Microscopy (SEM). Hasil: Karakterisasi SEM menunjukkan adanya variasi retakan pada permukaan sampel yang diperiksa dengan pembesaran 2000× dan 3500×. SIK modifikasi bubuk nanokitosan menunjukkan lebih banyak retakan pada permukaannya serta peningkatan rasio nanokitosan kumbang tanduk menunjukkan peningkatan keretakan pada morfologi permukaan SIK. Simpulan: Penambahan nanokitosan kumbang tanduk (Xylotrupes gideon) pada Semen Ionomer Kaca mengakibatkan perubahan morfologi permukaan SIK.Kata kunci: Semen ionomer kaca; kumbang tanduk; scanning electron microscopy ABSTRACTIntroduction: The addition of nanochitosan to the modification of dental restorative materials improves mechanical properties. Its surface structure influences the mechanical properties of a material. The restoration material that has been modified a lot is Glass Ionomer Cement (GIC), one of which is by adding nano chitosan. The source of nano chitosan can be derived from the exoskeleton of the rhinoceros beetle (Xylotrupes gideon). Rhinoceros beetle has a chitin content of 47%. This study aims to analyse the surface morphology of the glass ionomer cement with the modification of the addition of nano chitosan of rhinoceros beetle. Methods: This type of research was an experimental laboratory. The sample was cylindrical with 6 mm (height) × 4 mm (diameter). The sampling used was a purposive sampling technique. The minimum number of samples was one sample for each group, namely group (A) conventional (control) GIC, (B) modified GIC 10% vol/vol nanochitosan solution, (C) GIC modified 5% vol/vol nanochitosan solution, (D) GIC modification of 10% weight/weight of nanochitosan powder, and (E) modified GIC of 5% weight/weight of nanochitosan powder. Samples that have been made were stored in an incubator at 37°C. Characterisation of the surface morphology of the sample using Scanning Electron Microscopy (SEM). Results: SEM characterisation showed variations of cracks on the surface of the samples examined at 2000x and 3500x magnification. GIC modified nano chitosan powder showed more cracks on the surface, and an increase in the ratio of rhinoceros beetle nano chitosan showed an increase in cracks in the surface morphology of the GIC. Conclusions: The addition of nano chitosan of rhinoceros beetle to the GIC resulted in changes in the surface morphology.Keywords: Glass ionomer cement; rhinoceros beetle; scanning electron microscopy

Justification of the rotary working bodies of the cultivator for processing between the rows of plantations of lavender oilseed on the basis of agricultural biomechanics

The article presents the methods and results of modeling in agricultural biomechanics, which made it possible to substantiate models of cultivator working bodies adapted to the soil environment based on rotary discs with teeth. The biological prototype of this design is the burrowing limb of a rhinoceros beetle. It is proposed to solve the problems of improving the shape of rotary discs with teeth on the basis of the use of a mechanical-bionic approach, which allows to analytically describe the dependencies for determining the minimum number of steps of cutting notches between the teeth and the number of teeth on the disc, as well as the rational value of their length. The use of a new type of working bodies - a toothed flat disc, designed in a bionic manner, will increase the efficiency of weed control during inter-row tillage, and also reduce traction resistance.

The contents availability of N, P, K, and Mg in empty fruit composting of oil palms with symbiont bacteria from rhinoceros beetle larvae (Oryctes rhinoceros) (Coleoptera: Scarabidae)

The using of palm oil waste had not been optimal lately. It could be seen in oil empty fruit bunches (EFB). It was placed along the oil palm plantations. The condition was not only the trigger of air pollution but also could invite rhinoceros beetle pests (Oryctes rhinoceros) to lay their eggs and carry out reproductive activities due to availability organic matter of the trees. Oil palm plants required large amounts of macro nutrients, especially potassium. However, the potassium nutrient was found in EFB was too slow available because of its relatively long breakdown. That was the reason why it was needed a method of using EFB waste into a capable of high use value product, environmentally friendly, and could give a lot of benefits to oil palm farmers. The purpose of this study was to determine the availability of nutrient content in EFB composting by the using of symbiont bacteria from larvae O. rhinoceros. The research was experimentally conducted a factorial randomized block design (RBD) with 2 factors, namely the type of bacteria and the time of decomposition. The composting stage was carried out by coarsely chopping the EFB then 75 ml of bacterial culture was applied to 1 kg of EFB. Analysis, results indicated C/N ratio (35.56% and 36.97%) and high K content (1.64% and 1.48%). The EFB composting method is achievable in 6 weeks with activators of Bacillus stratosphericus and Bacillus siamensis.

Identification of Components of the Aggregation Pheromone of the Guam Strain of Coconut Rhinoceros Beetle, Oryctes rhinoceros, and Determination of Stereochemistry

The coconut rhinoceros beetle, Oryctes rhinoceros (Linnaeus 1758) (Coleoptera: Scarabaeidae: Dynastinae) (CRB), is endemic to tropical Asia where it damages both coconut and oil palm. A new invasion by CRB occurred on Guam in 2007 and eradication attempts failed using commonly applied Oryctes rhinoceros nudivirus (OrNV) isolates. This and subsequent invasive outbreaks were found to have been caused by a previously unrecognized haplotype, CRB-G, which appeared to be tolerant to OrNV. The male-produced aggregation pheromone of the endemic, susceptible strain of O. rhinoceros (CRB-S) was previously identified as ethyl 4-methyloctanoate. Following reports from growers that commercial lures containing this compound were not attractive to CRB-G, the aim of this work was to identify the pheromone of CRB-G. Initial collections of volatiles from virgin male and female CRB-G adults from the Solomon Islands failed to show any male- or female-specific compounds as candidate pheromone components. Only after five months were significant quantities of ethyl 4-methyloctanoate and 4-methyloctanoic acid produced by males but not by females. No other male-specific compounds could be detected, in particular methyl 4-methyloctanoate, 4-methyl-1-octanol, or 4-methyl-1-octyl acetate, compounds identified in volatiles from some other species of Oryctes. Ethyl 4-methyloctanoate elicited a strong electroantennogram response from both male and female CRB-G, but these other compounds, including 4-methyloctanoic acid, did not. The enantiomers of ethyl 4-methyloctanoate and 4-methyloctanoic acid were conveniently prepared by enzymatic resolution of the commercially-available acid, and the enantiomers of the acid, but not the ester, could be separated by gas chromatography on an enantioselective cyclodextrin phase. Using this approach, both ethyl 4-methyloctanoate and 4-methyloctanoic acid produced by male CRB-G were shown to be exclusively the (R)-enantiomers whereas previous reports had suggested male O. rhinoceros produced the (S)-enantiomers. However, re-examination of the ester and acid produced by male CRB-S from Papua New Guinea showed that these were also the (R)-enantiomers. In field trapping experiments carried out in the Solomon Islands, both racemic and ethyl (R)-4-methyloctanoate were highly attractive to both male and female CRB-G beetles. The (S)-enantiomer and the corresponding acids were only weakly attractive. The addition of racemic 4-methyloctanoic acid to ethyl 4-methyloctanoate did significantly increase attractiveness, but the addition of (R)- or (S)-4-methyloctanoic acid to the corresponding ethyl esters did not. Possible reasons for the difference in assignment of configuration of the components of the CRB pheromone are discussed along with the practical implications of these results.

Diverse Host Immune Responses of Different Geographical Populations of the Coconut Rhinoceros Beetle to Oryctes Rhinoceros Nudivirus (OrNV) Infection

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).

A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

Background: 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. 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. Results: 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. 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 = 99.11%). These quality metrics place our assembly as the most complete of the published Coleopteran genomes. The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes showing BUSCO completeness of 92.09%, as well as the expected number of non-coding RNAs and the number and structure of paralogous genes in a gene family like Sigma GST. Conclusions: 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. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.

Monitoring an invasive coconut rhinoceros beetle population using pheromone traps in Honiara, Solomon Islands

An invasive population of the coconut rhinoceros beetle (Oryctes rhinoceros; CRB) was discovered in Honiara, Guadalcanal, Solomon Islands in 2015. The beetle has caused severe damage to coconut palms in the outbreak area and its continued spread threatens the food security and livelihood of thousands of smallholder farmers in the region. Spread and abundance of the beetle were monitored using bucket traps baited with the aggregation pheromone, ethyl-4 methyloctanoate. Beetles were collected from traps approximately bi-weekly for two periods; one during 2017–18 and the other during 2019–2020. Trap catches showed that CRB was present throughout the whole survey region with significantly higher numbers of female CRB trapped than males. Results indicate a significant 1.5-fold increase in CRB trap catch numbers from 2017–2018 to 2019–2020 despite control efforts. The number of CRB adults trapped also varied between sites and months during both time periods but with no clear patterns. Removal of breeding sites along with strong local quarantine should remain the top priority of the local government to contain CRB expansion within Solomon Islands and beyond.