The transcriptome of Spodoptera exigua larvae exposed to different types of microbes

A novel broad-spectrum antibacterial and anti-malarial Anopheles gambiae Cecropin promotes microbial clearance during pupation

Anophelinae mosquitoes are exposed to a variety of microbes including Plasmodium parasites that cause malaria. When infected, mosquitoes mount versatile immune responses, including the production of antimicrobial peptides. Cecropins are one of the most widely distributed families of antimicrobial peptides in insects and all previously studied Anopheles members are playing roles in adult mosquito immunity. We have identified and characterized a novel member of the Anopheles gambiae cecropin family, cecropin D (CecD), that is uniquely expressed and immune-responsive at late larval stages to promote microbial clearance through its broad-spectrum antibacterial activity during larval-pupal developmental transition. Interestingly, Cecropin D also exhibited highly potent activity against Plasmodium falciparum sporozoites, the malaria parasite stage that is transmitted from mosquitoes and infects humans and thereby holds promise as a malaria transmission-blocking agent. Finally, we have defined unequivocal cecropin-specific molecular signatures to systematically organize the diversity of the cecropin family in malaria vectors.

Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers

The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.

Bursicon receptor gene HLGR2 as a potential RNA interference target for control of the fall webworm Hyphantria cunea

BACKGROUND

Insect G protein-coupled receptors (GPCRs) have been identified as a new generation of attractive targets for RNA interference (RNAi)-based pest control. A functional study of the leucine-rich repeat-containing (LGR2) gene in Hyphantria cunea (HLGR2) was performed to examine whether it can be used in the molecular control of this notorious pest.

RESULTS

The complementary DNA (cDNA) sequence and deduced amino acids of HLGR2 were obtained and analyzed in the present study. HLGR2 is a typical GPCR and shows high structural and sequence similarity with other insect LGR2 proteins. The spatiotemporal expression profiles of HLGR2 showed that HLGR2 was highly expressed at the egg stage and tissues of head and silk gland. After RNAi of HLGR2, distinct phenotypes were observed when HLGR2 expression was suppressed, indicating that HLGR2 is essential in pupation and eclosion. HLGR2 RNAi led to a low pupation rate (45.00%), body malformation, abnormal wing expansion, failed cuticle melanization (63.33%), and high mortality rate (48.33%). Furthermore, we identified eight genes that are regulated by HLGR2. The expression of these eight genes was induced by the HLGR2 signaling pathway and correlated well with cuticle sclerotization. Unlike LGR2 in other insect species, HLGR2 was found to play a crucial role in the control of H. cunea during ecdysis and postecdysial stages.

CONCLUSION

HLGR2 is essential for the growth and development and wing expansion and maturation in H. cunea, suggesting HLGR2 is a promising candidate for application in RNAi-based control of this notorious agriculture-forest pest. © 2021 Society of Chemical Industry.

Activation of the Host Immune Response in Hyphantria cunea (Drury) (Lepidoptera: Noctuidae) Induced by Serratia marcescens Bizio

Simple Summary

Hyphantria cunea (Drury) is a quarantine pest, due to its extensive host, leading to serious economic losses in the agricultural and forestry industries. To control this pest, it is increasingly important to use microbial pesticides because they are biologically active and ecologically safe. Serratia marcescens Bizio (SM1) is a potential biocontrol bacterium. Although SM1 has a pathogenic role in H. cunea, H. cunea self-defense reduces the pathogenic effect of SM1. In this study, immune-related differentially expressed genes (DEGs) in H. cunea were first identified after SM1 infection, and the immune regulation mode of H. cunea in response to SM1, including antimicrobial peptide synthesis pathways, melanization and cellular immunity, was revealed. According to the analysis, the immune system of H. cunea was induced by SM1. In summary, our study demonstrates how the immune systems of the H. cunea work to resist the infection of SM1, which provides the theoretical basis for researching more efficient microbial pesticides for H. cunea.

Abstract

Host–pathogen interactions are essential to our understanding of biological pesticides. Hyphantria cunea (Drury) is an important forest pest worldwide. The immune mechanism of the interaction between H. cunea and Serratia marcescens Bizio (SM1) is unclear. First, transcriptome sequencing and quantitative real-time PCR (qRT-PCR) analysis described the H. cunea immune response to SM1. A total of 234 immune-related differentially expressed genes (DEGs) were found. Many immune regulatory genes in three classical pathways were found. Antimicrobial peptides, including attacin B, cecropin A, gloverin, lebocin and diapausin, are involved in defending against SM1 challenge, and are mainly produced by Toll and immune deficiency (IMD) pathways. Some melanization genes were changed in H. cunea, which suggested that H. cunea melanization was activated by SM1. Furthermore, phagocytosis, autophagolysosome and apoptosis pathways in cellular immunity were activated in H. cunea against SM1. Finally, the expression patterns of 10 immune genes were analyzed systematically by qRT-PCR, and most of the genes were upregulated compared to the control. Our studies provide useful information about the immune response of H. cunea under the stress of SM1, which is important to understand how SM1 affects the immune system of H. cunea and provides new ideas to control H. cunea by using SM1.

Xenobiotic transcription factors CncC and maf regulate expression of CYP321A16 and CYP332A1 that mediate chlorpyrifos resistance in Spodoptera exigua

Insect cytochrome P450 s (P450 s) are associated with the metabolic detoxification of toxic xenobiotics and their constitutive upregulation is often associated with resistance to natural and synthetic toxicants. The P450 s CYP321A16 and CYP332A1 are constitutively overexpressed in an insecticide-resistant strain of beet armyworm, Spodoptera exigua. However, the function and upstream regulation of these two P450 s remain unknown. Here, we investigated the function of CYP321A16 and CYP332A1 in resistance to the organophosphate insecticide, chlorpyrifos and their regulation by the transcription factors CncC and Maf. Transgenic strains of Drosophila melanogaster expressing CYP321A16 or CYP332A1 showed higher levels of tolerance to chlorpyrifos than the control flies with the same genetic background. Furthermore, recombinant CYP321A16 and CYP332A1 proteins metabolized chlorpyrifos. Analysis of the putative promoter sequences of the genes coding for CYP321A16 and CYP332A1 revealed conserved CncC/Maf binding sites. Transfection of luciferase reporter plasmids containing the promoter of CYP450 gene together with CncC and Maf expression plasmids significantly enhanced the activity of the reporter. Promoter truncation identified a site in the promoter of CYP321A16 that is critical for the CncC/Maf binding. These data demonstrate that resistance to chlorpyrifos in S. exigua is conferred by the combined action of CYP321A16 and CYP332A1 and uncovered their regulation by the transcription factors CncC and Maf.

Pattern recognition receptors from lepidopteran insects and their biological functions

Lepidopteran insects have potent innate immunity to fight against the invading pathogens. As the initiation step, pattern recognition receptors (PRRs) recognize and bind microbial surface configurations known as pathogen-associated molecular patterns (PAMPs). Aftermath, they initiate both cellular and humoral immune responses, including phagocytosis, agglutination, nodulation, encapsulation, prophenoloxidase activation, and synthesis of antimicrobial peptides. In this review, we summarize the recent findings concerning PRRs in lepidoptaeran insects, mostly agriculture pests including Helicoverpa armigera, Plutella xylostella, and Spodoptera exigua. We mainly focus on the function and phylogeny of C-type lectins (CTLs), peptidoglycan recognition proteins (PGRPs), β-1,3-glucan recognition proteins (βGRPs), and galectins (GALEs). It enriches our understanding of the immune system of lepidopteran insects and provides directions in the future research.

iTRAQ-Based Comparative Proteomic Analysis of Larval Midgut From the Beet Armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) Challenged With the Entomopathogenic Bacteria Serratia marcescens

Entomopathogenic bacteria Serratia marcescens is widely used as an environmentally friendly biocontrol agent against various pests, including Spodoptera exigua. Understanding the immune defense mechanism of S. exigua through comparative proteomic analysis can identify the key proteins expressed in response to the microbial infection. Here, we employed the as isobaric tags for relative and absolute quantification (iTRAQ) technique to investigate the effects of S. marcescens on the proteomic expression of S. exigua. Based on the molecular functional analysis, the differentially expressed proteins (DEPs) were mainly involved in the binding process and catalytic activities. Further bioinformatics analysis revealed important DEPs that played a crucial role in innate immunity of S. exigua with recognition (C-type lectin), melanization (propanol oxidase 3, serine protease, Serine-type carboxypeptidase activity, clip domain serine protease 4), antimicrobial activity (lysozyme, lysozyme-like, gloverin, cecropin B), detoxification (acetyl-CoA C-acetyltransferase, 3-dehydroecdysone 3-alpha-reductase, glucuronosyltransferase, glutathione S-transferase) and others. The Quantitative real-time PCR (qRT-PCR) results further indicated the significant upregulation of the immune-related genes in Spodoptera exigua following S. marcescens infection. To the best of our knowledge, this is the first iTRAQ based study to characterize S. marcescens mediated proteomic changes in S. exigua and identified important immune-related DEPs. The results of this study will provide an essential resource for understanding the host-pathogen interactions and the development of novel microbial biopesticides against various pests.

Midgut de novo transcriptome analysis and gene expression profiling of Spodoptera exigua larvae exposed with sublethal concentrations of Cry1Ca protein

Spodoptera exigua (Hübner) is a polyphagous pest on agricultural crops, whose control is based mainly on the application of chemical insecticides. Bacillus thuringiensis (Bt) is one of the most important biological agents that have been successfully applied as a biological control, and Cry1Ca protein is considered to be active against S. exigua. Therefore, to understand the response of S. exigua to Cry1Ca protein, high-throughput sequencing was used to analyse the S. exigua larval midgut after treatment with sublethal concentrations of Cry1Ca protein. Transcriptome data showed that a total of 98,571 unigenes with an N50 value of 1135 bp and a mean length of 653 bp were obtained. Furthermore, 2962 differentially expressed genes (DEGs) were identified after Cry1Ca challenge, including 1508 up-regulated and 1454 down-regulated unigenes. Among these DEGs, detoxification (CYP, CarE, and GST) and Bt resistance (ALP, APN, and ABC transporter)-related genes were differentially expressed in the midgut of S. exigua after Cry1Ca treatment. However, most DEGs of protective enzymes were down-regulated, while most DEGs related with serine protease and REPAT were up-regulated. Furthermore, almost all DEGs related to the immune signaling pathway, antimicrobial protein, and lysozyme were up-regulated by Cry1Ca treatment. These results indicated that the detoxification enzyme, protective enzymes, Bt resistance-related genes, serine protease, REPAT, and the immune response might have been involved in the response of S. exigua to Cry1Ca protein. In summary, analysis of the transcriptomal expression of genes involved in Cry1Ca protein against S. exigua provided potential clues for elucidating the host response processes and defensive mechanisms underlying Cry1Ca toxicity.

Characterisation of GST genes from the Hyphantria cunea and their response to the oxidative stress caused by the infection of Hyphantria cunea nucleopolyhedrovirus (HcNPV)

The fall webworm, Hyphantria cunea (Drury) (Lepidoptera: Noctuidae), is a major pest found in forests. In this study, the effects of Hyphantria cunea nucleopolyhedrovirus (HcNPV) infection on the transcription levels and activities of glutathione S-transferases (GSTs) in H. cunea were determined. In the present study, 18 GST family genes were identified from the H. cunea transcriptome dataset by using bioinformatic analyses. These GST genes were classified into cytosolic (15 genes) and microsomal (three genes) classes. The 15 cytosolic GST genes belonged to four different subclasses (epsilon, sigma and delta). The all GST genes, especially GSTe4, showed high expression levels in egg and 1st~4th instar larval stage while their low expression levels in 5th~7th instar larvae using real-time quantitative PCR analysis. However, the expression levels of the 18 GST genes were varied after exposure to sublethal doses of HcNPV. The expression levels of most GSTs were downregulated and upregulated at low and high concentrations of HcNPV, respectively. The corresponding total GST activities also showed similar patterns. In H. cunea, changes in the expression levels and enzymatic activities of GSTs after exposure to HcNPV indicated that they may have important functions in the defense against HcNPV, and the stress, which may be reflected by the high GST enzymatic activities.

Transcriptomic analysis of the interactions between the Spodoptera exigua midgut and nucleopolyhedrovirus

Spodoptera exigua nucleopolyhedrovirus (SeNPV) has been successfully applied as a bioinsecticide against S. exigua, one of the most devastating pests worldwide. However, due to limited information, the molecular mechanisms underlying interactions between S. exigua and SeNPV remain to be elucidated. In this study, RNA-Seq and differentially expressed gene (DEG) analysis of the S. exigua larva midgut were performed to explore molecular responses to SeNPV infection. A total of 1785 DEGs, including 935 upregulated and 850 downregulated genes, were identified in the midgut of SeNPV-infected S. exigua larvae. Ultrastructural observations showed that after SeNPV infection, the peritrophic matrix (PM) became a loose and highly porous surface with many clear ruptures; these changes were most likely associated with upregulation of chitin deacetylases. In addition, 124 putative innate immunity-related DEGs were identified and divided into several groups, including pattern recognition proteins, signaling pathways, signal modulation, antimicrobial peptides and detoxification. Interestingly, upregulation of some pattern recognition proteins, induction of the JAK/STAT signaling pathway and promotion of REPAT synthesis might be the main innate immunity responses occurring in the S. exigua larva midgut after SeNPV infection. According to quantitative real-time PCR, the expression profiles of 19 random DEGs were consistent with those obtained by RNA-Seq. These findings provide important basic information for understanding the molecular mechanisms of SeNPV invasion and the anti-SeNPV responses of the S. exigua midgut, promoting the utility of SeNPV as a bioinsecticide for the effective control of S. exigua and related pests.

New insight into the molecular basis of Fe (III) stress responses of Procambarus clarkii by transcriptome analysis

Iron in excess can have toxic effects on living organisms. In China, the freshwater crayfish Procambarus clarkii is a source of aquatic food with high-quality protein and has significant commercial value. P. clarkii shows oxidative stress on exposure to heavy metals, and antioxidant enzymes, such as ubiquitination enzymes and proteasomes, play important roles in oxidative stress. To understand the antioxidant defense system of P. clarkii, we analyzed the hepatopancreas transcriptomes of P. clarkii after stimulation with FeCl₃. In total, 5199 differentially expressed genes (DEGs) were identified (2747 upregulated and 2452 downregulated). GO analysis revealed that these DEGs belonged to 16 cellular component, 16 molecular function, and 19 biological process subcategories. A total of 1069 DEGs were classified into 25 categories by using COG. Some antioxidant defense pathways, such as "Ubiquitin mediated proteolysis" and "Glutathione metabolism," were identified using KEGG. In addition, quantitative real time-PCR (qRT-PCR) substantiated the up-regulation of a random selection of DEGs including antioxidant and immune defense genes. We obtained information for P. clarkii transcriptome databases and new insights into the responses of P. clarkii hepatopancreas to heavy metals.

Transcription factors CncC/Maf and AhR/ARNT coordinately regulate the expression of multiple GSTs conferring resistance to chlorpyrifos and cypermethrin in Spodoptera exigua

BACKGROUND

Glutathione S-transferases (GSTs) are a superfamily of multifunctional dimeric proteins existing in both prokaryotic and eukaryotic organisms. They are involved in the detoxification of both endogenous and exogenous electrophiles, including insecticides. However, the molecular mechanisms underlying the regulation of GST genes in insects are poorly understood.

RESULTS

We first identified at least three GST genes involved in resistance to the insecticides chlorpyrifos and cypermethrin. Analysis of upstream sequences revealed that three GSTs (SeGSTo2, SeGSTe6 and SeGSTd3) harbor the same cap 'n' collar C/muscle aponeurosis fibromatosis (CncC/Maf) binding site, and SeGSTo2 and SeGSTe6 contain the aryl hydrocarbon receptor/aryl hydrocarbon receptor nuclear translocator (AhR/ARNT) binding site. Luciferase reporter assay showed co-transfection of reporter plasmid containing the SeGSTe6 promoter with CncC and/or Maf expressing constructs significantly boosted transcription. Similarly, AhR and/or ARNT expressing constructs also significantly increased the promoter activities. The co-transfection of mutated reporter plasmid with CncC/Maf or AhR/ARNT did not increase transcription activity anymore. Constitutive over-expression of CncC, Maf and AhR was also found in the HZ16 strain, which might be the molecular mechanism for up-regulated expression of multiple detoxification genes conferring resistance to insecticides.

CONCLUSION

These results suggest that CncC/Maf and AhR/ARNT coordinately regulate the expression of multiple GST genes involved in insecticide resistance in Spodoptera exigua. © 2019 Society of Chemical Industry.

The expression of Spodoptera exigua P450 and UGT genes: tissue specificity and response to insecticides

Cytochrome P450 and UDP-glucosyltransferase (UGT) as phase I and phase II metabolism enzymes, respectively, play vital roles in the breakdown of endobiotics and xenobiotics. Insects can increase the expression of detoxification enzymes to cope with the stress from xenobiotics including insecticides. However, the molecular mechanisms for insecticide detoxification in Spodoptera exigua remain elusive, and the genes conferring insecticide metabolisms in this species are less well reported. In this study, 68 P450 and 32 UGT genes were identified. Phylogenetic analysis showed gene expansions in CYP3 and CYP4 clans of P450 genes and UGT33 family of this pest. P450 and UGT genes exhibited specific tissue expression patterns. Insecticide treatments in fat body cells of S. exigua revealed that the expression levels of P450 and UGT genes were significantly influenced by challenges of abamectin, lambda-cyhalothrin, chlorantraniliprole, metaflumizone and indoxacarb. Multiple genes for detoxification were affected in expression levels after insecticide exposures. The results demonstrated that lambda-cyhalothrin, chlorantraniliprole, metaflumizone and indoxacarb induced similar responses in the expression of P450 and UGT genes in fat body cells; eight P450 genes and four UGT genes were co-up-regulated significantly, and no or only a few CYP/UGT genes were down-regulated significantly by these four insecticides. However, abamectin triggered a distinct response for P450 and UGT gene expression; more P450 and UGT genes were down-regulated by abamectin than by the other four compounds. In conclusion, P450 and UGT genes from S. exigua were identified, and different responses to abamectin suggest a different mechanism for insecticide detoxification.

Identification and expression analysis of the Spodoptera exigua neuropeptidome under different physiological conditions

Neuropeptides are small signalling molecules acting as neurohormones, neurotransmitters and neuromodulators. Being part of the chemical communication system between cells within an organism, they are involved in the regulation of different aspects of animal physiology and behaviour such as feeding, reproduction, development and locomotion. Transcriptomic data from larval and adult tissues have been obtained and mined to generate a comprehensive neuropeptidome for the polyphagous insect pest Spodoptera exigua. Sixty-three neuropeptides have been identified and described based on their tissue specificity and their regulation in response to different abiotic perturbations. Expression analyses have identified those neuropeptides involved in ingestive and digestive behaviour of S. exigua larvae and revealed a general pattern of upregulation in the midgut during larval starvation. Our results represent a comprehensive neuropeptidome of a lepidopteran species that will be highly relevant to future studies and provide novel information of the insect's perception of its environment.

Transcriptomic analysis of interactions between Hyphantria cunea larvae and nucleopolyhedrovirus

BACKGROUND

Hyphantria cunea is a destructive forest pest. To utilise H. cunea nucleopolyhedrovirus (HcNPV) for biological control, understanding insect-virus interactions is essential.

RESULTS

Four cDNA libraries were constructed from H. cunea larvae (two HcNPV-infected and two uninfected groups) and 76 004 expressed genes were obtained by next-generation sequencing. Compared with controls, 272 differentially expressed genes (DEGs) were identified in infected groups, including 162 up-regulated and 110 down-regulated genes. Transcription levels of 20 random DEGs were consistent with the Solexa expression profiles obtained by quantitative real-time PCR. DEGs associated with innate immunity were grouped into several categories, including pattern recognition proteins, heat-shock proteins, UDP-glycosyltransferases, cytochrome P450s, antimicrobial peptides and hormonal signalling proteins. Interestingly, up-regulated host genes included farnesoic acid O-methyltransferase, two juvenile hormone (JH) binding proteins, and a circadian clock-controlled protein related to JH regulation. Pathway enrichment analysis indicates that mitogen-activated protein kinase (MAPK) signalling pathways, key candidate genes and important biological pathways may be associated with molecular modification in H. cunea larvae in response to virus stress.

CONCLUSION

These findings provide insight for future research on the molecular mechanisms of HcNPV invasion and anti-HcNPV mechanisms in H. cunea. A better understanding of gene regulation following HcNPV invasion could help to develop the virus as a bio-insecticide. © 2018 Society of Chemical Industry.

Insecticides induce the co-expression of glutathione S-transferases through ROS/CncC pathway in Spodoptera exigua

Glutathione S-transferases (GSTs) are a family of multifunctional enzymes that are involved in detoxification of electrophilic toxic compounds. Although the co-induced expression of GST genes by insecticides in insects has been documented in recent years, the underlying regulatory mechanisms are not understood. In this study, a total of thirty-one cytosolic S. exigua GSTs (SeGSTs) was cloned and identified. The bioinformatics and gene expression patterns were also analyzed. Out of them, SeGSTe9, SeGSTs6, SeGSTe1, SeGSTe6, SeGSTe8, SeGSTe14, and SeGSTd1 were significantly co-expressed following exposure to three insecticides (lambda-cyhalothrin, chlorpyrifos and chlorantraniliprole). The analysis of upstream sequences revealed that all of these seven SeGSTs harbored CncC/Maf binding site. The luciferase reporter assay showed that the pGL3-SeGST promoter construct exhibited a significant increase in luciferase activities after exposure to insecticides, and mutation of CncC/Maf binding site diminish the induction effect. These data indicate that CncC/Maf pathway regulates the co-expression of GST genes in response to different insecticides in S. exigua. Insecticides significantly enhanced the ROS content and treatment with the ROS inhibitor N-acetylcysteine (NAC) decreased the insecticide-induced luciferase activities of the PGL3-GSTe6 promoter construct, but not the CncC-mutated construct. These results indicate that ROS mediates GST gene expression after exposure to insecticides through CncC/Maf pathway. Overall, these data show that insecticides induce the co-expression of glutathione S-transferases through the ROS/CncC pathway in S. exigua.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537 Mb total length was assembled into 68,292 scaffolds (N50 = 164 kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).

A new approach for detecting adventitious viruses shows Sf-rhabdovirus-negative Sf-RVN cells are suitable for safe biologicals production

Background

Adventitious viral contamination in cell substrates used for biologicals production is a major safety concern. A powerful new approach that can be used to identify adventitious viruses is a combination of bioinformatics tools with massively parallel sequencing technology. Typically, this involves mapping or BLASTN searching individual reads against viral nucleotide databases. Although extremely sensitive for known viruses, this approach can easily miss viruses that are too dissimilar to viruses in the database. Moreover, it is computationally intensive and requires reference cell genome databases. To avoid these drawbacks, we set out to develop an alternative approach. We reasoned that searching genome and transcriptome assemblies for adventitious viral contaminants using TBLASTN with a compact viral protein database covering extant viral diversity as the query could be fast and sensitive without a requirement for high performance computing hardware.

Results

We tested our approach on Spodoptera frugiperda Sf-RVN, a recently isolated insect cell line, to determine if it was contaminated with one or more adventitious viruses. We used Illumina reads to assemble the Sf-RVN genome and transcriptome and searched them for adventitious viral contaminants using TBLASTN with our viral protein database. We found no evidence of viral contamination, which was substantiated by the fact that our searches otherwise identified diverse sequences encoding virus-like proteins. These sequences included Maverick, R1 LINE, and errantivirus transposons, all of which are common in insect genomes. We also identified previously described as well as novel endogenous viral elements similar to ORFs encoded by diverse insect viruses.

Conclusions

Our results demonstrate TBLASTN searching massively parallel sequencing (MPS) assemblies with a compact, manually curated viral protein database is more sensitive for adventitious virus detection than BLASTN, as we identified various sequences that encoded virus-like proteins, but had no similarity to viral sequences at the nucleotide level. Moreover, searches were fast without requiring high performance computing hardware. Our study also documents the enhanced biosafety profile of Sf-RVN as compared to other Sf cell lines, and supports the notion that Sf-RVN is highly suitable for the production of safe biologicals.

Electronic supplementary material

The online version of this article (doi: 10.1186/s12896-017-0412-z) contains supplementary material, which is available to authorized users.

Characterization of two groups of Spodoptera exigua Hübner (Lepidoptera: Noctuidae) C-type lectins and insights into their role in defense against the densovirus JcDV

Insect innate immunity relies on numerous soluble and membrane-bound receptors, named pattern recognition proteins (PRPs), which enable the insect to recognize pathogen-associated molecular patterns. C-type lectins are among the best-studied PRPs and constitute the most diverse family of animal lectins. Here we have characterized two groups of Spodoptera exigua C-type lectins that differ in their phylogeny, domain architecture, and expression pattern. One group includes C-type lectins with similar characteristics to other lepidopteran lectins, and a second group includes bracoviral-related lectins (bracovirus-like lectins, Se-BLLs) recently acquired by horizontal gene transfer. Subsequently, we have investigated the potential role of some selected lectins in the susceptibility to Junonia coenia densovirus (JcDV). For this purpose, three of the bracoviral-related lectins were expressed, purified, and their effect on the densovirus infection to two different Spodoptera species was assessed. The results showed that Se-BLL3 specifically reduce the mortality of Spodoptera frugiperda larvae caused by JcDV. In contrast, no such effect was observed with S. exigua larvae. In a previous work, we have also shown that Se-BLL2 increased the tolerance of S. exigua larvae to baculovirus infection. Taken together, these results confirm the implication of two different C-type lectins in antiviral response and reflect the biological relevance of the acquisition of bracoviral genes in Spodoptera spp.

Microscopic cuticle structure comparison of pupal melanic and wild strain of Spodoptera exigua and their gene expression profiles in three time points

The beet armyworm, Spodoptera exigua (Hubner), is one of the major crop pests and is a target for current pest control approaches using insecticides. S. exigua melanic mutants (SEM) spontaneously occurred in the S. exigua wild type (SEW) strain and have been maintained under laboratory conditions on an artificial diet. Scanning electron microscopy showed that the inner cuticle of the SEM had a denser and less orderly structure. We investigated the cuticle protein genes using RNA-seq at three different developmental stages of both SEM and SEW. Comparison of cDNA libraries showed that 7257 CPs were significantly up-regulated and 664 genes were significantly downregulated in SEM at the developmental stage of 46-h in the fifth instar. In addition, 460 genes were significantly up-regulated and 439 genes were significantly down-regulated in the SEM at the development stage of 4-h before pupation. Moreover, 162 genes were significantly up-regulated and 293 genes were significantly downregulated in the SEM, just after pupation. Two genes CPR63 and CPR97 were identified from RNA sequences to verify the differentially expressed gene (DEG) results through quantitative real-time PCR (qRT-PCR). The results show that expression of both CPR63 and CPR97 structural cuticular proteins were significantly different between SEM and SEW. This functional analysis may help in understanding the role that these genes play in the cuticle pattern of the SEM.

Changes in gene expression and apoptotic response in Spodoptera exigua larvae exposed to sublethal concentrations of Vip3 insecticidal proteins

The insecticidal Vip3 proteins from Bacillus thuringiensis (Bt), along with the classical Bt Cry proteins, are currently used in Bt-crops to control insect pests, since they do not share the same mode of action. Here we characterized the response of Spodoptera exigua larvae after Vip3 challenge. The expression profile of 47 genes was analyzed in larvae challenged with three concentrations of Vip3Ca. Results showed that the up-regulated genes were mainly involved in immune response, whereas the down-regulated genes were mainly involved in the digestion process. Other mechanisms of cellular response to the damage such as apoptosis were analyzed. For this analysis, sections from the midguts were examined by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. The nuclei of the midgut epithelial cells were stained at the highest concentration of the Vip3Ca protein and at lower concentrations of Vip3Aa in agreement with the different potency of the two proteins. In addition, apoptosis was also examined by the analysis of the expression of five caspase genes. The present study shows that exposure of S. exigua larvae to sublethal concentrations of Vip3 proteins activates different insect response pathways which trigger the regulation of some genes, APN shedding, and apoptotic cell death.

Co-infection with iflaviruses influences the insecticidal properties of Spodoptera exigua multiple nucleopolyhedrovirus occlusion bodies: Implications for the production and biosecurity of baculovirus insecticides

Biological insecticides based on Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) can efficiently control S. exigua larvae on field and greenhouse crops in many parts of the world. Spanish wild populations and laboratory colonies of S. exigua are infected by two iflaviruses (SeIV-1 and SeIV-2). Here we evaluated the effect of iflavirus co-infection on the insecticidal characteristics of SeMNPV occlusion bodies (OBs). Overall, iflavirus co-inoculation consistently reduced median lethal concentrations (LC50) for SeMNPV OBs compared to larvae infected with SeMNPV alone. However, the speed of kill of SeMNPV was similar in the presence or absence of the iflaviruses. A reduction of the weight gain (27%) associated with iflavirus infection resulted in a 30% reduction in total OB production per larva. Adult survivors of SeMNPV OB inoculation were examined for covert infection. SeMNPV DNA was found to be present at a high prevalence in all SeIV-1 and SeIV-2 co-infection treatments. Interestingly, co-inoculation of SeMNPV with SeIV-2 alone or in mixtures with SeIV-1 resulted in a significant increase in the SeMNPV load of sublethally infected adults, suggesting a role for SeIV-2 in vertical transmission or reactivation of sublethal SeMNPV infections. In conclusion, iflaviruses are not desirable in insect colonies used for large scale baculovirus production, as they may result in diminished larval growth, reduced OB production and, depending on their host-range, potential risks to non-target Lepidoptera.

Oral immune priming with Bacillus thuringiensis induces a shift in the gene expression of Tribolium castaneum larvae

Background

The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evidence, knowledge of its mechanistic underpinnings is currently very limited. Here we used the system of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus thuringiensis (Bt) to further our molecular understanding of the oral immune priming phenomenon. We addressed how ingestion of bacterial cues (derived from spore supernatants) of an orally pathogenic and non-pathogenic Bt strain affects gene expression upon later challenge exposure, using a whole-transcriptome sequencing approach.

Results

Whereas gene expression of individuals primed with the orally non-pathogenic strain showed minor changes to controls, we found that priming with the pathogenic strain induced regulation of a large set of distinct genes, many of which are known immune candidates. Intriguingly, the immune repertoire activated upon priming and subsequent challenge qualitatively differed from the one mounted upon infection with Bt without previous priming. Moreover, a large subset of priming-specific genes showed an inverse regulation compared to their regulation upon challenge only.

Conclusions

Our data demonstrate that gene expression upon infection is strongly affected by previous immune priming. We hypothesise that this shift in gene expression indicates activation of a more targeted and efficient response towards a previously encountered pathogen, in anticipation of potential secondary encounter.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3705-7) contains supplementary material, which is available to authorized users.

Transcriptomic alterations in Sitophilus zeamais in response to allyl isothiocyanate fumigation

To study the fumigation mechanisms of Allyl isothiocyanate (AITC) a promising biorational alternative to present fumigants (phosphine and methyl bromide), and provide theoretical basis for its further development in the control of stored grain pests, this research presents a transcriptome analysis of Sitophilus zeamais fumigated with AITC at the concentration of LC₅₀ (5.69μg/mL) and control over 8h. 21,869,022 and 23,873,110 clean reads in insects fumigated with AITC and control were gained, respectively. The results of RNA-seq were confirmed by qRT-PCR determination of the expression levels of NADH dehydrogenase subunit 6 and Vacuolar ATP synthase subunit B in the insects fumigated with AITC at different concentrations. After enrichment analysis of differentially expressed genes, 117 over-expressed and 271 down-regulated transcripts were gained. Following GO enrichment, these transcripts were classified into 38 GO subgroups (at level 2), and the majority enriched GO terms were "Binding" "Cell process" and "metabolic". KEGG enrichment analysis showed that the majority enriched pathway were "Folding, sorting and degradation", "Transport and catabolism", "Energy metabolism", and "Carbohydrate metabolism". Connected with previous researches on mechanisms of isothiocyanates, cytoskeleton collapse and mitochondria dysfunction are proposed to be significant lethal mechanisms of AITC.

High Bacterial Agglutination Activity in a Single-CRD C-Type Lectin from Spodoptera exigua (Lepidoptera: Noctuidae)

Lectins are carbohydrate-interacting proteins that play a pivotal role in multiple physiological and developmental aspects of all organisms. They can specifically interact with different bacterial and viral pathogens through carbohydrate-recognition domains (CRD). In addition, lectins are also of biotechnological interest because of their potential use as biosensors for capturing and identifying bacterial species. In this work, three C-type lectins from the Lepidoptera Spodoptera exigua were produced as recombinant proteins and their bacterial agglutination properties were characterized. The lowest protein concentration producing bacterial agglutination against a panel of different Gram+ and Gram− as well as their carbohydrate binding specificities was determined for the three lectins. One of these lectins, BLL2, was able to agglutinate cells from a broad range of bacterial species at an extremely low concentration, becoming a very interesting protein to be used as a biosensor or for other biotechnological applications involving bacterial capture.

De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.

Characterization and functional study of a Cecropin-like peptide from the Chinese oak silkworm, Antheraea pernyi

In present study, a Cecropin-like peptide from Antheraea pernyi (ApCec) was cloned and characterized. The full-length ApCec cDNA encoded a protein with 64 amino acids including a putative 22-amino-acid signal peptide, a 4-amino-acid propeptide, and a 38-amino-acid mature peptide. ApCec gene was highly expressed in Malpighian tubules of A. pernyi after induction for 24 h by Escherichia coli in PBS. Pro-ApCec (including propeptide and mature peptide) and M-ApCec (just mature peptide) were synthesized chemically and analyzed by HPLC and mass spectroscopy. The antibacterial activity of M-ApCec is more potent than pro-ApCec against E. coli K12 or B. subtilus in both minimum inhibitory concentration and inhibition zone assays. Hemolytic assay results showed M-ApCec possessed a low cytotoxicity to mammalian cells. The secondary structure of M-ApCec forms α-helical structure, shown by circular dichroism spectroscopy. Transmission electron microscopy analysis suggested that M-ApCec killed bacteria by disrupting bacterial cell membrane integrity. Our results indicate ApCec may play an important role in defending from pathogenic bacteria in A. pernyi, and it may be as a potential candidate for applications in antibacterial drug development and agriculture.

A novel baculovirus-derived promoter with high activity in the baculovirus expression system

The baculovirus expression vector system (BEVS) has been widely used to produce a large number of recombinant proteins, and is becoming one of the most powerful, robust, and cost-effective systems for the production of eukaryotic proteins. Nevertheless, as in any other protein expression system, it is important to improve the production capabilities of this vector. The orf46 viral gene was identified among the most highly abundant sequences in the transcriptome of Spodoptera exigua larvae infected with its native baculovirus, the S. exigua multiple nucleopolyhedrovirus (SeMNPV). Different sequences upstream of the orf46 gene were cloned, and their promoter activities were tested by the expression of the GFP reporter gene using the Autographa californica nucleopolyhedrovirus (AcMNPV) vector system in different insect cell lines (Sf21, Se301, and Hi5) and in larvae from S. exigua and Trichoplusia ni. The strongest promoter activity was defined by a 120 nt sequence upstream of the ATG start codon for the orf46 gene. On average, GFP expression under this new promoter was more than two fold higher than the expression obtained with the standard polyhedrin (polh) promoter. Additionally, the orf46 promoter was also tested in combination with the polh promoter, revealing an additive effect over the polh promoter activity. In conclusion, this new characterized promoter represents an excellent alternative to the most commonly used baculovirus promoters for the efficient expression of recombinant proteins using the BEVS.

Transcriptional profiling analysis of Spodoptera litura larvae challenged with Vip3Aa toxin and possible involvement of trypsin in the toxin activation

Vip proteins, a new group of insecticidal toxins produced by Bacillus thuringiensis, are effective against specific pests including Spodoptera litura. Here, we report construction of a transcriptome database of S. litura by de novo assembly along with detection of the transcriptional response of S. litura larvae to Vip3Aa toxin. In total, 56,498 unigenes with an N50 value of 1,853 bp were obtained. Results of transcriptome abundance showed that Vip3Aa toxin provoked a wide transcriptional response of the S. litura midgut. The differentially expressed genes were enriched for immunity-related, metabolic-related and Bt-related genes. Twenty-nine immunity-related genes, 102 metabolic-related genes and 62 Bt-related genes with differential expression were found. On the basis of transcriptional profiling analysis, we focus on the functional validation of trypsin which potentially participated in the activation of Vip3Aa protoxin. Zymogram analysis indicated that the presence of many proteases, including trypsin, in S. litura larvae midgut. Results of enzymolysis in vitro of Vip3Aa by trypsin, and bioassay and histopathology of the trypsin-digested Vip3Aa toxin showed that trypsin was possibly involved in the Vip3Aa activation. This study provides a transcriptome foundation for the identification and functional validation of the differentially expressed genes in an agricultural important pest, S. litura.

Iflavirus increases its infectivity and physical stability in association with baculovirus

Virus transmission and the prevalence of infection depend on multiple factors, including the interaction with other viral pathogens infecting the same host. In this study, active replication of an iflavirus, Spodoptera exigua iflavirus 1 (order Picornavirales) was observed in the offspring of insects that survived following inoculation with a pathogenic baculovirus, Spodoptera exigua multiple nucleopolyhedrovirus. Tracking the origin of the iflavirus suggested the association of this virus with the occlusion bodies of the baculovirus. Here we investigated the effect of this association on the stability and infectivity of both viruses. A reduction in baculovirus pathogenicity, without affecting its infectivity and productivity, was observed when associated with the iflavirus. In contrast, viral association increased the infectivity of the iflavirus and its resistance to ultraviolet radiation and high temperature, two of the main factors affecting virus stability in the field. In addition, electron microscopy analysis revealed the presence of particles resembling iflavirus virions inside the occlusion bodies of the baculovirus, suggesting the possible co-occlusion of both viruses. Results reported here are indicative of facultative phoresis of a virus and suggest that virus–virus interactions may be more common than currently recognized, and may be influential in the ecology of baculovirus and host populations and in consequence in the use of baculoviruses as biological insecticides.

Gasmin (BV2-5), a polydnaviral-acquired gene in Spodoptera exigua. Trade-off in the defense against bacterial and viral infections

Thousands of Hymenopteran endoparasitoids have developed a unique symbiotic relationship with viruses named polydnavirus (PDVs). These viruses immunocompromise the lepidopteran host allowing the survival of the wasp eggs. In a previous work, we have shown the horizontal transfer of some polydnaviral genes into the genome of the Lepidoptera, Spodoptera exigua. One of these genes, BV2-5 (named gasmin) interferes with actin polymerization, negatively affecting the multiplication of baculovirus in cell culture. In this work, we have focused in the study of the effect of Gasmin expression on different aspects of the baculovirus production. In addition, and since actin polymerization is crucial for phagocytosis, we have studied the effect of Gasmin expression on the larval interaction with bacterial pathogens. Over-expression of Gasmin on hemocytes significantly reduces their capacity to phagocytize the pathogenic bacteria Bacillus thuringiensis. According to these results, gasmin domestication negatively affects baculovirus replication, but increases larvae susceptibility to bacterial infections as pay off. Although the effect of Gasmin on the insect interaction with other pathogens or parasitoids remain unknown, the opposite effects described here could shape the biological history of this species based on the abundance of certain type of pathogens as suggested by the presence of truncated forms of this protein in several regions of the world.

Transcriptome Analysis and Discovery of Genes Relevant to Development in Bradysia odoriphaga at Three Developmental Stages

Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive (Allium tuberosum) in Asia; however, the molecular genetics are poorly understood. To explore the molecular biological mechanism of development, Illumina sequencing and de novo assembly were performed in the third-instar, fourth-instar, and pupal B. odoriphaga. The study resulted in 16.2 Gb of clean data and 47,578 unigenes (≥125 bp) contained in 7,632,430 contigs, 46.21% of which were annotated from non-redundant protein (NR), Gene Ontology (GO), Clusters of Orthologous Groups (COG), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. It was found that 19.67% of unigenes matched the homologous species mainly, including Aedes aegypti, Culex quinquefasciatus, Ceratitis capitata, and Anopheles gambiae. According to differentially expressed gene (DEG) analysis, 143, 490, and 309 DEGs were annotated as involved in the developmental process in the GO database respectively, in the comparisons of third-instar and fourth-instar larvae, third-instar larvae and pupae, and fourth-instar larvae and pupae. Twenty-five genes were closely related to these processes, including developmental process, reproduction process, and reproductive organs development and programmed cell death (PCD). The information of unigenes assembled in B. odoriphaga through transcriptome and DEG analyses could provide a detailed genetic basis and regulated information for elaborating the developmental mechanism from the larval, pre-pupal to pupal stages of B. odoriphaga.

Continuous Influx of Genetic Material from Host to Virus Populations

Many genes of large double-stranded DNA viruses have a cellular origin, suggesting that host-to-virus horizontal transfer (HT) of DNA is recurrent. Yet, the frequency of these transfers has never been assessed in viral populations. Here we used ultra-deep DNA sequencing of 21 baculovirus populations extracted from two moth species to show that a large diversity of moth DNA sequences (n = 86) can integrate into viral genomes during the course of a viral infection. The majority of the 86 different moth DNA sequences are transposable elements (TEs, n = 69) belonging to 10 superfamilies of DNA transposons and three superfamilies of retrotransposons. The remaining 17 sequences are moth sequences of unknown nature. In addition to bona fide DNA transposition, we uncover microhomology-mediated recombination as a mechanism explaining integration of moth sequences into viral genomes. Many sequences integrated multiple times at multiple positions along the viral genome. We detected a total of 27,504 insertions of moth sequences in the 21 viral populations and we calculate that on average, 4.8% of viruses harbor at least one moth sequence in these populations. Despite this substantial proportion, no insertion of moth DNA was maintained in any viral population after 10 successive infection cycles. Hence, there is a constant turnover of host DNA inserted into viral genomes each time the virus infects a moth. Finally, we found that at least 21 of the moth TEs integrated into viral genomes underwent repeated horizontal transfers between various insect species, including some lepidopterans susceptible to baculoviruses. Our results identify host DNA influx as a potent source of genetic diversity in viral populations. They also support a role for baculoviruses as vectors of DNA HT between insects, and call for an evaluation of possible gene or TE spread when using viruses as biopesticides or gene delivery vectors.

While gene exchange is known to occur between viruses and their hosts, this phenomenon has never been studied at the level of the viral population. Here we report that each time a virus from the Baculoviridae family infects a moth, a large number (dozens to hundreds) and high diversity of moth DNA sequences (86 different sequences) can integrate into replicating viral genomes. These findings show that viral populations carry a measurable load of host DNA sequences, further supporting the role of viruses as vectors of horizontal transfer of DNA between insect species. The potential uncontrolled gene spread associated with the use of viruses produced in insect cells as gene delivery vectors and/or biopesticides should therefore be evaluated.

An insulin-binding protein from the venom of a solitary wasp Eumenes pomiformis binds to apolipophorin III in lepidopteran hemolymph

EpIBP, an insulin-like peptide-binding protein, is a major protein component of the venom of a solitary hunting wasp, Eumenes pomiformis. To evaluate the bioactivity, bacteria-expressed EpIBP was injected into Spodoptera exigua larvae, resulting in a higher survival rate and reduced loss of body weight under starvation conditions than control larvae. EpIBP was found to interact with apolipophorin III (apoLp III), implying that EpIBP might function by altering the apoLp III-mediated metabolism of prey.

Novel genetic factors involved in resistance to Bacillus thuringiensis in Plutella xylostella

The widespread and sustainable exploitation of the entomopathogen Bacillus thuringiensis (Bt) in pest control is threatened by the evolution of resistance. Although resistance is often associated with loss of binding of the Bt toxins to the insect midgut cells, other factors have been implicated. Here we used suppressive subtractive hybridization and gene expression suppression to identify additional molecular components involved in Bt-resistance in Plutella xylostella. We isolated transcripts from genes that were differentially expressed in the midgut of larvae from a resistant population, following ingestion of a Bt kurstaki HD1 strain-based commercial formulation (DiPel), and compared with a genetically similar susceptible population. Quantitative real-time polymerase-chain reaction (RT-PCR) analysis confirmed the differential basal expression of a subset of these genes. Gene expression suppression of three of these genes (P. xylostella cyclin-dependent kinase 5 regulatory subunit associated protein 1-like 1, stromal cell-derived factor 2-like 1 and hatching enzyme-like 1) significantly increased the pathogenicity of HD1 to the resistant population. In an attempt to link the multitude of factors reportedly influencing resistance to Bt with the well-characterized loss of toxin binding, we also considered Bt-resistance models in P. xylostella and other insects.

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses

Bracoviruses are symbiotic viruses associated with tens of thousands of species of parasitic wasps that develop within the body of lepidopteran hosts and that collectively parasitize caterpillars of virtually every lepidopteran species. Viral particles are produced in the wasp ovaries and injected into host larvae with the wasp eggs. Once in the host body, the viral DNA circles enclosed in the particles integrate into lepidopteran host cell DNA. Here we show that bracovirus DNA sequences have been inserted repeatedly into lepidopteran genomes, indicating this viral DNA can also enter germline cells. The original mode of Horizontal Gene Transfer (HGT) unveiled here is based on the integrative properties of an endogenous virus that has evolved as a gene transfer agent within parasitic wasp genomes for ≈100 million years. Among the bracovirus genes thus transferred, a phylogenetic analysis indicated that those encoding C-type-lectins most likely originated from the wasp gene set, showing that a bracovirus-mediated gene flux exists between the 2 insect orders Hymenoptera and Lepidoptera. Furthermore, the acquisition of bracovirus sequences that can be expressed by Lepidoptera has resulted in the domestication of several genes that could result in adaptive advantages for the host. Indeed, functional analyses suggest that two of the acquired genes could have a protective role against a common pathogen in the field, baculovirus. From these results, we hypothesize that bracovirus-mediated HGT has played an important role in the evolutionary arms race between Lepidoptera and their pathogens.

Eukaryotes are generally thought to evolve mainly through the modification of existing genetic information. However, evidence of horizontal gene transfer (HGT) in eukaryotes-the accidental acquisition of a novel gene from another species, allowing acquisition of novel traits—is now recognized as an important factor in their evolution. We show here that in several lineages, lepidopteran genomes have acquired genes from a bracovirus that is symbiotically used by parasitic wasps to inhibit caterpillar host immune defences. Integration of parts of the viral genome into host caterpillar DNA strongly suggests that integration can sporadically occur in the germline, leading to the production of lepidopteran lineages that harbor bracovirus sequences. Moreover, some of the transferred bracovirus genes reported here originate from the wasp genome, demonstrating that a gene flux exists between the two insect orders Hymenoptera and Lepidoptera that diverged ≈300 MYA. As bracovirus gene organisation has evolved to allow expression in Lepidoptera, these transferred genes can be readily domesticated. Additionally, we present functional analyses suggesting that some of the acquired genes confer to caterpillars a protection toward baculovirus, a very common pathogen in the field. This phenomenon may have implications for understanding how caterpillars acquire resistance against baculoviruses used in biological control.

Dissimilar Regulation of Antimicrobial Proteins in the Midgut of Spodoptera exigua Larvae Challenged with Bacillus thuringiensis Toxins or Baculovirus

Antimicrobial peptides (AMPs) and lysozymes are the main effectors of the insect immune system, and they are involved in both local and systemic responses. Among local responses, midgut immune reaction plays an important role in fighting pathogens that reach the insect body through the oral route, as do many microorganisms used in pest control. Under this point of view, understanding how insects defend themselves locally during the first phases of infections caused by food-borne pathogens is important to further improve microbial control strategies. In the present study, we analyzed the transcriptional response of AMPs and lysozymes in the midgut of Spodoptera exigua (Lepidoptera: Noctuidae), a polyphagous pest that is commonly controlled by products based on Bacillus thuringiensis (Bt) or baculovirus. First, we comprehensively characterized the transcripts encoding AMPs and lysozymes expressed in S. exigua larval midgut, identifying 35 transcripts that represent the S. exigua arsenal against microbial infection. Secondly, we analyzed their expression in the midgut after ingestion of sub-lethal doses of two different pore-forming B. thuringiensis toxins, Cry1Ca and Vip3Aa, and the S. exigua nucleopolyhedrovirus (SeMNPV). We observed that both Bt toxins triggered a similar, wide and in some cases high transcriptional activation of genes encoding AMPs and lysozymes, which was not reflected in the activation of the classical systemic immune-marker phenoloxidase in hemolymph. Baculovirus ingestion resulted in the opposed reaction: Almost all transcripts coding for AMPs and lysozymes were down-regulated or not induced 96 hours post infection. Our results shed light on midgut response to different virulence factors or pathogens used nowadays as microbial control agents and point out the importance of the midgut immune response contribution to the larval immunity.

Sequence diversity and evolution of antimicrobial peptides in invertebrates

Antimicrobial peptides (AMPs) are evolutionarily ancient molecules that act as the key components in the invertebrate innate immunity against invading pathogens. Several AMPs have been identified and characterized in invertebrates, and found to display considerable diversity in their amino acid sequence, structure and biological activity. AMP genes appear to have rapidly evolved, which might have arisen from the co-evolutionary arms race between host and pathogens, and enabled organisms to survive in different microbial environments. Here, the sequence diversity of invertebrate AMPs (defensins, cecropins, crustins and anti-lipopolysaccharide factors) are presented to provide a better understanding of the evolution pattern of these peptides that play a major role in host defense mechanisms.

In search of pathogens: transcriptome-based identification of viral sequences from the pine processionary moth (Thaumetopoea pityocampa)

Thaumetopoea pityocampa (pine processionary moth) is one of the most important pine pests in the forests of Mediterranean countries, Central Europe, the Middle East and North Africa. Apart from causing significant damage to pinewoods, T. pityocampa occurrence is also an issue for public and animal health, as it is responsible for dermatological reactions in humans and animals by contact with its irritating hairs. High throughput sequencing technologies have allowed the fast and cost-effective generation of genetic information of interest to understand different biological aspects of non-model organisms as well as the identification of potential pathogens. Using these technologies, we have obtained and characterized the transcriptome of T. pityocampa larvae collected in 12 different geographical locations in Turkey. cDNA libraries for Illumina sequencing were prepared from four larval tissues, head, gut, fat body and integument. By pooling the sequences from Illumina platform with those previously published using the Roche 454-FLX and Sanger methods we generated the largest reference transcriptome of T. pityocampa. In addition, this study has also allowed identification of possible viral pathogens with potential application in future biocontrol strategies.

Rapid cold hardening of Thrips palmi (Thysanoptera: Thripidae)

Cold tolerance of the palm thrips, Thrips palmi Karny, was investigated to predict its survival in field during winter. Supercooling points of T. palmi were varied among the developmental stages and ranged from -26.4 to -18.4°C. However, the cold injuries occurred above supercooling points in terms of higher mortality. The exposure to subzero temperatures (-5° to -15°C) resulted in significant mortalities to all developmental stages of T. palmi. A preexposure to a low temperature (4°C) for 7 h significantly increased the cold tolerance of all stages of T. palmi with respect to survival at -10°C and supercooling capacity. The rapid cold hardening (RCH) was dependent on the duration of the preexposure period at 4°C in adult stage. Polyol and sugar analysis using an high-performance liquid chromatography analysis showed that 4°C preexposure caused accumulation of glycerol, trehalose, mannitol, and mannose in the adults. The increase in trehalose levels was more significant than the others. This study suggests that all stages of T. palmi are able to become cold-hardy by RCH, in which several polyols and sugars may play crucial roles as cryoprotectants.

Novel Drosophila viruses encode host-specific suppressors of RNAi

The ongoing conflict between viruses and their hosts can drive the co-evolution between host immune genes and viral suppressors of immunity. It has been suggested that an evolutionary ‘arms race’ may occur between rapidly evolving components of the antiviral RNAi pathway of Drosophila and viral genes that antagonize it. We have recently shown that viral protein 1 (VP1) of Drosophila melanogaster Nora virus (DmelNV) suppresses Argonaute-2 (AGO2)-mediated target RNA cleavage (slicer activity) to antagonize antiviral RNAi. Here we show that viral AGO2 antagonists of divergent Nora-like viruses can have host specific activities. We have identified novel Nora-like viruses in wild-caught populations of D. immigrans (DimmNV) and D. subobscura (DsubNV) that are 36% and 26% divergent from DmelNV at the amino acid level. We show that DimmNV and DsubNV VP1 are unable to suppress RNAi in D. melanogaster S2 cells, whereas DmelNV VP1 potently suppresses RNAi in this host species. Moreover, we show that the RNAi suppressor activity of DimmNV VP1 is restricted to its natural host species, D. immigrans. Specifically, we find that DimmNV VP1 interacts with D. immigrans AGO2, but not with D. melanogaster AGO2, and that it suppresses slicer activity in embryo lysates from D. immigrans, but not in lysates from D. melanogaster. This species-specific interaction is reflected in the ability of DimmNV VP1 to enhance RNA production by a recombinant Sindbis virus in a host-specific manner. Our results emphasize the importance of analyzing viral RNAi suppressor activity in the relevant host species. We suggest that rapid co-evolution between RNA viruses and their hosts may result in host species-specific activities of RNAi suppressor proteins, and therefore that viral RNAi suppressors could be host-specificity factors.

Viruses and their hosts can engage in an evolutionary arms race. Viruses may select for hosts with more effective immune responses, whereas the immune response of the host may select for viruses that evade the immune system. These viral counter-defenses may in turn drive adaptations in host immune genes. A potential outcome of this perpetual cycle is that the interaction between virus and host becomes more specific. In insects, the host antiviral RNAi machinery exerts strong evolutionary pressure that has led to the evolution of viral proteins that can antagonize the RNAi response. We have identified novel viruses that infect different fruit fly species and we show that the RNAi suppressor proteins of these viruses can be specific to their host. Furthermore, we show that these proteins can enhance virus replication in a host-specific manner. These results are in line with the hypothesis that virus-host co-evolution shapes the genomes of both virus and host. Moreover, our results suggest that RNAi suppressor proteins have the potential to determine host specificity of viruses.

De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae)

Background

Anopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq).

Methods

To provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs).

Results

Approximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species.

Conclusions

Our data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis.

Simultaneous occurrence of covert infections with small RNA viruses in the lepidopteran Spodoptera exigua

Viral covert infections in invertebrates have been traditionally attributed to sublethal infections that were not able to establish an acute infection. Recent studies are revealing that, although true for some viruses, other viruses may follow the strategy of establishing covert or persistent infections without producing the death of the host. Recently, and due to the revolution in the sequencing technologies, a large number of viruses causing covert infections in all type of hosts have been identified. The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae) is a worldwide pest that causes significant losses to agricultural and ornamental plant industries. In a previous project we used NGS to obtain a comprehensive transcriptome of the larval stage, revealing the presence of an important number of unigenes belonging to novel RNA viruses, most of them from the order Picornavirales. In order to characterize S. exigua viral complex, in this work we have completed the genomic sequences of two picorna-like viruses, and compared them to a SeIV1, a member of Iflaviridae previously described by our group. We performed additional studies to determine virus morphology, horizontal transmission, tissue and life stage distribution and abundance in the hosts. We discuss the role of virus persistent infections on insect populations.

ABCC transporters mediate insect resistance to multiple Bt toxins revealed by bulk segregant analysis

BACKGROUND

Relatively recent evidence indicates that ABCC2 transporters play a main role in the mode of action of Bacillus thuringiensis (Bt) Cry1A-type proteins. Mapping of major Cry1A resistance genes has linked resistance to the ABCC2 locus in Heliothis virescens, Plutella xylostella, Trichoplusia ni and Bombyx mori, and mutations in this gene have been found in three of these Bt-resistant strains.

RESULTS

We have used a colony of Spodoptera exigua (Xen-R) highly resistant to a Bt commercial bioinsecticide to identify regions in the S. exigua genome containing loci for major resistance genes by using bulk segregant analysis (BSA). Results reveal a region containing three genes from the ABCC family (ABBC1, ABBC2 and ABBC3) and a mutation in one of them (ABBC2) as responsible for the resistance of S. exigua to the Bt commercial product and to its key Spodoptera-active ingredients, Cry1Ca. In contrast to all previously described mutations in ABCC2 genes that directly or indirectly affect the extracellular domains of the membrane protein, the ABCC2 mutation found in S. exigua affects an intracellular domain involved in ATP binding. Functional analyses of ABBC2 and ABBC3 support the role of both proteins in the mode of action of Bt toxins in S. exigua. Partial silencing of these genes with dsRNA decreased the susceptibility of wild type larvae to both Cry1Ac and Cry1Ca. In addition, reduction of ABBC2 and ABBC3 expression negatively affected some fitness components and induced up-regulation of arylphorin and repat5, genes that respond to Bt intoxication and that are found constitutively up-regulated in the Xen-R strain.

CONCLUSIONS

The current results show the involvement of different members of the ABCC family in the mode of action of B. thuringiensis proteins and expand the role of the ABCC2 transporter in B. thuringiensis resistance beyond the Cry1A family of proteins to include Cry1Ca.

The de novo transcriptome and its analysis in the worldwide vegetable pest, Delia antiqua (Diptera: Anthomyiidae)

The onion maggot Delia antiqua is a major insect pest of cultivated vegetables, especially the onion, and a good model to investigate the molecular mechanisms of diapause. To better understand the biology and diapause mechanism of the insect pest species, D. antiqua, the transcriptome was sequenced using Illumina paired-end sequencing technology. Approximately 54 million reads were obtained, trimmed, and assembled into 29,659 unigenes, with an average length of 607 bp and an N50 of 818 bp. Among these unigenes, 21,605 (72.8%) were annotated in the public databases. All unigenes were then compared against Drosophila melanogaster and Anopheles gambiae. Codon usage bias was analyzed and 332 simple sequence repeats (SSRs) were detected in this organism. These data represent the most comprehensive transcriptomic resource currently available for D. antiqua and will facilitate the study of genetics, genomics, diapause, and further pest control of D. antiqua.

Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing

The pine processionary moth Thaumetopoea pityocampa is a Mediterranean lepidopteran defoliator that experiences a rapid range expansion towards higher latitudes and altitudes due to the current climate warming. Its phenology - the time of sexual reproduction - is certainly a key trait for the local adaptation of the processionary moth to climatic conditions. Moreover, an exceptional case of allochronic differentiation was discovered ca. 15 years ago in this species. A population with a shifted phenology (the summer population, SP) co-exists near Leiria, Portugal, with a population following the classical cycle (the winter population, WP). The existence of this population is an outstanding opportunity to decipher the genetic bases of phenology. No genomic resources were so far available for T. pityocampa. We developed a high-throughput sequencing approach to build a first reference transcriptome, and to proceed with comparative analyses of the sympatric SP and WP. We pooled RNA extracted from whole individuals of various developmental stages, and performed a transcriptome characterisation for both populations combining Roche 454-FLX and traditional Sanger data. The obtained sequences were clustered into ca. 12,000 transcripts corresponding to 9265 unigenes. The mean transcript coverage was 21.9 reads per bp. Almost 70% of the de novo assembled transcripts displayed significant similarity to previously published proteins and around 50% of the transcripts contained a full-length coding region. Comparative analyses of the population transcriptomes allowed to investigate genes specifically expressed in one of the studied populations only, and to identify the most divergent homologous SP/WP transcripts. The most divergent pairs of transcripts did not correspond to obvious phenology-related candidate genes, and 43% could not be functionally annotated. This study provides the first comprehensive genome-wide resource for the target species T. pityocampa. Many of the assembled genes are orthologs of published Lepidoptera genes, which allows carrying out gene-specific re-sequencing. Data mining has allowed the identification of SNP loci that will be useful for population genomic approaches and genome-wide scans of population differentiation to identify signatures of selection.

Identification of immunity-related genes in Ostrinia furnacalis against entomopathogenic fungi by RNA-seq analysis

BACKGROUND

The Asian corn borer (Ostrinia furnacalis (Guenée)) is one of the most serious corn pests in Asia. Control of this pest with entomopathogenic fungus Beauveria bassiana has been proposed. However, the molecular mechanisms involved in the interactions between O. furnacalis and B. bassiana are unclear, especially under the conditions that the genomic information of O. furnacalis is currently unavailable. So we sequenced and characterized the transcriptome of O. furnacalis larvae infected by B. bassiana with special emphasis on immunity-related genes.

METHODOLOGY/PRINCIPAL FINDINGS

Illumina Hiseq2000 was used to sequence 4.64 and 4.72 Gb of the transcriptome from water-injected and B. bassiana-injected O. furnacalis larvae, respectively. De novo assembly generated 62,382 unigenes with mean length of 729 nt. All unigenes were searched against Nt, Nr, Swiss-Prot, COG, and KEGG databases for annotations using BLASTN or BLASTX algorithm with an E-value cut-off of 10(-5). A total of 35,700 (57.2%) unigenes were annotated to at least one database. Pairwise comparisons resulted in 13,890 differentially expressed genes, with 5,843 up-regulated and 8,047 down-regulated. Based on sequence similarity to homologs known to participate in immune responses, we totally identified 190 potential immunity-related unigenes. They encode 45 pattern recognition proteins, 33 modulation proteins involved in the prophenoloxidase activation cascade, 46 signal transduction molecules, and 66 immune responsive effectors, respectively. The obtained transcriptome contains putative orthologs for nearly all components of the Toll, Imd, and JAK/STAT pathways. We randomly selected 24 immunity-related unigenes and investigated their expression profiles using quantitative RT-PCR assay. The results revealed variant expression patterns in response to the infection of B. bassiana.

CONCLUSIONS/SIGNIFICANCE

This study provides the comprehensive sequence resource and expression profiles of the immunity-related genes of O. furnacalis. The obtained data gives an insight into better understanding the molecular mechanisms of innate immune processes in O. furnacalis larvae against B. bassiana.