The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface

Identification of Multifunctional Putative Bioactive Peptides in the Insect Model Red Palm Weevil (Rhynchophorus ferrugineus)

Innate immunity, the body's initial defense against bacteria, fungi, and viruses, heavily depends on antimicrobial peptides (AMPs), which are small molecules produced by all living organisms. Insects, with their vast biodiversity, are one of the most abundant and innovative sources of AMPs. In this study, AMPs from the red palm weevil (RPW) Rhynchophorus ferrugineus (Coleoptera: Curculionidae), a known invasive pest of palm species, were examined. The AMPs were identified in the transcriptomes from different body parts of male and female adults, under different experimental conditions, including specimens collected from the field and those reared in the laboratory. The RPW transcriptomes were examined to predict antimicrobial activity, and all sequences putatively encoding AMPs were analyzed using several machine learning algorithms available in the CAMPR3 database. Additionally, anticancer, antiviral, and antifungal activity of the peptides were predicted using iACP, AVPpred, and Antifp server tools, respectively. Physicochemical parameters were assessed using the Antimicrobial Peptide Database Calculator and Predictor. From these analyses, 198 putatively active peptides were identified, which can be tested in future studies to validate the in silico predictions. Genome-wide analysis revealed that several AMPs have predominantly emerged through gene duplication. Noticeably, we detect a newly originated defensin allele from an ancestral defensin via the deletion of two amino acids following gene duplication in RPW, which may confer an enhanced resilience to microbial infection. Our study shed light on AMP gene families and shows that high duplication and deletion rates are essential to achieve a diversity of antimicrobial mechanisms; hence, we propose the RPW AMPs as a model for exploring gene duplication and functional variations against microbial infection.

Chromosome-Level Genome Assembly of Apoderus dimidiatus Voss (Coleoptera: Attelabidae): Insights into Evolution and Behavior

Attelabidae insects have attracted much attention due to their unique leaf rolling behavior before oviposition. However, the lack of genomic data makes it difficult to understand the molecular mechanism behind their behavior and their evolutionary relationship with other species. To address this gap, we utilized Illumina and Nanopore sequencing platforms along with Hi-C technology to establish a highly accurate whole genome of A. dimidiatus at the chromosome level. The resulting genome size was determined to be 619.26 Mb, with a contig N50 of 50.89 Mb and GC content of 33.89%. Moreover, a total of 12,572 genes were identified, with 82.59% being functionally annotated, and 64.78% designated as repeat sequences. Our subsequent phylogenetic tree analysis revealed that Attelabidae's divergence from Curculionidae occurred approximately 161.52 million years ago. Furthermore, the genome of A. dimidiatus contained 334 expanded gene families and 1718 contracted gene families. In addition, using Phylogenetic Analysis by Maximum Likelihood (PAML), we identified 106 rapidly evolved genes exhibiting significant signals and 540 positively selected genes. Our research endeavors to serve as an invaluable genomic data resource for the study of Attelabidae, offering fresh perspectives for the exploration of its leaf rolling behavior.

Taxonomy, Biology, Symbionts, Omics, and Management of Rhynchophorus Palm Weevils (Coleoptera: Curculionidae: Dryophthorinae)

Palm weevils, Rhynchophorus spp., are destructive pests of native, ornamental, and agricultural palm species. Of the 10 recognized species, two of the most injurious species, Rhynchophorus ferrugineus and Rhynchophorus palmarum, both of which have spread beyond their native range, are the best studied. Due to its greater global spread and damage to edible date industries in the Middle East, R. ferrugineus has received more research interest. Integrated pest management programs utilize traps baited with aggregation pheromone, removal of infested palms, and insecticides. However, weevil control is costly, development of resistance to insecticides is problematic, and program efficacy can be impaired because early detection of infestations is difficult. The genome of R. ferrugineus has been sequenced, and omics research is providing insight into pheromone communication and changes in volatile and metabolism profiles of weevil-infested palms. We outline how such developments could lead to new control strategies and early detection tools.

Near-chromosomal-level genome of the red palm weevil (Rhynchophorus ferrugineus), a potential resource for genome-based pest control

The red palm weevil (RPW) is a highly destructive pest that mainly affects palms, particularly date palms (Phoenix dactylifera), in the Arabian Gulf region. In this study, we present a near-chromosomal-level genome assembly of the RPW using a combination of PacBio HiFi and Dovetail Omini-C reads. The final genome assembly is around 779 Mb in size, with an N50 of ~43 Mb, consistent with our previous flow cytometry estimates. The completeness of the genome was confirmed through BUSCO analysis, which indicates the presence of 99.5% of BUSCO single copy orthologous genes. The genome annotation identified a total of 29,666 protein-coding, 1,091 tRNA and 543 rRNA genes. Overall, the proposed genome assembly is significantly superior to existing assemblies in terms of contiguity, integrity, and genome completeness.

Host-Encoded Aminotransferase Import into the Endosymbiotic Bacteria Nardonella of Red Palm Weevil

Symbiotic systems are intimately integrated at multiple levels. Host-endosymbiont metabolic complementarity in amino acid biosynthesis is especially important for sap-feeding insects and their symbionts. In weevil-Nardonella endosymbiosis, the final step reaction of the endosymbiont tyrosine synthesis pathway is complemented by host-encoded aminotransferases. Based on previous results from other insects, we suspected that these aminotransferases were likely transported into the Nardonella cytoplasm to produce tyrosine. Here, we identified five aminotransferase genes in the genome of the red palm weevil. Using quantitative real-time RT-PCR, we confirmed that RfGOT1 and RfGOT2A were specifically expressed in the bacteriome. RNA interference targeting these two aminotransferase genes reduced the tyrosine level in the bacteriome. The immunofluorescence-FISH double labeling localization analysis revealed that RfGOT1 and RfGOT2A were present within the bacteriocyte, where they colocalized with Nardonella cells. Immunogold transmission electron microscopy demonstrated the localization of RfGOT1 and RfGOT2A in the cytosol of Nardonella and the bacteriocyte. Our data revealed that RfGOT1 and RfGOT2A are transported into the Nardonella cytoplasm to collaborate with genes retained in the Nardonella genome in order to synthesize tyrosine. The results of our study will enhance the understanding of the integration of host and endosymbiont metabolism in amino acid biosynthesis.

Evolutionary genomics of three agricultural pest moths reveals rapid evolution of host adaptation and immune-related genes

BACKGROUND

Understanding the genotype of pest species provides an important baseline for designing integrated pest management (IPM) strategies. Recently developed long-read sequence technologies make it possible to compare genomic features of nonmodel pest species to disclose the evolutionary path underlying the pest species profiles. Here we sequenced and assembled genomes for 3 agricultural pest gelechiid moths: Phthorimaea absoluta (tomato leafminer), Keiferia lycopersicella (tomato pinworm), and Scrobipalpa atriplicella (goosefoot groundling moth). We also compared genomes of tomato leafminer and tomato pinworm with published genomes of Phthorimaea operculella and Pectinophora gossypiella to investigate the gene family evolution related to the pest species profiles.

RESULTS

We found that the 3 solanaceous feeding species, P. absoluta, K. lycopersicella, and P. operculella, are clustered together. Gene family evolution analyses with the 4 species show clear gene family expansions on host plant-associated genes for the 3 solanaceous feeding species. These genes are involved in host compound sensing (e.g., gustatory receptors), detoxification (e.g., ABC transporter C family, cytochrome P450, glucose-methanol-choline oxidoreductase, insect cuticle proteins, and UDP-glucuronosyl), and digestion (e.g., serine proteases and peptidase family S1). A gene ontology enrichment analysis of rapid evolving genes also suggests enriched functions in host sensing and immunity.

CONCLUSIONS

Our results of family evolution analyses indicate that host plant adaptation and pathogen defense could be important drivers in species diversification among gelechiid moths.

Host plant recognition by two odorant-binding proteins in Rhynchophorus ferrugineus (Coleoptera: Curculionidae)

BACKGROUND

Rhynchophorus ferrugineus, the red palm weevil (RPW), is a key pest that attacks many economically important palm species and that has evolved a sensitive and specific olfactory system to seek palm hosts. Odorant-binding proteins (OBPs) not only play crucial roles in its olfactory perception process but are also important molecular targets for the development of new approaches for pest management.

RESULTS

Analysis of the tissue expression profiles of RferOBP8 and RferOBP11 revealed that these two Rhynchophorus ferrugineus odorant binding proteins (RferOBPs) exhibited high expression in the antennae and showed sexual dimorphism. We analyzed the volatiles of seven host plants by gas chromatography-mass spectrometry and screened 13 potential ligands by molecular docking. The binding affinity of two recombinant OBPs to aggregation pheromones and 13 palm odorants was tested by fluorescence competitive binding assays. The results revealed that eight tested palm volatiles and ferrugineol have high binding affinities with RferOBP8 or RferOBP11. Behavioral trials showed that these eight odor compounds could elicit an attraction response in adult RPW. RNA interference analysis indicated that the reduction in the expression levels of the two RferOBPs led to a decrease in behavioral responses to these volatiles.

CONCLUSION

These results suggest that RferOBP8 and RferOBP11 are involved in mediating the responses of RPW to palm volatiles and to aggregation pheromones and may play important roles in RPW host-seeking. This study also provides a theoretical foundation for the promising application of novel molecular targets in the development of new behavioral interference strategies for RPW management in the future. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Computational insights of the molecular recognition between volatile molecules and odorant binding proteins from the red palm weevil Rhynchophorus ferrugineus

The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is one of the most harmful pests for palm trees, causing serious economic damage worldwide. The present work aims to model and study the 3D structures of highly expressed odorant binding proteins from R. ferrugineus (RferOBPs) and identify possible binding modes and ligand release mechanism by docking and molecular dynamics. Highly confident 3D structures of a total of 11 odorant binding proteins (OBPs) were obtained with AlphaFold2. All 3D RferOBPs modeled structures displayed six characteristic α-helices, except for RfeOBP7 and RfeOBP10, which had an extra terminal α-helix. Among the eleven modeled RferOBPs, RferOBP4 was highly expressed in the antennae and subsequently selected for further analyses. Molecular docking analyses demonstrated that ferruginol, α-pinene, DEET, and picaridin can favorably bind the RferOBP4 cavity with low affinity energies. Molecular dynamic simulations of RferOBP4 bound to ferruginol at different pH values showed that low pH environments dictate a structural change into an apo-state that modifies the number of tunnels where the ligand can coexist, further triggering ligand release by a pH-dependent mechanism. This is the first report concerning the modelling and study of ligand binding modes and release mechanism of R. ferrugineus OBPs.Communicated by Ramaswamy H. Sarma.

A Review on Digestive System of Rhynchophorus ferrugineus as Potential Target to Develop Control Strategies

Rhynchophorus ferrugineus, commonly known as red palm weevil (RPW), is a high-risk insect pest that has become a threat to many important palm species. There are several dominant factors that lead to the successful infestation of RPW, including its stealthy lifestyle, highly chitinized mouthpart, and high fecundity rate. Due to that, millions of dollars of losses have been suffered by many countries invaded by RPW. Several methods have been designed to control its invasion, including the usage of insecticides, but many cause resistance and environmental pollution. Therefore, an environmentally friendly insecticide that targets specific systems or pathways in RPW is urgently needed. One of the potential targets is the digestive system of RPW, as it is the major interface between the insect and its plant host. The related knowledge of RPW's digestive system, such as the anatomy, microflora, transcriptomic analysis, and proteomic analysis, is important to understand its effects on RPW's survival. Several data from different omics regarding the digestive systems of RPW have been published in separate reports. Some of the potential targets have been reported to be inhibited by certain potential insecticides, while other targets have not yet been tested with any inhibitors. Hence, this review may lead to a better understanding on managing infestations of RPW using the system biology approach for its digestive system.

Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing

The world's largest butterfly is the microendemic Papua New Guinean Ornithoptera alexandrae. Despite years of conservation efforts to protect its habitat and breed this up-to-28-cm butterfly, this species still figures as endangered in the IUCN Red List and is only known from two allopatric populations occupying a total of only ∼140 km². Here we aim at assembling reference genomes for this species to investigate its genomic diversity, historical demography and determine whether the population is structured, which could provide guidance for conservation programs attempting to (inter)breed the two populations. Using a combination of long and short DNA reads and RNA sequencing, we assembled six reference genomes of the tribe Troidini, with four annotated genomes of O. alexandrae and two genomes of related species Ornithoptera priamus and Troides oblongomaculatus. We estimated the genomic diversity of the three species, and we proposed scenarios for the historical population demography using two polymorphism-based methods taking into account the characteristics of low-polymorphic invertebrates. Indeed, chromosome-scale assemblies reveal very low levels of nuclear heterozygosity across Troidini, which appears to be exceptionally low for O. alexandrae (lower than 0.01%). Demographic analyses demonstrate low and steadily declining Ne throughout O. alexandrae history, with a divergence into two distinct populations about 10,000 years ago. These results suggest that O. alexandrae distribution has been microendemic for a long time. It should also make local conservation programs aware of the genomic divergence of the two populations, which should not be ignored if any attempt is made to cross the two populations.

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest

The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.

Insight into weevil biology from a reference quality genome of the boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae)

The boll weevil, Anthonomus grandis grandis Boheman, is one of the most historically impactful insects due to its near destruction of the US cotton industry in the early 20th century. Contemporary efforts to manage this insect primarily use pheromone baited traps for detection and organophosphate insecticides for control, but this strategy is not sustainable due to financial and environmental costs. We present a high-quality boll weevil genome assembly, consisting of 306 scaffolds with approximately 24,000 annotated genes, as a first step in the identification of gene targets for novel pest control. Gene content and transposable element distribution are similar to those found in other Curculionidae genomes; however, this is the most contiguous and only assembly reported to date for a member in the species-rich genus Anthonomus. Transcriptome profiles across larval, pupal, and adult life stages led to identification of several genes and gene families that could present targets for novel control strategies.

Genome analysis of Phrixothrix hirtus (Phengodidae) railroad worm shows the expansion of odorant-binding gene families and positive selection on morphogenesis and sex determination genes

Among bioluminescent beetles of the Elateroidea superfamily, Phengodidae is the third largest family, with 244 bioluminescent species distributed only in the Americas, but is still the least studied from the phylogenetic and evolutionary points of view. The railroad worm Phrixothrix hirtus is an essential biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing the first source of genomic information and a framework for comparative analyses of the bioluminescent system in Elateroidea. This is the largest genome described in the Elateroidea superfamily, with an estimated size of ∼3.4 Gb, displaying 32 % GC content, and 67 % transposable elements. Comparative genomic analyses showed a positive selection of genes and gene family expansion events of growths and morphogenesis gene products, which could be associated with the atypical anatomical development and morphogenesis found in paedomorphic females and underdeveloped males. We also observed gene family expansion among distinct odorant-binding receptors, which could be associated with the pheromone communication system typical of these beetles, and retrotransposable elements. Common genes putatively regulating bioluminescence production and control, including two luciferase genes corresponding to lateral lanterns green-emitting and head lanterns red-emitting luciferases with 7 exons and 6 introns, and genes potentially involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea.

Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops

Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.

Insights Into Chemosensory Proteins From Non-Model Insects: Advances and Perspectives in the Context of Pest Management

Nowadays, insect chemosensation represents a key aspect of integrated pest management in the Anthropocene epoch. Olfaction-related proteins have been the focus of studies due to their function in vital processes, such ashost finding and reproduction behavior. Hence, most research has been based on the study of model insects, namely Drosophila melanogaster, Bombyx mori or Tribolium castaneum. Over the passage of time and the advance of new molecular techniques, insects considered non-models have been studied, contributing greatly to the knowledge of insect olfactory systems and enhanced pest control methods. In this review, a reference point for non-model insects is proposed and the concept of model and non-model insects is discussed. Likewise, it summarizes and discusses the progress and contribution in the olfaction field of both model and non-model insects considered pests in agriculture.

A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae) provides insights into the evolution of a detoxification system

The orange wheat blossom midge Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae), an economically important pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. A high-quality chromosome-level genome for S. mosellana was assembled using PacBio long read, Illumina short read, and Hi-C sequencing technologies. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored 4 pseudochromosomes, accounting for 99.67% of the assembled genome. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that S. mosellana and its close relative, the swede midge Contarinia nasturtii, diverged about 32.7 MYA. The S. mosellana genome showed high chromosomal synteny with the genome of Drosophila melanogaster and Anopheles gambiae. The key gene families involved in the detoxification of plant secondary chemistry were analyzed. The high-quality S. mosellana genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges, as well as insect–plant interactions and coevolution.

Role of Genes in Regulating Host Plants Expansion in Tephritid Fruit Flies (Diptera) and Potential for RNAi-Based Control

Host plant expansion is an important survival strategy for tephritids as they expand their range. Successful host expansion requires tephritids to adapt to the chemical and nonchemical properties of a novel host fruit, such as fruit color, phenology, and phytochemicals. These plant properties trigger a series of processes in tephritids, with each process having its own genetic basis, which means that various genes are involved in regulating host plant expansion by tephritids. This review summarizes current knowledge on the categories and roles of genes involved in host plant expansion in several important tephritid species, including genes related to chemoreception (olfactory and gustation), vision, digestion, detoxification, development, ribosomal and energy metabolism. Chemoreception- and detoxification- and digestion-related genes are stimulated by volatile chemicals and secondary chemicals of different hosts, respectively, which are involved in the regulation of nervous signal transduction that triggers behavioral, physical, and chemical responses to the novel host fruit. Vision-, nerve-, and development-related genes and metabolism-associated genes are activated in response to nonchemical stimuli from different hosts, such as color and phenology, to regulate a comprehensive adaptation of the extending host for tephritids. The chemical and nonchemical signals of hosts activate ribosomal and energy-related genes that result in the basic regulation of many processes of host expansion, including detoxification and development. These genes do not regulate novel host use individually, but multiple genes regulate multilevel adaptation to novel host fruits via multiple mechanisms. These genes may also be potential target genes for RNAi-based control of tephritid pests.

Satellitome of the Red Palm Weevil, Rhynchophorus ferrugineus (Coleoptera: Curculionidae), the Most Diverse Among Insects

The red palm weevil, Rhynchophorus ferrugineus, is the most harmful species among those pests affecting palm trees. Its impact causes important economic losses around the World. Nevertheless, the genetic information of Rh. ferrugineus is very scarce. Last year, the first genome assembly was published including a rough description of its repeatome. However, no information has been added about one of the main components of repeated DNA, the satellite DNA. Herein, we presented the characterization of the satellitome of this important species that includes 112 satellite DNA families, the largest number in an insect genome. These satellite DNA families made up around 25% of the genome while the most abundant family, RferSat01-169, alone represented 20.4%. Chromosomal location of most abundant satellite DNA families performed by fluorescence in situ hybridization showed that all of them are dispersed in the euchromatin on all chromosomes but some of them are also specifically accumulated either on the pericentromeric heterochromatic regions of all chromosomes or on specific chromosomes. Finally, the transcription of satellitome families was analyzed through Rh. ferrugineus development. It was found that 55 out of 112 satellite DNA families showed transcription, some families seemed to be transcribed across all stages while a few appeared to be stage-specific, indicating a possible role of those satellite DNA sequences in the development of this species.

The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont

The highly diverse insect family of true weevils, Curculionidae, includes many agricultural and forest pests. Pissodes strobi, commonly known as the spruce weevil or white pine weevil, is a major pest of spruce and pine forests in North America. Pissodes strobi larvae feed on the apical shoots of young trees, causing stunted growth and can destroy regenerating spruce or pine forests. Here, we describe the nuclear and mitochondrial Pissodes strobi genomes and their annotations, as well as the genome of an apparent Wolbachia endosymbiont. We report a substantial expansion of the weevil nuclear genome, relative to other Curculionidae species, possibly driven by an abundance of class II DNA transposons. The endosymbiont observed belongs to a group (supergroup A) of Wolbachia species that generally form parasitic relationships with their arthropod host.

Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892)

BACKGROUND

Members of the genus Novius Mulsant, 1846 (= Rodolia Mulsant, 1850) (Coleoptera, Coccinellidae), play important roles in the biological control of cotton cushion scale pests, especially those belonging to Icerya. Since the best-known species, the vedalia beetle Novius cardinalis (Mulsant, 1850) was introduced into California from Australia, more than a century of successful use in classical biological control, some species of Novius have begun to exhibit some field adaptations to novel but related prey species. Despite their economic importance, relatively little is known about the underlying genetic adaptations associated with their feeding habits. Knowledge of the genome sequence of Novius is a major step towards further understanding its biology and potential applications in pest control.

RESULTS

We report the first high-quality genome sequence for Novius pumilus (Weise, 1892), a representative specialist of Novius. Computational Analysis of gene Family Evolution (CAFE) analysis showed that several orthogroups encoding chemosensors, digestive, and immunity-related enzymes were significantly expanded (P < 0.05) in N. pumilus compared to the published genomes of other four ladybirds. Furthermore, some of these orthogroups were under significant positive selection pressure (P < 0.05). Notably, transcriptome profiling demonstrated that many genes among the significantly expanded and positively selected orthogroups, as well as genes related to detoxification were differentially expressed, when N. pumilus feeding on the nature prey Icerya compared with the no feeding set. We speculate that these genes are vital in the Icerya adaptation of Novius species.

CONCLUSIONS

We report the first Novius genome thus far. In addition, we provide comprehensive transcriptomic resources for N. pumilus. The results from this study may be helpful for understanding the association of the evolution of genes related to chemosensing, digestion, detoxification and immunity with the prey adaptation of insect predators. This will provide a reference for future research and utilization of Novius in biological control programs. Moreover, understanding the possible molecular mechanisms of prey adaptation also inform mass rearing of N. pumilus and other Novius, which may benefit pest control.

The transposable element-rich genome of the cereal pest Sitophilus oryzae

BACKGROUND

The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions.

RESULTS

We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis.

CONCLUSIONS

Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.

Chromosome-Level Genome Assembly of Cyrtotrachelus buqueti and Mining of Its Specific Genes

Background: The most severe insect damage to bamboo shoots is the bamboo-snout beetle (Cyrtotrachelus buqueti). Bamboo is a perennial plant that has significant economic value. C. buqueti also plays a vital role in the degradation of bamboo lignocellulose and causing damage. The genome sequencing and functional gene annotation of C. buqueti are of great significance to reveal the molecular mechanism of its efficient degradation of bamboo fiber and the development of the bamboo industry.

Results: The size of C. buqueti genome was close to 600.92 Mb by building a one paired-end (PE) library and k-mer analysis. Then, we developed nine 20-kb SMRTbell libraries for genome sequencing and got a total of 51.12 Gb of the original PacBio sequel reads. Furthermore, after filtering with a coverage depth of 85.06×, clean reads with 48.71 Gb were obtained. The final size of C. buqueti genome is 633.85 Mb after being assembled and measured, and the contig N50 of C. buqueti genome is 27.93 Mb. The value of contig N50 shows that the assembly quality of C. buqueti genome exceeds that of most published insect genomes. The size of the gene sequence located on chromosomes reaches 630.86 Mb, accounting for 99.53% of the genome sequence. A 1,063 conserved genes were collected at this assembled genome, comprising 99.72% of the overall genes with 1,066 using the Benchmark Uniform Single-Copy Orthology (BUSCO). Moreover, 63.78% of the C. buqueti genome is repetitive, and 57.15% is redundant with long-term elements. A 12,569 protein-coding genes distributed on 12 chromosomes were acquired after function annotation, of which 96.18% were functional genes. The comparative genomic analysis results revealed that C. buqueti was similar to D. ponderosae. Moreover, the comparative analysis of specific genes in C. buqueti genome showed that it had 244 unique lignocellulose degradation genes and 240 genes related to energy production and conversion. At the same time, 73 P450 genes and 30 GST genes were identified, respectively, in the C. buqueti genome.

Conclusion: The high-quality C. buqueti genome has been obtained in the present study. The assembly level of this insect’s genome is higher than that of other most reported insects’ genomes. The phylogenetic analysis of P450 and GST gene family showed that C. buqueti had a vital detoxification function to plant chemical components.

Chromosome-level genome assemblies of two cotton-melon aphid Aphis gossypii biotypes unveil mechanisms of host adaption

The cotton-melon aphid Aphis gossypii is a sap-sucking insect that is considered a serious global pest. The species is distributed over a large geographical range and uses a wide variety of hosts, with some populations being specialized to attack different plant species. Here, we provide de novo chromosome-level genome assemblies of a cotton specialist population (Hap1) and a cucurbit specialist population (Hap3). We achieved this by using a combination of third-generation sequencing platforms, namely Illumina and Hi-C sequencing technologies. We were able to anchor a total of 334.89 Mb (scaffold N50 of 89.13 Mb) and 359.95 Mb (scaffold N50 of 68.88 Mb) to four chromosomes for Hap1 and Hap3, respectively. Moreover, our results showed that the X-chromosome of Hap3 (113.01 Mb) was significantly longer than that of Hap1 (100.26 Mb), with a high level of sequence conservation between the aphid species. We also report variation in the number of protein-coding genes and repeat sequences between Hap1 and Hap3. In particular, olfactory and gustatory receptor genes underwent a high level of gene duplication and expansion events in A. gossypii, including between Hap1 and Hap3. Moreover, we identified two glutathione S-transferase genes which underwent single gene duplications in Hap3, and tandem duplication and inversion events affecting the cytochrome P450 monooxygenase between Hap1 and Hap3, all of which include the CYP3 family. Our results illustrate the variance in the genomic composition of two specialized A. gossypii populations and provide a helpful resource for the study of aphid population evolution, host adaption and insecticide resistance.

Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato

Fruit production is negatively affected by a wide range of frugivorous insects, among them tephritid fruit flies are one of the most important. As a replacement for pesticide-based controls, enhancing natural fruit resistance through biotechnology approaches is a poorly researched but promising alternative. The use of quantitative reverse transcription PCR (RT-qPCR) is an approach to studying gene expression which has been widely used in studying plant resistance to pathogens and non-frugivorous insect herbivores, and offers a starting point for fruit fly studies. In this paper, we develop a gene selection pipe-line for known induced-defense genes in tomato fruit, Solanum lycopersicum, and putative detoxification genes in Queensland fruit fly, Bactrocera tryoni, as a basis for future RT-qPCR research. The pipeline started with a literature review on plant/herbivore and plant/pathogen molecular interactions. With respect to the fly, this was then followed by the identification of gene families known to be associated with insect resistance to toxins, and then individual genes through reference to annotated B. tryoni transcriptomes and gene identity matching with related species. In contrast for tomato, a much better studied species, individual defense genes could be identified directly through literature research. For B. tryoni, gene selection was then further refined through gene expression studies. Ultimately 28 putative detoxification genes from cytochrome P450 (P450), carboxylesterase (CarE), glutathione S-transferases (GST), and ATP binding cassette transporters (ABC) gene families were identified for B. tryoni, and 15 induced defense genes from receptor-like kinase (RLK), D-mannose/L-galactose, mitogen-activated protein kinase (MAPK), lipoxygenase (LOX), gamma-aminobutyric acid (GABA) pathways and polyphenol oxidase (PPO), proteinase inhibitors (PI) and resistance (R) gene families were identified from tomato fruit. The developed gene selection process for B. tryoni can be applied to other herbivorous and frugivorous insect pests so long as the minimum necessary genomic information, an annotated transcriptome, is available.

The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. This large amount of reshuffling within chromosomes with few inter-chromosomal events contrasts with patterns seen in mammals in which the chromosomes tend to exchange larger blocks of material more readily. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta in a phylogenetic framework. For the first time, we find that synteny decays at an exponential rate relative to phylogenetic distance. Additionally, there are significant differences in decay rates between insect orders, this pattern was not driven by Lepidoptera alone which has a substantially different rate.

Genome-Wide Identification of the Gustatory Receptor Gene Family of the Invasive Pest, Red Palm Weevil, Rhynchophorus ferrugineus (Olivier, 1790)

The red palm weevil (Rhynchophorus ferrugineus) is a highly destructive pest of oil palm, date, and coconut in many parts of Asia, Europe, and Africa. The Food and Agriculture Organization of the United Nations has called for international collaboration to develop a multidisciplinary strategy to control this invasive pest. Previous research focused on the molecular basis of chemoreception in this species, particularly olfaction, to develop biosensors for early detection and more effective bait traps for mass trapping. However, the molecular basis of gustation, which plays an essential role in discriminating food and egg-laying sites and chemical communication in this species, is limited because its complete gustatory receptor gene family still has not been characterized. We manually annotated the gene family from the recently available genome and transcriptome data and reported 50 gustatory receptor genes encoding 65 gustatory receptors, including 7 carbon dioxide, 9 sugar, and 49 bitter receptors. This study provides a platform for future functional analysis and comparative chemosensory study. A better understanding of gustation will improve our understanding of this species' complex chemoreception, which is an important step toward developing more effective control methods.

Complete Genome Sequence of Rhynchophorus ferrugineus Endocytobiont "Candidatus Nardonella dryophthoridicola" Strain NardRF

We report the complete genome sequence and annotation of “Candidatus Nardonella dryophthoridicola” strain NardRF, obtained by sequencing its host bacteriome, Rhynchophorus ferrugineus, using Oxford Nanopore technology.

Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus

The red palm weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae) is an economically-important invasive species that attacks multiple species of palm trees around the world. A better understanding of gene content and function in R. ferrugineus has the potential to inform pest control strategies and thereby mitigate economic and biodiversity losses caused by this species. Using 10x Genomics linked-read sequencing, we produced a haplotype-resolved diploid genome assembly for R. ferrugineus from a single heterozygous individual with modest sequencing coverage (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sim$$\end{document}∼ 62x). Benchmarking against conserved single-copy Arthropod orthologs suggests both pseudo-haplotypes in our R. ferrugineus genome assembly are highly complete with respect to gene content, and do not suffer from haplotype-induced duplication artifacts present in a recently published hybrid assembly for this species. Annotation of the larger pseudo-haplotype in our assembly provides evidence for 23,413 protein-coding loci in R. ferrugineus, including over 13,000 predicted proteins annotated with Gene Ontology terms and over 6000 loci independently supported by high-quality Iso-Seq transcriptomic data. Our assembly also includes 95% of R. ferrugineus chemosensory, detoxification and neuropeptide-related transcripts identified previously using RNA-seq transcriptomic data, and provides a platform for the molecular analysis of these and other functionally-relevant genes that can help guide management of this widespread insect pest.

First phylogenetic analysis of Dryophthorinae (Coleoptera, Curculionidae) based on structural alignment of ribosomal DNA reveals Cenozoic diversification

Dryophthorinae is an economically important, ecologically distinct, and ubiquitous monophyletic group of pantropical weevils with more than 1,200 species in 153 genera. This study provides the first comprehensive phylogeny of the group with the aim to provide insights into the process and timing of diversification of phytophagous insects, inform classification and facilitate predictions. The taxon sampling is the most extensive to date and includes representatives of all five dryophthorine tribes and all but one subtribe. The phylogeny is based on secondary structural alignment of 18S and 28S rRNA totaling 3,764 nucleotides analyzed under Bayesian and maximum likelihood inference. We used a fossil-calibrated relaxed clock model with two approaches, node-dating and fossilized birth-death models, to estimate divergence times for the subfamily. All tribes except the species-rich Rhynchophorini were found to be monophyletic, but higher support is required to ascertain the paraphyly of Rhynchophorini with more confidence. Nephius is closely related to Dryophthorini and Stromboscerini, and there is strong evidence for paraphyly of Sphenophorina. We find a large gap between the divergence of Dryophthorinae from their sister group Platypodinae in the Jurassic-Cretaceous boundary and the diversification of extant species in the Cenozoic, highlighting the role of coevolution with angiosperms in this group.

Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri

BACKGROUND

The ladybird beetle Cryptolaemus montrouzieri Mulsant, 1853 (Coleoptera, Coccinellidae) is used worldwide as a biological control agent. It is a predator of various mealybug pests, but it also feeds on alternative prey and can be reared on artificial diets. Relatively little is known about the underlying genetic adaptations of its feeding habits.

RESULTS

We report the first high-quality genome sequence for C. montrouzieri. We found that the gene families encoding chemosensors and digestive and detoxifying enzymes among others were significantly expanded or contracted in C. montrouzieri in comparison to published genomes of other beetles. Comparisons of diet-specific larval development, survival and transcriptome profiling demonstrated that differentially expressed genes on unnatural diets as compared to natural prey were enriched in pathways of nutrient metabolism, indicating that the lower performance on the tested diets was caused by nutritional deficiencies. Remarkably, the C. montrouzieri genome also showed a significant expansion in an immune effector gene family. Some of the immune effector genes were dramatically downregulated when larvae were fed unnatural diets.

CONCLUSION

We suggest that the evolution of genes related to chemosensing, digestion, and detoxification but also immunity might be associated with diet adaptation of an insect predator. These findings help explain why this predatory ladybird has become a successful biological control agent and will enable the optimization of its mass rearing and use in biological control programs.

Evaluating insect-host interactions as a driver of species divergence in palm flower weevils

Plants and their specialized flower visitors provide valuable insights into the evolutionary consequences of species interactions. In particular, antagonistic interactions between insects and plants have often been invoked as a major driver of diversification. Here we use a tropical community of palms and their specialized insect flower visitors to test whether antagonisms lead to higher population divergence. Interactions between palms and the insects visiting their flowers range from brood pollination to florivory and commensalism, with the latter being species that feed on decaying-and presumably undefended-plant tissues. We test the role of insect-host interactions in the early stages of diversification of nine species of beetles sharing host plants and geographical ranges by first delimiting cryptic species and then using models of genetic isolation by environment. The degree to which insect populations are structured by the genetic divergence of plant populations varies. A hierarchical model reveals that this variation is largely uncorrelated with the kind of interaction, showing that antagonistic interactions are not associated with higher genetic differentiation. Other aspects of host use that affect plant-associated insects regardless of the outcomes of their interactions, such as sensory biases, are likely more general drivers of insect population divergence.

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3' end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.