RNA-seq data of Elaeidobius kamerunicus from North Sumatera and Central Kalimantan in Indonesia.

Since introduced from West Africa at 40 years ago, Elaeidobius kamerunicus Faust. (Coleoptera: Curculionidae) is still the main pollinator agent of oil palm plantation in Indonesia until now. Unfortunately, the success rate of pollination in various regions in Indonesia is relatively different, for example in Sumatra and Kalimantan. The oil palm fruit set formed in Kalimantan tends to be lower than in Sumatra. Preliminary studies show that weevils from Kalimantan visit female flowers less than from Sumatra. However, the molecular mechanisms involved in regulating insect behavior, especially in their role as pollinating agents, are not yet clearly understood. Therefore, a transcriptomic study was carried out to obtain raw data to determine gene expression differences in studying the behavior of the same weevil from two different regions. Here, we present two data sets of RNA seq reads which are available in GenBank Sequence Read Archive (SRA) database with accession number of SRR21521626 and SRR21521625 for weevil from North Sumatra and Central Kalimantan respectively.

RNA-seq data of tea mosquito bugs, Helopeltis bradyi, antennae.

Tea Mosquito Bug (TMB), Helopeltis bradyi (Hemiptera: Miridae) is one of the major pest infesting tea and cocoa plantations worldwide. Developing olfaction-based control methods was urges as an alternative to commonly used but non-environmental friendly chemical pesticides. However, the molecular mechanisms underlying TMB reception mechanism are still lacking. Here, we collected a pooled male and female TMB antennae for RNA extraction followed by sequencing using the BGISEQ-500 platform and de novo assembly. TMB antennae RNA-seq data yielded 32,142 unigenes with N50 and GC (%) were 2322 and 40.25; subsequently. The RNA-seq data are available in GenBank Sequence Read Archive (SRA) database with accession number SRR13327229. De novo transcriptome analysis had identified several genes involved in TMB odorant reception includes; 39 OBPs (odorant binding proteins), 10 CSPs (chemosensory proteins), 81 Ors (odorant receptors), 1 Orcos (co-receptors), 9 SNMPs (sensory neuron membrane proteins), 3 GRs (gustatory receptors) and 4 IRs (ionotropic receptors). Our study presents the first RNA seq for TMB antennae, which serve the primary molecular resources data, which will facilitate further research to develop olfaction-based control methods, potentially contribute to TMB management strategies.

Transcriptomic data of the Musa balbisiana cultivar Kepok inoculated with Ralstonia syzigii subsp. celebesensis and Ralstonia solanacearum.

The increasing production of banana is hampered by the spread of banana plant diseases, one of which is caused by a group of bacteria, including those of causing wilt diseases. In Indonesia, blood disease is one of the important banana wilt diseases since loss due to the infection can reach up to 50%. There are numerous publications on the pathogen identification causing banana blood disease based on the molecular approach, however to date, no detailed molecular data are available for the interaction of banana host plant against the pathogen. Here, we present three raw data sets of the total RNA-seq from the inoculated Musa balbisiana cutivar kepok (ABB genome) inoculated with Ralstonia syzigii subsp. celebesensis, Ralstonia solanacearum and mock. The data provide essential knowledge for differentiating the banana response against pathogen, reveal pathogenesis-related genes and gene functions in the plant system, and research development to design blood disease-resistance of banana as one of the management strategies. Raw reads of RNA-seq data can be found in NCBI's Sequence Read Archive (SRA) database with the accession number of SRR10547839 (RSC), SRR10547840 (RS), and SRR10547841 (Mock).

RNA-seq data of banana bunchy top virus (BBTV) viruliferous and non-viruliferous banana aphid (Pentalonia nigronervosa).

Banana bunchy top disease (BBT) is one of the most economically serious viral diseases of banana caused by banana bunchy top virus (BBTV: Nanoviridae: Babuvirus). BBTV is a circular, ssDNA virus which is suitable in the phloem tissue and currently only being transmitted by the banana aphid (Pentalonia nigronervosa) in a persistent, non-propagative, circulative manner. Interaction of BBTV and banana aphid had been studied in several ways, such as transmission and translocation of BBTV inside the banana aphid body at cellular level. However, the molecular mechanism underlying the interaction between BBTV and banana aphid have been poorly understood. Therefore, this transcriptomic study was conducted to obtain the raw data for differential genes expression study in BBTV viruliferous (Vr) and non-viruliferous (NVr) banana aphid. Here, we present two data sets of RNA seq raw reads which is available in GenBank Sequence Read Archive (SRA) database with accession number of SRX6918251 and SRX6918252 for the Vr and NVr banana aphid respectively.

Evolutionary Analysis of the Highly Conserved Insect Odorant Coreceptor (Orco) Revealed a Positive Selection Mode, Implying Functional Flexibility.

Odorant coreceptor (Orco) represents one of the essential genes in the insect olfactory system, which facilitates signal transduction and heterodimerization with different odorant receptors (Ors) in the insect antennal dendritic membrane. Evolutionary analysis by detecting positive selection is important to examine the functional flexibility of Orco that potentially supports insect survival. The maximum likelihood codon substitution model was applied using CODEML program as implemented in PAML ver 4.9e package across 59 Orco codon sequences available from GenBank. These sequences represented five major insect orders and two reproductive systems (holometabola and nonholometabola). In the site model that identified common ω values for Orco, it was clearly shown that Orco was under strong purifying selection, indicated by the ω value that was far from 1 (ω: 0.03). However, in to the branch model, positive selection was detected to be acting on Dipteran lineages, whereas in the branch-site model, several sites were under significant positive selection occurring in the following four clades: Coleoptera, Diptera, Lepidoptera, and Psocodea. The typical evolutionary mode acting on Orco was consistent with the entropy value [H(x)], confirming that 48.9% of the Orco site was under conservation (H(x) < 0.5), whereas 26.9% of the Orco sites was under high variation (H(x) > 1). These findings confirmed that Orco genes are generally highly conserved and can possibly be used for the manipulation of insect pest control programs. However, positive selection that acts on certain lineages suggested future adaptive evolutionary ability of Orco to anticipate flexible functions for successful olfactory processes.

Silencing the Olfactory Co-Receptor RferOrco Reduces the Response to Pheromones in the Red Palm Weevil, Rhynchophorus ferrugineus.

The red palm weevil (RPW, Rhynchophorus ferrugineus), one of the most widespread of all invasive insect pest species, is a major cause of severe damage to economically important palm trees. RPW exhibits behaviors very similar to those of its sympatric species, the Asian palm weevil (R. vulneratus), which is restricted geographically to the southern part of Southeast Asia. Although efficient and sustainable control of these pests remains challenging, olfactory-system disruption has been proposed as a promising approach for controlling palm weevils. Here, we report the cloning and sequencing of an olfactory co-receptor (Orco) from R. ferrugineus (RferOrco) and R. vulneratus (RvulOrco) and examine the effects of RferOrco silencing (RNAi) on odorant detection. RferOrco and RvulOrco encoding 482 amino acids showing 99.58% identity. The injection of double-stranded RNA (dsRNA) from RferOrco into R. ferrugineus pupae significantly reduced RferOrco gene expression and led to the failure of odor-stimulus detection, as confirmed through olfactometer and electroantennography (EAG) assays. These results suggest that olfactory-system disruption leading to reduced pheromone detection holds great potential for RPW pest-control strategies.

Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis.

BACKGROUND: The Red Palm Weevil (RPW) Rhynchophorus ferrugineus (Oliver) is one of the most damaging invasive insect species in the world. This weevil is highly specialized to thrive in adverse desert climates, and it causes major economic losses due to its effects on palm trees around the world. RPWs locate palm trees by means of plant volatile cues and use an aggregation pheromone to coordinate a mass-attack. Here we report on the high throughput sequencing of the RPW antennal transcriptome and present a description of the highly expressed chemosensory gene families. RESULTS: Deep sequencing and assembly of the RPW antennal transcriptome yielded 35,667 transcripts with an average length of 857 bp and identified a large number of highly expressed transcripts of odorant binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors/co-receptors (ORs/Orcos), sensory neuron membrane proteins (SNMPs), gustatory receptors (GRs) and ionotropic receptors (IRs). In total, 38 OBPs, 12 CSPs, 76 ORs, 1 Orco, 6 SNMPs, 15 GRs and 10 IRs were annotated in the R. ferrugineus antennal transcriptome. A comparative transcriptome analysis with the bark beetle showed that 25% of the blast hits were unique to R. ferrugineus, indicating a higher, more complete transcript coverage for R. ferrugineus. We categorized the RPW ORs into seven subfamilies of coleopteran ORs and predicted two new subfamilies of ORs. The OR protein sequences were compared with those of the flour beetle, the cerambycid beetle and the bark beetle, and we identified coleopteran-specific, highly conserved ORs as well as unique ORs that are putatively involved in RPW aggregation pheromone detection. We identified 26 Minus-C OBPs and 8 Plus-C OBPs and grouped R. ferrugineus OBPs into different OBP-subfamilies according to phylogeny, which indicated significant species-specific expansion and divergence in R. ferrugineus. We also identified a diverse family of CSP proteins, as well as a coleopteran-specific CSP lineage that diverged from Diptera and Lepidoptera. We identified several extremely diverged IR orthologues as well as highly conserved insect IR co-receptor orthologous transcripts in R. ferrugineus. Notably, GR orthologous transcripts for CO2-sensing and sweet tastants were identified in R. ferrugineus, and we found a great diversity of GRs within the coleopteran family. With respect to SNMP-1 and SNMP-2 orthologous transcripts, one SNMP-1 orthologue was found to be strikingly highly expressed in the R. ferrugineus antennal transcriptome. CONCLUSION: Our study presents the first comprehensive catalogue of olfactory gene families involved in pheromone and general odorant detection in R. ferrugineus, which are potential novel targets for pest control strategies.

Genes involved in sex pheromone biosynthesis of Ephestia cautella, an important food storage pest, are determined by transcriptome sequencing.

BACKGROUND: Insects use pheromones, chemical signals that underlie all animal behaviors, for communication and for attracting mates. Synthetic pheromones are widely used in pest control strategies because they are environmentally safe. The production of insect pheromones in transgenic plants, which could be more economical and effective in producing isomerically pure compounds, has recently been successfully demonstrated. This research requires information regarding the pheromone biosynthetic pathways and the characterization of pheromone biosynthetic enzymes (PBEs). We used Illumina sequencing to characterize the pheromone gland (PG) transcriptome of the Pyralid moth, Ephestia cautella, a destructive storage pest, to reveal putative candidate genes involved in pheromone biosynthesis, release, transport and degradation. RESULTS: We isolated the E. cautella pheromone compound as (Z,E)-9,12-tetradecadienyl acetate, and the major pheromone precursors 16:acyl, 14:acyl, E14-16:acyl, E12-14:acyl and Z9,E12-14:acyl. Based on the abundance of precursors, two possible pheromone biosynthetic pathways are proposed. Both pathways initiate from C16:acyl-CoA, with one involving ∆14 and ∆9 desaturation to generate Z9,E12-14:acyl, and the other involving the chain shortening of C16:acyl-CoA to C14:acyl-CoA, followed by ∆12 and ∆9 desaturation to generate Z9,E12-14:acyl-CoA. Then, a final reduction and acetylation generates Z9,E12-14:OAc. Illumina sequencing yielded 83,792 transcripts, and we obtained a PG transcriptome of ~49.5 Mb. A total of 191 PBE transcripts, which included pheromone biosynthesis activating neuropeptides, fatty acid transport proteins, acetyl-CoA carboxylases, fatty acid synthases, desaturases, ß-oxidation enzymes, fatty acyl-CoA reductases (FARs) and fatty acetyltransferases (FATs), were selected from the dataset. A comparison of the E. cautella transcriptome data with three other Lepidoptera PG datasets revealed that 45% of the sequences were shared. Phylogenetic trees were constructed for desaturases, FARs and FATs, and transcripts that clustered with the ∆14, ∆12 and ∆9 desaturases, PG-specific FARs and potential candidate FATs, respectively, were identified. Transcripts encoding putative pheromone degrading enzymes, and candidate pheromone carrier and receptor proteins expressed in the E. cautella PG, were also identified. CONCLUSIONS: Our study provides important background information on the enzymes involved in pheromone biosynthesis. This information will be useful for the in vitro production of E. cautella sex pheromones and may provide potential targets for disrupting the pheromone-based communication system of E. cautella to prevent infestations.