Genome mapping coupled with CRISPR gene editing reveals a P450 gene confers avermectin resistance in the beet armyworm

The evolution of insecticide resistance represents a global constraint to agricultural production. Because of the extreme genetic diversity found in insects and the large numbers of genes involved in insecticide detoxification, better tools are needed to quickly identify and validate the involvement of putative resistance genes for improved monitoring, management, and countering of field-evolved insecticide resistance. The avermectins, emamectin benzoate (EB) and abamectin are relatively new pesticides with reduced environmental risk that target a wide number of insect pests, including the beet armyworm, Spodoptera exigua, an important global pest of many crops. Unfortunately, field resistance to avermectins recently evolved in the beet armyworm, threatening the sustainable use of this class of insecticides. Here, we report a high-quality chromosome-level assembly of the beet armyworm genome and use bulked segregant analysis (BSA) to identify the locus of avermectin resistance, which mapped on 15–16 Mbp of chromosome 17. Knockout of the CYP9A186 gene that maps within this region by CRISPR/Cas9 gene editing fully restored EB susceptibility, implicating this gene in avermectin resistance. Heterologous expression and in vitro functional assays further confirm that a natural substitution (F116V) found in the substrate recognition site 1 (SRS1) of the CYP9A186 protein results in enhanced metabolism of EB and abamectin. Hence, the combined approach of coupling gene editing with BSA allows for the rapid identification of metabolic resistance genes responsible for insecticide resistance, which is critical for effective monitoring and adaptive management of insecticide resistance.     

Chromosome-level genome assembly of an agricultural pest,the rice leaffolder Cnaphalocrocis exigua (Crambidae,Lepidoptera)

The rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera) is an important agricultural pest that damages rice crops and other members of related grass families. C. exigua exhibits a very similar morphological phenotype and feeding behaviour to C. medinalis, another species of rice leaffolder whose genome was recently reported. However, genomic information for C. exigua remains extremely limited. Here, we used a hybrid strategy combining different sequencing technologies, including Illumina, PacBio, 10× Genomics, and Hi – C scaffolding, to generate a high-quality chromosome-level genome assembly of C. exigua. We initially obtained a 798.8 Mb assembly with a contig N50 size of 2.9 Mb, and the N50 size was subsequently increased to 25.7 Mb using Hi – C technology to anchor 1413 scaffolds to 32 chromosomes. We detected a total of 97.7% Benchmarking Universal Single-Copy Orthologues (BUSCO) in the genome assembly, which was comprised of ~52% repetitive sequence and annotated 14,922 protein-coding genes. Of note, the Z and W sex chromosomes were assembled and identified. A comparative genomic analysis demonstrated that despite the high synteny observed between the two rice leaffolders, the species have distinct genomic features associated with expansion and contraction of gene families and selection pressure. In summary, our chromosome-level genome assembly and comparative genomic analysis of C. exigua provide novel insights into the evolution and ecology of this rice insect pests and offer useful information for pest control.     

Characterization of the gut microbiome in the beet armyworm Spodoptera exigua in response to the short-term thermal stress

The gut microbiota is critical for energy and nutrient utilization and plays a role in host immunity in response to environmental changes. The beet armyworm Spodoptera exigua is a worldwide polyphagous agricultural pest and has frequently experienced potentially stressful temperature fluctuations under natural environmental conditions. However, little is known about the effects of thermal stress on the gut microbiome of this moth pest. Therefore, we investigated the gut microbiome variations, composition and community structure of S. exigua among low-temperature (10 °C), control (26 °C) and high temperature (35 °C) treatments using 16S amplicon sequencing. Overall, 1,192,707 high-quality reads and 762 operational taxonomic units (OTUs) were detected from 15 samples. A total of 289 genera belonging to 19 bacterial phyla were captured, with Firmicutes and Proteobacteria being the most prominent phyla. Alpha diversity metrics indicated no significant differences in the gut bacterial diversity of S. exigua among the three temperature treatments. Principal coordinates and hierarchical cluster analysis revealed significant differences in the structure of gut microbiota between the low-temperature treatment and the other two temperature treatments. In addition, PICRUSt2 analysis demonstrated that the predicted metagenomes associated with the gut microbiome were amino carbohydrate transport and metabolism, acid transport and metabolism, inorganic ion transport and metabolism and cellular processes. Our study showed that thermal stress induced changes in the gut microbiome of the beet armyworm, which may contribute to better understanding the ecological adaptation of S. exigua under changing temperature trends and to evaluating the use of gut microorganisms as biocontrol agents for this pest.     

Eicosanoids influence insect susceptibility to nucleopolyhedroviruses

Nine pharmaceutical inhibitors of eicosanoid biosynthesis (e.g., bromophenacyl bromide, clotrimazole, diclofenamic acid, esculetin, flufenamic acid, indomethacin, nimesulide, sulindac, tolfenamic acid) that increased the susceptibility of the gypsy moth, Lymantria dispar (L.), to the nucleopolyhedrovirus LdMNPV were tested against the beet armyworm Spodoptera exigua (Hübner), the corn earworm Helicoverpa zea (Boddie) and the fall armyworm Spodoptera frugiperda (J.E. Smith) and their respective NPVs to determine whether these compounds also alter the susceptibility of these insects. The susceptibility of the beet armyworm was increased by six inhibitors (bromophenacyl bromide, clotrimazole, diclofenic acid, esculetin, flufenamic acid, nimesulide). The susceptibility of the fall armyworm was increased by seven inhibitors, (bromophenacyl bromide, diclofenamic acid, esculetin, indomethacin, nimesulide, sulindac, tolfenamic acid), whereas the susceptibility of the corn earworm was increased by only one inhibitor (sulindac). The influence of the cyclooxygenase inhibitor, indomethacin was expressed in a concentration-related manner in beet armyworms. We infer from these findings that eicosanoids, including prostaglandins and lipoxygenase products, act in insect anti-viral defenses.     

Chromosome-level de novo genome assembly of two conifer-parasitic wasps,Megastigmus duclouxiana and Megastigmus sabinae,reveals genomic imprints of adaptation to hosts

Conifers make up about one third of global forests but are threatened by seed parasitoid wasp species. Many of these wasps belong to the genus Megastigmus, yet little is known about their genomic background. In this study, we provide chromosome-level genome assemblies for two oligophagous conifer parasitoid species of Megastigmus, which represent the first two chromosome-level genomes of the genus. The assembled genomes of Megastigmus duclouxiana and M. sabinae are 878.48 Mb (scaffold N50 of 215.60 Mb) and 812.98 Mb (scaffold N50 of 139.16 Mb), respectively, which are larger than the genome size of most hymenopterans due to the expansion of transposable elements. Expanded gene families highlight the difference in sensory-related genes between the two species, reflecting the difference in their hosts. We further found that these two species have fewer family members but more single-gene duplications than polyphagous congeners in the gene families of ATP-binding cassette transporter (ABC), cytochrome P450 (P450) and olfactory receptors (OR). These findings shed light on the pattern of adaptation to a narrow spectrum of hosts in oligophagous parasitoids. Our findings suggest potential drivers underlying genome evolution and parasitism adaptation, and provide valuable resources for understanding the ecology, genetics and evolution of Megastigmus, as well as for the research and biological control of global conifer forest pests.     

Response of multiple generations of beet armyworm,Spodoptera exigua (Hübner), feeding on transgenic Bt cotton

Development, reproduction and food utilization of three successive generations of beet armyworm, Spodoptera exigua (Hübner), fed on transgenic and non‐transgenic Bt cotton were examined. Significantly longer larval life‐span and lower pupal weight were observed in three successive generations of S. exigua fed on transgenic Bt cotton compared with non‐transgenic Bt cotton. Significantly higher survival rate and adult fecundity of S. exigua were found in three successive generations of S. exigua fed on transgenic Bt cotton compared with non‐transgenic Bt cotton. The survival rate and adult fecundity of S. exigua were occurred significant increase in the third generation compared with the first generation after feeding on transgenic Bt cotton. Significantly lower consumption, frass and relative growth rate (RGR) were observed in three successive generations of S. exigua fed on transgenic Bt cotton compared with non‐transgenic Bt cotton. Cotton variety significantly affected all indices of larval consumption and utilization in three successive generations of S. exigua, except for efficiency of conversion of ingested food. However, beet armyworm generation only significantly affected RGR of S. exigua. The results of this study indicated food quality on the diet‐utilization efficiency of S. exigua was different along with beet armyworm generation. Measuring multigenerational development and food utilization of S. exigua at individual and population level in response to Bacillus thuringiensis (Bt) can provide a more meaningful evaluation of long‐term population dynamics than experiments on a single generation. It is imperative to develop an appropriate multigenerational pest management tactic to monitor the field population dynamics of non‐target pests (e.g., beet armyworm) in agricultural Bt cotton ecosystem.     

Epizootiology of virus diseases in three lepidopterous insect species of alfalfa

Summary The incidence of virus infections in three lepidopterous insect species was studied from 1965 to 1968 in alfalfa fields in California. The insects were the alfalfa caterpillar,Colias eurytheme; the beet armyworm,Spodoptera exigua; and the alfalfa looper,Autographa californica. InC. eurytheme, the major virus was a nuclear polyhedrosis virus (NPV); inS. exigua, a granulosis virus (GV) and an NPV; inA. californica, a GV. Virus epizootics did not develop in very high densities ofC. eurytheme. Virus epizootics occurred in low host densities of the three insect species, especially in populations ofA. californica. The virus acted as a density-dependent factor in the regulation of the populations ofS. exigua andA. californica. Temperature, humidity and rainfall had no marked effect on the incidence of virus infections.     

The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability

Background and AimsPlant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes.MethodsWe identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization.Key resultsAll 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes – mechanisms that likely caused Cassandra’s subfamily formation and diversification.ConclusionsWe traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.     

The chromosome-scale assembly of endive (Cichorium endivia) genome provides insights into the sesquiterpenoid biosynthesis

Endive (Cichorium endivia L.) is a leafy vegetable in the Asteraceae family. Sesquiterpene lactones (STLs) in endive leaves bring a bitter taste that varies between varieties. Despite their importance in breeding varieties with unique flavours, sesquiterpenoid biosynthesis pathways in endive are poorly understood. We assembled a chromosome-scale endive genome of 641 Mb with a contig N50 of 5.16 Mb and annotated 46,711 protein-coding genes. Several gene families, especially terpene synthases (TPS) genes, expanded significantly in the C. endivia genome. STLs biosynthesis-related genes and TPS genes in more bitter varieties have shown a higher level of expression, which could be attributed to genomic variations. Our results penetrate the origin and diversity of bitter taste and facilitate the molecular breeding of endive varieties with unique bitter tastes. The high-quality endive assembly would provide a reference genome for studying the evolution and diversity of Asteraceae.     

Bumblebee Venom Serine Protease Increases Fungal Insecticidal Virulence by Inducing Insect Melanization

Insect-killing (entomopathogenic) fungi have high potential for controlling agriculturally harmful pests. However, their pathogenicity is slow, and this is one reason for their poor acceptance as a fungal insecticide. The expression of bumblebee, Bombus ignitus, venom serine protease (VSP) by Beauveria bassiana (ERL1170) induced melanization of yellow spotted longicorn beetles (Psacothea hilaris) as an over-reactive immune response, and caused substantially earlier mortality in beet armyworm (Spodopetra exigua) larvae when compared to the wild type. No fungal outgrowth or sporulation was observed on the melanized insects, thus suggesting a self-restriction of the dispersal of the genetically modified fungus in the environment. The research is the first use of a multi-functional bumblebee VSP to significantly increase the speed of fungal pathogenicity, while minimizing the dispersal of the fungal transformant in the environment.     

Selection of nuclear polyhedrosis viruses as biological control agents ofSpodoptera exigua [Lep.: Noctuidae]

The virulence of 5 nuclear polyhedrosis viruses infectious for larvae of beet armyworm,Spodoptera exigua, was studied and their potential as biological control agents of this accidentally introduced pest in Dutch greenhouse crops is discussed. Three of the virus isolates were collected from deceased beet armyworm larvae found in Dutch greenhouses. Based on restriction endonuclease patterns of their DNA they appeared to be closely related toMamestra brassicae nuclear polyhedrosis virus (MbMNPV) and therefore were named MbMNPV-NL80, MbMNPV-NL82 and MbMNPV-NL83. These isolates were not related toAutographa californica MNPV (AcMNPV) or toSpodoptera exigua MNPV (SeMNPV), both originating from the USA. Comparison of the oiological activity of these 5 isolates showed that the SeMNPV was more virulent against beet armyworm than the other isolates. There was no significant difference in virulence between MbMNPV-NL80, NL82, NL83 and AcMNPV forS. exigua. The LD-50 values of the 5 isolates for 2nd instar larvae were 3, 26, 14, 17 and 18 polyhedra, respectively. Despite compensating qualities of the other MNPVs, such as a broader host range and potential production in alternate hosts or cell-lines, SeMNPV is considered to be the most suitable candidate as biological control agent of beet armyworm.      

An Entomopathogenic Bacterium,Xenorhabdus nematophila K1, Enhances Baculovirus Pathogenicity against Spodoptera exigua and Plutella xylostella

This is a report to demonstrate a pathogenicity enhancement by two microbial agents. Baculovirus pathogenicity was attenuated with larval development of both lepidopteran species: the beet armyworm, Spodoptera exigua, and the diamondback moth, Plutella xylostella. The addition of an entomopathogenic bacterium, Xenorhabdus nematophila Kl, to the baculovirus treatment significantly enhanced the viral pathogenicity in both lepidopteran species. The synergistic pathogenicity may result from their independent pathogenic targets in the insects.     

Identification of Bacillus thuringiensis Delta-Endotoxin Cry1C Domain III Amino Acid Residues Involved in Insect Specificity

Cry1C domain III amino acid residues involved in specificity for beet armyworm (Spodoptera exigua) were identified. For this purpose, intradomain III hybrids between Cry1E (nontoxic) and Cry1E-Cry1C hybrid G27 (toxic) were made. Crossover points of these hybrids defined six sequence blocks containing between 1 and 19 of the amino acid differences between Cry1E and G27. Blocks B, C, D, and E of G27 were shown to be required for optimal activity against S. exigua. Block E was also required for optimal activity against the tobacco hornworm (Manduca sexta), whereas block D had a negative effect on toxicity for this insect. The mutagenesis of individual amino acids in block B identified Trp-476 as the only amino acid in this block essential, although not sufficient by itself, for full S. exigua activity. In block D, we identified a seven-amino-acid insertion in G27 that was not in Cry1E. The deletion of either one of two groups of four consecutive amino acids in this insertion completely abolished activity against S. exigua but resulted in higher activity against M. sexta. Alanine substitutions of the first group had little effect on toxicity, whereas alanine substitutions of the second group had the same effect as its deletion. These results identify groups of amino acids as well as some individual residues in Cry1C domain III, which are strongly involved in S. exigua-specific activity as well as sometimes involved in M. sexta-specific activity.     

Roles of Peroxinectin in PGE2-Mediated Cellular Immunity in Spodoptera exigua

Background

Prostaglandins (PGs) mediate insect immune responses to infections and invasions. Although the presence of PGs has been confirmed in several insect species, their biosynthesis in insects remains a conundrum because orthologs of the mammalian cyclooxygenases (COXs) have not been found in the known insect genomes. PG-mediated immune reactions have been documented in the beet armyworm, Spodoptera exigua. The purpose of this research is to identify the source of PGs in S. exigua.

Principal Findings

Peroxidases (POXs) are a sister group of COX genes. Ten putative POXs (SePOX-A ∼ SePOX-J) were expressed in S. exigua. Expressions of SePOX-F and -H were induced by bacterial challenge and expressed in the hemocytes and the fat body. RNAi of each POX was performed by hemocoelic injection of their specific double-stranded RNAs. dsPOX-F or, separately, dsPOX-H, but not the other eight dsRNA constructs, specifically suppressed hemocyte-spreading behavior and nodule formation; these two reactions were also inhibited by aspirin, a COX inhibitor. PGE₂, but not arachidonic acid, treatment rescued the immunosuppression. Sequence analysis indicated that both POX genes were clustered with peroxinectin (Pxt) and their cognate proteins shared some conserved domains corresponding to the Pxt of Drosophila melanogaster.

Conclusions

SePOX-F and -H are Pxt-like genes associated with PG biosynthesis in S. exigua.     

Forecasting the potential distribution of Spodoptera exigua and S. littoralis (Lepidoptera,Noctuidae) in Iran

The beet armyworm, Spodoptera exigua (Hübner, 1808) and the Egyptian cotton leafworm, S. littoralis (Boisduval, 1833), are amongst the most notorious agricultural pest species in Iran. Spodoptera exigua is considered a serious pest of different crops, whereas S. littoralis is known as an important pest of cotton.In this paper, the potential distribution areas of these species in Iran and the important climatic factors affecting their distribution were predicted using the MaxEnt model and the ArcGIS. The results indicate that the main environmental variables contributing to S. exigua’s distribution were precipitation of the coldest quarter (bio19), average wind speed in April (wind4), and annual precipitation (bio12). Also, minimum temperature of the coldest month (bio6), mean temperature of coldest quarter (bio11), altitude and average wind speed in May (wind5) were dominant climatic factors that affected the potential distribution of S. littoralis. These species overlapped in most parts of coastal areas in the southern and northern parts of Iran, with an average overlapping range of 33.2%. Considering their preferred host plants in Iran, it is necessary to strengthen biosurveillance programes and management of these two species in their suitable areas to prevent further invasion, which endangers agricultural security.