Hybridization and gene flow in the mega-pest lineage of moth, Helicoverpa

Homology-based characterization of the cis-regulatory elements modulate flavone induction of CYP321A1 in Helicoverpa armigera

Xenobiotic response element (XRE) to flavone was the cis- regulatory elements that mediates the induction of the allelochemical-metabolizing CYP321A1 gene from Helicoverpa zea. However, it was unknown whether the XRE-Fla element existed in other species. Recently we have identified and cloned the CYP321A1 gene with promoter region in a related species, Helicoverpa armigera. Sequence similarity of two orthologous CYP321A1 genes was 97.27%, but the promoter sequence similarity was only 56.32%. Sequence alignment showed the XRE-Fla like element owns three mutations in H. armigera compared with H. zea. Progressive 5' deletions and internal mutation indicated that H. armigera XRE-Fla was the essential element of CYP321A1 gene in response to flavone. XRE-Fla mutations and EMSA analysis confirmed that the H. armigera XRE-Fla element binding factor was stronger than H. zea. The findings indicate the XRE element mutations mainly contribute to the differences between the flavone-induced expressions of two CYP321A1 genes, which improve the flexibility and adaptability for allelochemical response of H. armigera.

An Improved Bulk DNA Extraction Method for Detection of Helicoverpa armigera (Lepidoptera: Noctuidae) Using Real-Time PCR

Helicoverpa armigera is among the most problematic agricultural pests worldwide due to its polyphagy and ability to evolve pesticide resistance. Molecular detection methods for H. armigera have been developed to track its spread, as such methods allow for rapid and accurate differentiation from the native sibling species H. zea. Droplet digital PCR (ddPCR) is a preferred method for bulk screening due to its accuracy and tolerance to PCR inhibitors; however, real-time PCR is less expensive and more widely available in molecular labs. Improvements to DNA extraction yield, purity, and throughput are crucial for real-time PCR assay optimization. Bulk DNA extractions have recently been improved to where real-time PCR sensitivity can equal that of ddPCR, but these new methods require significant time and specialized equipment. In this study, we improve upon previously published bulk DNA extraction methods by reducing bench time and materials. Our results indicate that the addition of caffeine and RNase A improves DNA extraction, resulting in lower Cq values during real-time PCR while reducing the processing time and cost per specimen. Such improvements will enable the use of high throughput screening methods across multiple platforms to improve the probability of detection of H. armigera.

Differentiation in detoxification gene complements, including neofunctionalization of duplicated cytochrome P450 genes, between lineages of cotton bollworm, Helicoverpa armigera

Here we investigate the evolutionary dynamics of five enzyme superfamilies (CYPs, GSTs, UGTs, CCEs and ABCs) involved in detoxification in Helicoverpa armigera. The reference assembly for an African isolate of the major lineages, H. a. armigera, has 373 genes in the five superfamilies. Most of its CYPs, GSTs, UGTs and CCEs and a few of its ABCs occur in blocks and most of the clustered genes are in subfamilies specifically implicated in detoxification. Most of the genes have orthologues in the reference genome for the Oceania lineage, H. a. conferta. However, clustered orthologues and subfamilies specifically implicated in detoxification show greater sequence divergence and less constraint on non-synonymous differences between the two assemblies than do other members of the five superfamilies. Two duplicated CYPs, which were found in the H. a. armigera but not H. a. conferta reference genome, were also missing in 16 Chinese populations spanning two different lineages of H. a. armigera. The enzyme produced by one of these duplicates has higher activity against esfenvalerate than a previously described chimeric CYP mutant conferring pyrethroid resistance. Various transposable elements were found in the introns of most detoxification genes, generating diverse gene structures. Extensive resequencing data for the Chinese H. a. armigera and H. a. conferta lineages also revealed complex copy number polymorphisms in 17 CCE001s in a cluster also implicated in pyrethroid metabolism, with substantial haplotype differences between all three lineages. Our results suggest that cotton bollworm has a versatile complement of detoxification genes which are evolving in diverse ways across its range.

Rapid Adaptation and Interspecific Introgression in the North American Crop Pest Helicoverpa zea

Insect crop pests threaten global food security. This threat is amplified through the spread of nonnative species and through adaptation of native pests to control measures. Adaptations such as pesticide resistance can result from selection on variation within a population, or through gene flow from another population. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has evolved resistance to a wide range of pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid-resistance gene CYP337B3 to South American H. zea via adaptive introgression. To understand whether this could contribute to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites. We report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4 Mbp region containing CYP337B3. Next, we identify signatures of selection in the panmictic population of nonadmixed H. zea, identifying a selective sweep at a second cytochrome P450 gene: CYP333B3. We estimate that its derived allele conferred a ∼5% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a ∼20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Overall, we document two mechanisms of rapid adaptation: the introduction of fitness-enhancing alleles through interspecific introgression, and selection on intraspecific variation.

Hybrids of two destructive subterranean termites established in the field, revealing a potential for gene flow between species

Hybridization between invasive pest species may lead to significant genetic and economic impacts that require close monitoring. The two most invasive and destructive termite species worldwide, Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann), have the potential for hybridization in the field. A three-year field survey conducted during the dispersal flight season of Coptotermes in Taiwan identified alates with atypical morphology, which were confirmed as hybrids of the two Coptotermes species using microsatellite and mitochondrial analyses. Out of 27,601 alates collected over three years, 4.4% were confirmed as hybrid alates, and some advanced hybrids (>F1 generations) were identified. The hybrid alates had a dispersal flight season that overlapped with the two parental species 13 out of 15 times. Most of the hybrid alates were females, implying that mating opportunities beyond F1 may primarily be possible through female hybrids. However, the incipient colony growth results from all potential mating combinations suggest that only backcross colonies with hybrid males could sometimes lead to brood development. The observed asymmetrical viability and fertility of hybrid alates may critically reduce the probability of advanced-hybrid colonies being established in the field.

Is there hybridization between 2 species of the same genus in sympatry?-The genetic relationships between Anoplophora glabripennis, Anoplophora chinensis, and putative hybrids

Anoplophora glabripennis (Asian longhorn beetle, ALB) and Anoplophora chinensis (Citrus longhorn beetle, CLB) are native forest pests in China; they have become important international quarantine pests. They are found using the same Salix aureo-pendula host tree of Cixi, Zhejiang province, China. On this host tree, we collected additional beetles that appeared to be morphologically intermediate between ALB and CLB. By using a stereoscope, we observed that there were several bumps on the base of the elytra, which was inconsistent with ALB, which typically has a smooth elytral base, but was more like CLB, which has numerous short tubercles on the elytral base. Given their sympatry and intermediate morphology, we hypothesized that these may represent ALB × CLB hybrids. We studied the genomic profiles for 46 samples (ALB, CLB, and putative hybrids) using genotyping-by-sequencing (GBS) providing a reduced representation of the entire genome. Employing principal component analyses on the 163 GBS-derived single nucleotide polymorphism data, we found putative hybrids tightly clustered with ALB, but genetically distinct from the CLB individuals. Therefore, our initial hybrid hypothesis was not supported by genomic data. Further, while mating experiments between adult ALB and CLB were successful in 4 separate years (2017, 2018, 2020, and 2021), and oviposition behavior was observed, no progeny was produced. Having employed population genomic analysis and biological hybridization experiments, we conclude that the putative hybrids represent newly discovered morphological variants within ALB. Our approach further confirmed the advantage of genome-wide information for Anoplophora species assignment in certain ambiguous classification cases.

Accurate identification of Helicoverpa armigera-Helicoverpa zea hybrids using genome admixture analysis: implications for genomic surveillance

Helicoverpa armigera, the cotton bollworm moth, is one of the world's most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive H. armigera has been reported to hybridize with local populations of Helicoverpa zea. The correct identification of H. armigera-H. zea hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate H. zea pesticide resistance and host plant range via introgression of H. armigera genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two H. armigera-H. zea F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% H. armigera for the two F1 hybrids, confirming its accuracy. Genome sequences from five H. zea and one H. armigera that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four H. zea genomes generated from a previous study are predicted to possess a proportion of H. armigera genetic material. Using unsupervised clustering to identify non-hybridized H. armigera and H. zea genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor H. armigera component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of H. armigera-H. zea hybrids, and suggest measures that will improve such analyses.

The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest

Sequence capture is a genomic technique that selectively enriches target sequences before high throughput next-generation sequencing, to generate specific sequences of interest. Off-target or 'bycatch' data are often discarded from capture experiments, but can be leveraged to address evolutionary questions under some circumstances. Here, we investigated the effects of missing data on a variety of evolutionary analyses using bycatch from an exon capture experiment on the global pest moth, Helicoverpa armigera. We added > 200 new samples from across Australia in the form of mitogenomes obtained as bycatch from targeted sequence capture, and combined these into an additional larger dataset to total > 1000 mitochondrial cytochrome c oxidase subunit I (COI) sequences across the species' global distribution. Using discriminant analysis of principal components and Bayesian coalescent analyses, we showed that mitogenomes assembled from bycatch with up to 75% missing data were able to return evolutionary inferences consistent with higher coverage datasets and the broader literature surrounding H. armigera. For example, low-coverage sequences broadly supported the delineation of two H. armigera subspecies and also provided new insights into the potential for geographic turnover among these subspecies. However, we also identified key effects of dataset coverage and composition on our results. Thus, low-coverage bycatch data can offer valuable information for population genetic and phylodynamic analyses, but caution is required to ensure the reduced information does not introduce confounding factors, such as sampling biases, that drive inference. We encourage more researchers to consider maximizing the potential of the targeted sequence approach by examining evolutionary questions with their off-target bycatch where possible-especially in cases where no previous mitochondrial data exists-but recommend stratifying data at different genome coverage thresholds to separate sampling effects from genuine genomic signals, and to understand their implications for evolutionary research.

Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification

The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid molting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown, and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and we also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. Our evolutionary analyses provide hypotheses of function and a robust framework for future experimental studies of the EcKL gene family. They also open promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied coevolution of butterflies with their host plants.

Performance of cotton expressing Cry1Ac, Cry1F and Vip3Aa19 insecticidal proteins against Helicoverpa armigera, H. zea and their hybrid progeny, and evidence of reduced susceptibility of a field population of H. zea to Cry1 and Vip3Aa in Brazil

The genetically modified cotton DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 expressing Cry1Ac, Cry1F and Vip3Aa19 from Bacillus thuringiensis Berliner (Bt) has been cultivated in Brazil since the 2020/2021 season. Here, we assessed the performance of DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 cotton expressing Cry1Ac, Cry1F and Vip3Aa19 against Helicoverpa armigera (Hübner), Helicoverpa zea (Boddie), and their hybrid progeny. We also carried out evaluations with DAS-21023-5 × DAS-24236-5 cotton containing Cry1Ac and Cry1F. In leaf-disk bioassays, DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 was effective in controlling neonates from laboratory colonies of H. armigera, H. zea and the hybrid progeny (71.9%-100% mortality). On floral bud bioassays using L2 larvae, H. zea presented complete mortality, whereas H. armigera and the hybrid progeny showed <55% mortality. On DAS-21023-5 × DAS-24236-5 cotton, the mortality of H. armigera on leaf-disk and floral buds ranged from 60% to 73%, whereas mortality of hybrids was <46%. This Bt cotton caused complete mortality of H. zea larvae from a laboratory colony in the early growth stages, but mortalities were <55% on advanced growth stages and on floral buds. In field studies conducted from 2014 to 2019, DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 cotton was also effective at protecting plants against H. armigera. In contrast, a population of H. zea collected in western Bahia in 2021/2022 on Bt cotton expressing Cry1 and Vip3Aa proteins, showed 63% mortality after 30 d, with insects developing into fifth and sixth instars, on DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 cotton. We conclude that H. armigera, H. zea, and their hybrid progeny can be managed with DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 cotton; however we found the first evidence in Brazil of a significant reduction in the susceptibility to DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 cotton of a population of H. zea collected from Bt cotton in Bahia in 2021/2022.

Adaptive evolution to the natural and anthropogenic environment in a global invasive crop pest, the cotton bollworm

The cotton bollworm, Helicoverpa armigera, is set to become the most economically devastating crop pest in the world, threatening food security and biosafety as its range expands across the globe. Key to understanding the eco-evolutionary dynamics of H. armigera, and thus its management, is an understanding of population connectivity and the adaptations that allow the pest to establish in unique environments. We assembled a chromosome-scale reference genome and re-sequenced 503 individuals spanning the species range to delineate global patterns of connectivity, uncovering a previously cryptic population structure. Using a genome-wide association study (GWAS) and cell line expression of major effect loci, we show that adaptive changes in a temperature- and light-sensitive developmental pathway enable facultative diapause and that adaptation of trehalose synthesis and transport underlies cold tolerance in extreme environments. Incorporating extensive pesticide resistance monitoring, we also characterize a suite of novel pesticide and Bt resistance alleles under selection in East China. These findings offer avenues for more effective management strategies and provide insight into how insects adapt to variable climatic conditions and newly colonized environments.

Evolutionary shifts in pheromone receptors contribute to speciation in four Helicoverpa species

Male moths utilize their pheromone communication systems to distinguish potential mates from other sympatric species, which contributes to maintaining reproductive isolation and even drives speciation. The molecular mechanisms underlying the evolution of pheromone communication systems are usually studied between closely-related moth species for their similar but divergent traits associated with pheromone production, detection, and/or processing. In this study, we first identified the functional differentiation in two orthologous pheromone receptors, OR14b, and OR16, in four Helicoverpa species, Helicoverpa armigera, H. assulta, H. zea, and H. gelotopoeon. To understand the substrate response specificity of these two PRs, we performed all-atom molecular dynamics simulations of OR14b and OR16 based on AlphaFold2 structural prediction, and molecular docking, allowing us to predict a few key amino acids involved in substrate binding. These candidate residues were further tested and validated by site-directed mutagenesis and functional analysis. These results together identified two hydrophobic amino acids at positions 164 and 232 are the determinants of the response specificity of HarmOR14b and HzeaOR14b to Z9-14:Ald and Z9-16:Ald by directly interacting with the substrates. Interestingly, in OR16 orthologs, we found that position 66 alone determines the specific binding of Z11-16:OH, likely via allosteric interactions. Overall, we have developed an effective integrated method to identify the critical residues for substrate selectivity of ORs and elucidated the molecular mechanism of the diversification of pheromone recognition systems.

Field-based recombinase polymerase amplification and lab-based qPCR assays for detection of Helicoverpa armigera

Helicoverpa armigera (Hübner) is a major crop pest native to Europe, Asia, Australia, and Africa which has recently invaded South America and has caused billions of dollars in agricultural losses. Because of challenges in differentiating between H. armigera and Helicoverpa zea (Boddie), a closely related species native to North and South America, genetic tests have previously been developed to detect H. armigera DNA in pooled samples of moth legs. In this study, a field-based recombinase polymerase amplification (RPA) assay using a lateral flow strip and a qPCR melt curve assay were developed for specific detection of H. armigera DNA in pooled moth samples. In addition, a crude DNA extraction protocol for whole moths was developed to allow rapid preparation of DNA samples. The RPA field test was able to detect ≥ 10 pg of purified H. armigera DNA and the crude DNA of one H. armigera sample in a background of 999 H. zea equivalents. The qPCR assay was able to detect ≥ 100 fg of purified H. armigera DNA and the crude DNA of one H. armigera sample in a background of up to 99,999 H. zea equivalents. Both RPA and qPCR assays detected H. armigera in the crude DNA extracted in the field from a pool of one H. armigera moth and 999 H. zea moths. These newly developed molecular assays to detect H. armigera will contribute to large-scale surveillance programs of H. armigera.

Genomics reveals widespread hybridization across insects with ramifications for species boundaries and invasive species

As the amount of genomic data for non-model taxa grows, it is increasingly clear that gene flow across species barriers in insects is much more common than previously thought. In recent years, the decreased cost and increased accuracy of long-read sequencing has enabled the assembly of high-quality, reference genomes and chromosome maps for non-model insects. With this long-read data we can now not only compare variation across the genome among homologous genes between species, which has been the basis of phylogenetics for more than thirty years, but also tease apart evidence of ancient and recent hybridization and gene flow. The implications of hybridization for species adaptation may be more positive than previously considered, explaining its prevalence across many groups of insects. Unfortunately, due to anthropogenic actions, some pest species appear to be benefitting from hybridization and gene flow, facilitating future invasions.

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

Structural variation has been associated with genetic diversity and adaptation. Despite these observations, it is not clear what their relative importance is for evolution, especially in rapidly adapting species. Here, we examine the significance of structural polymorphisms in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, we develop highly contiguous reference genomes to characterize structural variation. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral nonpest individuals. We identify >200,000 structural variations, which appear to be nonrandomly distributed across the genome as they co-occur with transposable elements and genes. Structural variations intersect with exons in a large proportion of gene annotations (~20%) that are associated with insecticide resistance (including cytochrome P450s), development, and transcription. To understand the role structural variations play in adaptation, we measure their allele frequencies among an additional 57 individuals using whole genome resequencing data, which represents pest and nonpest populations of North America. Incorporating multiple independent tests to detect the signature of natural selection using SNP data, we identify 14 genes that are probably under positive selection, include structural variations, and SNPs of elevated frequency within the pest lineages. Among these, three are associated with insecticide resistance based on previous research. One of these genes, CYP4g15, is coinduced during insecticide exposure with glycosyltransferase-13, which is a duplicated gene enclosed within a structural variant adjacent to the CYP4g15 genic region. These results demonstrate the significance of structural variations as a genomic feature to describe species history, genetic diversity, and adaptation.

Spodoptera frugiperda: Ecology, Evolution, and Management Options of an Invasive Species

The fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera, Noctuidae), is a well-known agricultural pest in its native range, North and South America, and has become a major invasive pest around the globe in the past decade. In this review, we provide an overview to update what is known about S. frugiperda in its native geographic ranges. This is followed by discussion of studies from the invaded areas to gain insights into S. frugiperda's ecology, specifically its reproductive biology, host plant use, status of insecticide resistance alleles, and biocontrol methods in native and invasive regions. We show that reference to host strains is uninformative in the invasive populations because multidirectional introduction events likely underpinned its recent rapid spread. Given that recent genomic analyses show that FAW is much more diverse than was previously assumed, and natural selection forces likely differ geographically, region-specific approaches will be needed to control this global pest.

Complex multiple introductions drive fall armyworm invasions into Asia and Australia

The fall armyworm (FAW) Spodoptera frugiperda is thought to have undergone a rapid 'west-to-east' spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations in this study were overwhelmingly C- and R-strain hybrids (n = 252/262). SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved 'bridgehead populations' in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the 'African origin spread' nor the 'Myanmar source population to China' hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.

Resistance Bioassays and Allele Characterization Inform Analysis of Spodoptera frugiperda (Lepidoptera: Noctuidae) Introduction Pathways in Asia and Australia

The fall armyworm (FAW) Spodoptera frugiperda (Smith; Lepidoptera: Noctuidae) is present in over 70 countries in Africa, Asia, and Oceania. Its rapid dispersal since 2016 when it was first reported in western Africa, and associated devastation to agricultural productivity, highlight the challenges posed by this pest. Currently, its management largely relies on insecticide sprays and transgenic Bacillus thuringiensis toxins, therefore understanding their responses to these agents and characteristics of any resistance genes enables adaptive strategies. In Australia, S. frugiperda was reported at the end of January 2020 in northern Queensland and by March 2020, also in northern Western Australia. As an urgent first response we undertook bioassays on two Australian populations, one each from these initial points of establishment. To assist with preliminary sensitivity assessment, two endemic noctuid pest species, Helicoverpa armigera (Hübner; Lepidoptera, Noctuidae) and Spodoptera litura (Fabricius; Lepidoptera, Noctuidae), were concurrently screened to obtain larval LC50 estimates against various insecticides. We characterized known resistance alleles from the VGSC, ACE-1, RyR, and ABCC2 genes to compare with published allele frequencies and bioassay responses from native and invasive S. frugiperda populations. An approximately 10× LC50 difference for indoxacarb was detected between Australian populations, which was approximately 28× higher than that reported from an Indian population. Characterization of ACE-1 and VGSC alleles provided further evidence of multiple introductions in Asia, and multiple pathways involving genetically distinct individuals in Australia. The preliminary bioassay results and resistance allele patterns from invasive S. frugiperda populations suggest multiple introductions have contributed to the pest's spread and challenge the axiom of its rapid 'west-to-east' spread.

Subspecific Synonym of Monochamus alternatus (Coleoptera: Cerambycidae): Population Genetics and Morphological Reassessment

Monochamus alternatus Hope, 1842, is a major forest pest that hosts the pathogenic pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner and Buhrer, 1934) Nickle 1970. Taxonomically, M. alternatus is currently divided into two subspecies, based on morphology and geography: Monochamus alternatus alternatus Hope, 1842 in China, Taiwan, Tibet, Vietnam, and Laos and Monochamus alternatus endai Makihara, 2004 in South Korea and Japan. Despite their economic importance, the subspecies taxonomy of M. alternatus has never been tested after the first description. In this study, we aimed to reassess the subspecies taxonomy of M. alternatus using molecular and morphological data. For morphological analysis, we examined three major morphological characters (pronotal longitudinal band, granulation on humeri, and elytral proximomedial spine) from 191 individuals from China, Korea, and Taiwan. Population genetic structures were examined using 85 de novo sequences and 82 public COI sequences from China, Korea, Japan, Malaysia, Taiwan, and a few intercepted specimens from the United States. All the genetic data were aligned as three different multiple sequence alignments. Individuals from each subspecies were morphologically and genetically scattered, not clustered according to subspecies in any of the analyses. Therefore, a new synonymy is proposed: Monochamus alternatus Hope, 1842 = Monochamus alternatus endai, syn. n. This study suggests a more robust classification of M. alternatus for the first time and ultimately will pose a substantial impact on implementing quarantine or forestry policies.

Helicoverpa genus on the edge of the continental U.S.: Flight phenology, analysis of hybrid presence, and insecticide performance in high-input field crops in Puerto Rico

The genus Helicoverpa includes several agricultural pests globally. Helicoverpa armigera was reported in several countries in South America in 2013, and in Puerto Rico, in 2014. This territory is considered an agricultural hub, with a high-input system of seed production in the southern region of the island, and also at the edge of the continental U.S. Possible natural dispersion of populations of H. armigera from the Caribbean or other Central American regions poses a continuing risk to the U.S. This study was performed during the post-detection scenario of H. armigera in Puerto Rico, from 2018 to 2021. A year-round pheromone trapping program of adult males indicated an increase in the population from October to March and differences in the occurrence of Helicoverpa spp. between the municipalities Juan Diaz and Salinas. The proportion of H. armigera/H. zea and detection of congeneric hybrids between these species were assessed based on genital morphology and DNA analysis. Interestingly, neither H. armigera nor expected hybrids were detected in the present study. The susceptibility of H. zea populations to the insecticides Spinetoram, Emamectin benzoate, Chlorantraniliprole, and Esfenvalerate was assessed, and an overall significant effect of insecticide susceptibility was detected. Chlorantraniliprole and Emamectin benzoate had the highest efficacy. These results contribute to the Integrated Pest Management and Insect resistance management programs to Helicoverpa spp. in Puerto Rico. In addition, provide validated information to be considered in mitigation plans, in the scenario of an invasion of H. armigera in the continental U.S.

Utility and challenges of using whole-genome resequencing to detect emerging insect and mite resistance in agroecosystems

Arthropods that invade agricultural ecosystems systematically evolve resistance to the control measures used against them, and this remains a significant and ongoing challenge for sustainable food production systems. Early detection of resistance evolution could prompt remedial action to slow the spread of resistance alleles in the landscape. Historical approaches used to detect emerging resistance included phenotypic monitoring of agricultural pest populations, as well as monitoring of allele frequency changes at one or a few candidate pesticide resistance genes. In this article, I discuss the successes and limitations of these traditional monitoring approaches and then consider whether whole-genome scanning could be applied to samples collected from agroecosystems over time for resistance monitoring. I examine the qualities of agroecosystems that could impact application of this approach to pesticide resistance monitoring and describe a recent retrospective analysis where genome scanning successfully detected an oligogenic response to selection by pesticides years prior to pest management failure. I conclude by considering areas of further study that will shed light on the feasibility of applying whole-genome scanning for resistance risk monitoring in agricultural pest species.

Genetic Variation and Population Structure of the Old World Bollworm Helicoverpa armigera (Hübner, 1808) (Lepidoptera: Noctuidae) in Ethiopia

Helicoverpa armigera is one of the most destructive insect pests of economically valuable crops in the world. Despite its economic importance, the population genetic structure of this insect remains unexplored in Ethiopia. To investigate the genetic diversity and population structure of H. armigera, we sampled 170 individuals from 15 populations throughout Ethiopia. We sequenced a fragment of the mitochondrial cytochrome b (cyt b) gene and five exon-primed intron-crossing (EPIC) markers. Twenty cyt b haplotypes with low-to-moderate haplotype diversity (mean Hd = 0.537) and high nucleotide diversity (mean Pi = 0.00339) were identified. The most frequently observed and widely distributed cyt b haplotype was designated as Hap_1 (67.058%), which is identical to sequences found across the globe. Tajima's D and Fu's F for the cyt b data were negative, supporting a model of population expansion. Within populations, a mean of 2.493 alleles/locus was recorded across the five EPIC loci, ranging from 1.200 to 3.600 alleles/locus. The highest mean effective number of alleles/population was 2.369 and the lowest was 1.178. The mean observed heterozygosity (HO) of the five loci (0-0.289; mean 0.104 ± 0.020) was lower than the expected heterozygosity (HE) (0.095-0.523; mean 0.258 ± 0.028). AMOVA detected significant genetic structure with 61% of the total molecular genetic variation of EPIC genotypes occurring between populations, suggesting a considerable degree of differentiation among populations. STRUCTURE analyses clustered the H. armigera populations into three distinct population groups but very low isolation by distance (R2 = 0.0132, P < 0.05).

Genomic evidence of contemporary hybridization between Schistosoma species

Hybridization between different species of parasites is increasingly being recognised as a major public and veterinary health concern at the interface of infectious diseases biology, evolution, epidemiology and ultimately control. Recent research has revealed that viable hybrids and introgressed lineages between Schistosoma spp. are prevalent across Africa and beyond, including those with zoonotic potential. However, it remains unclear whether these hybrid lineages represent recent hybridization events, suggesting hybridization is ongoing, and/or whether they represent introgressed lineages derived from ancient hybridization events. In human schistosomiasis, investigation is hampered by the inaccessibility of adult-stage worms due to their intravascular location, an issue which can be circumvented by post-mortem of livestock at abattoirs for Schistosoma spp. of known zoonotic potential. To characterise the composition of naturally-occurring schistosome hybrids, we performed whole-genome sequencing of 21 natural livestock infective schistosome isolates. To facilitate this, we also assembled a de novo chromosomal-scale draft assembly of Schistosoma curassoni. Genomic analyses identified isolates of S. bovis, S. curassoni and hybrids between the two species, all of which were early generation hybrids with multiple generations found within the same host. These results show that hybridization is an ongoing process within natural populations with the potential to further challenge elimination efforts against schistosomiasis.

Genetic evidence of transoceanic migration of the small brown planthopper between China and Japan

BACKGROUND

The small brown planthopper, Laodelphax striatellus (Fallén), is an important pest of rice. It is suspected of migrating over the sea from China to Japan. However, where in China it comes from and how it affects Japanese populations remain unclear.

RESULTS

Here, we studied the genetic structure of 15 L. striatellus populations sampled from Japan and China using single nucleotide polymorphisms generated by the double digest restriction site-associated DNA sequencing technique. We found weak genetic differentiation between the Chinese and Japanese populations. Our data revealed migration signals of L. striatellus from China to southern and northern Japan. However, the source regions of the immigrants remain unclear due to the low genetic differentiation between populations. Our results also pointed to the possibility of backward gene flow from Japanese to Chinese populations. We suspect that the south-eastern wind associated with the East Asian summer monsoon may facilitate the reverse migration of L. striatellus from Japan to China. Interestingly, we found that the X chromosome displayed relatively higher genetic differentiation among populations and suffered more intensive selection pressure than autosomes.

CONCLUSION

We provide genetic evidence of transoceanic migration of L. striatellus from China to Japan and found that the X chromosome can aid the deciphering of the migration trajectories of species with low genetic differentiation. These findings have implications for forecasting the outbreak of this pest and also provide insights into how to improve the tracking of the migration routes of small insects via population genomics. © 2022 Society of Chemical Industry.

Global population genomic signature of Spodoptera frugiperda (fall armyworm) supports complex introduction events across the Old World

Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by its chronological detection across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range. 870 high-quality nuclear single nucleotide polymorphic DNA markers identified five distinct New World population clusters, broadly reflecting FAW native geographical ranges and the absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinning the pest’s global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated the potential of population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

This population genomics study identifies the complex multiple introduction history of Spodoptera frugiperda (fall armyworm) from the Americas, into Africa and Asia. This provides new insight into the ‘east-to-west’ directionality of gene flow, and suggests ample genomic exchange at the nuclear level.

Helicoverpa armigera and Helicoverpa zea hybridization: constraints, heterosis, and implications for pest management

BACKGROUND

The invasion of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) into the New World has made it possible for this pest to hybridize with a native American species, H. zea (Boddie), under natural conditions. We investigated the viability and development of hybrids of these two Helicoverpa species. We reared the parental species and evaluated crosses between H. armigera males and H. zea females and vice versa, two intercrosses between hybrids, and eight backcrosses between hybrids and parental species. We estimated the length of immature stages, fecundity, survival, sex ratio, and heterosis.

RESULTS

Although hybridization occcurred, with heterosis during the development of immatures, reproductive incompatibilities also were observed between the parental species and between hybrids from subsequent crosses. The interspecific crosses between hybrids and backcrosses confirmed the possibility of introgression events and their perpetuation in field populations. The results indicate that hybridization events are favored at high population levels, while at low population levels the 'species identities' will be maintained.

CONCLUSIONS

The possibility of interspecific gene flow and its perpetuation through successive crosses and backcrosses suggests several recommenations for management. Populations of both species should be maintained at an equilibrium level to reduce the chance of interspecific crosses, which are presumably more likely to occur during pest outbreaks. The existence of hybridization and resistance to different active pesticide ingredients should be monitored. All practices related to managing the resistance of these pests to chemical and biological insecticides should be systematized to reduce the chance of selecting for resistant individuals.

Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle

Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.

Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm

The cotton bollworm Helicoverpa armigera is a cosmopolitan pest and its diverse habitats plausibly contribute to the formation of diverse lineages. Despite the significant threat it poses to economic crops worldwide, its evolutionary history and genetic basis of local adaptation are poorly understood. In this study, we de novo assembled a high-quality chromosome-level reference genome of H. a. armigera (contig N50 = 7.34 Mb), with 99.13% of the HaSCD2 assembly assigned into 31 chromosomes (Z-chromosome + 30 autosomes). We constructed an ultra-dense variation map across 14 cotton bollworm populations and identified a novel lineage in northwestern China. Historical inference showed that effective population size changes coincided with global temperature fluctuation. We identified nine differentiated genes in the three H. armigera lineages (H. a. armigera, H. a. conferta, and the new northwestern Chinese lineage), of which per and clk genes are involved in circadian rhythm. Selective sweep analyses identified a series of GO categories related to climate adaptation, feeding behavior and insecticide tolerance. Our findings reveal fundamental knowledge of the local adaptation of different cotton bollworm lineages and will guide the formulation of cotton bollworm management measures at different scales.

Determinants of Insecticide Resistance Evolution: Comparative Analysis Among Heliothines

It is increasingly clear that pest species vary widely in their propensities to develop insecticide resistance. This review uses a comparative approach to analyze the key pest management practices and ecological and biochemical or genetic characteristics of the target that contribute to this variation. We focus on six heliothine species, three of which, Helicoverpa armigera, Heliothis virescens, and Helicoverpa zea, have developed resistances to many pesticide classes. The three others, Helicoverpa punctigera, Helicoverpa assulta, and Helicoverpa gelotopoeon, also significant pests, have developed resistance to very few pesticide classes. We find that host range and movement between alternate hosts are key ecological traits that influence effective selection intensities for resistance. Operational issues are also critical; area-wide, cross-pesticide management practices that account for these ecological factors are key to reducing selection intensity. Without such management, treatment using broad-spectrum chemicals serves to multiply the effects of host plant preference, preadaptive detoxification ability, and high genetic diversity to create a pesticide treadmill for the three high-propensity species.Without rigorous ongoing management, such a treadmill could still develop for newer, more selective chemistries and insecticidal transgenic crops.

Involvement of CYP2 and mitochondrial clan P450s of Helicoverpa armigera in xenobiotic metabolism

Insect CYP2 and mitochondrial clan P450s are relatively conserved genes encoding enzymes generally thought to be involved in biosynthesis or metabolism of endobiotics. However, emerging evidence argues they have potential roles in chemical defense as well, but their actual detoxification functions remain largely unknown. Here, we focused on the full complement of 8 CYP2 and 10 mitochondrial P450s in the generalist herbivore, Helicoverpa armigera. Their varied spatiotemporal expression profiles were analyzed and reflected their specific functions. For functional study of the mitochondrial clan P450s, the redox partners, adrenodoxin reductase (AdR) and adrenodoxin (Adx), were identified from genomes of eight insects and an efficient in vitro electron transfer system of mitochondrial P450 was established by co-expression with Adx and AdR of H. armigera. All CYP2 clan P450s and 8 mitochondrial P450s were successfully expressed in Sf9 cells and compared functionally. In vitro metabolism assays showed that two CYP2 clan P450s (CYP305B1 and CYP18A1) and CYP333B3 (mito clan) could epoxidize aldrin to dieldrin, while CYP305B1 and CYP339A1 (mito clan) have limited but significant hydroxylation capacities to esfenvalerate. CYP303A1 of the CYP2 clan exhibits high metabolic efficiency to 2-tridecanone. Screening the xenobiotic metabolism competence of CYP2 and mitochondrial clan P450s not only provides new insights on insect chemical defense but also can give indications on their physiological functions in H. armigera and other insects.

Hybridization Potential of Two Invasive Asian Longhorn Beetles

The Asian longhorned beetle (ALB), Anoplophora glabripennis (Motschulsky) and citrus longhorned beetle (CLB), Anoplophora chinensis (Förster) (both Coleoptera: Cerambycidae: Lamiinae), are high-risk invasive pests that attack various healthy hardwood trees. These two species share some similar host plants and overlapping distributions in large parts of their native ranges in China and the Korean peninsula as well as similar reproductive behaviors. The original Anoplophora malasiaca (Thomson) occurs in Japan and has been synonymized as CLB (hereafter referred to JCLB). In this study, a 30-min behavioral observation of paired adults, followed by a four-week exposure to host bolts, showed that ALB could not successfully cross with CLB. Mating was observed between female CLB and male ALB but not between female ALB and male CLB, no laid eggs hatched. JCLB males successfully crossed with ALB females to produce viable eggs although the overall percentage of hatched eggs was lower than those from conspecific mating pairs. However, ALB males could not successfully cross with JCLB females. CLB and JCLB mated and produced viable hybrid offspring and the hybrid F1 offspring eggs were fertile. These results suggest an asymmetrical hybridization between ALB and JCLB, and that both CLB and JCLB might be considered as two subspecies with different hybridization potential with congeneric ALB. Given their potential impacts on ecosystems and many economically important tree hosts, invasion of these geographically isolated species (ALB and JCLB) or distant subspecies (CLB and JCLB) into the same region may facilitate potential hybridization, which could be a potential concern for the management of these two globally important invasive forest pests. Further studies are needed to determine if fertile hybrid offspring are capable of breeding continually or backcrossing with parental offspring successfully.

Assay Optimization Can Equalize the Sensitivity of Real-Time PCR with ddPCR for Detection of Helicoverpa armigera (Lepidoptera: Noctuidae) in Bulk Samples

Simple Summary

Invasive species are a constant threat to agriculture throughout the world against which early detection is one of the primary defenses. The Old World bollworm is one of the most important invasive agricultural pests in the world. While historically absent from the Americas, this species was first found in South America in 2013 and poses an ongoing threat of spreading into North America. Surveys are conducted each year, which result in hundreds or thousands of traps that must be screened for this species. Unfortunately, the most common non-target is the native corn earworm, which is nearly identical morphologically to the Old World bollworm and cannot be easily separated. Molecular methods have been developed to screen these trap samples, but the required equipment is expensive and not commonly available. This study details improvements to current molecular methods that will allow for screening of bulk trap samples using standard laboratory instruments and protocols. The ability to perform these methods in nearly any molecular biology lab will greatly enhance our ability to detect and exclude this important pest.

Abstract

Helicoverpa armigera (Hübner) is one of the most important agricultural pests in the world. This historically Old World species was first reported in Brazil in 2013 and has since spread throughout much of South America and into the Caribbean. Throughout North America, H. armigera surveys are ongoing to detect any incursions. Each trap is capable of capturing hundreds of native Helicoverpa zea (Boddie). The two species cannot be separated without genitalic dissection or molecular methods. A ddPCR assay is currently used to screen large trap samples, but this equipment is relatively uncommon and expensive. Here, we optimized a newly designed assay for accurate and repeatable detection of H. armigera in bulk samples across both ddPCR and less costly, and more common, real-time PCR methods. Improvements over previously designed assays were sought through multiple means. Our results suggest bulk real-time PCR assays can be improved through changes in DNA extraction and purification, so that real-time PCR can be substituted for ddPCR in screening projects. While ddPCR remains a more sensitive method for detection of H. armigera in bulk samples, the improvements in assay design, DNA extraction, and purification presented here also enhance assay performance over previous protocols.

An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae)

An optimized high-quality DNA isolation protocol was developed using body segment tissue from the Fall Armyworm (Spodoptera frugiperda), that will allow documenting genetic variability based on biotypes, facilitating studies on the appearance, distribution and population dynamics of the fall armyworm at the molecular level. The resulting protocol is an easy-to-use, timesaving method that can rapidly achieve high quality, high-yielding total genomic DNA, using chemicals and everyday consumables available in a molecular laboratory. This new method of DNA extraction avoids the contamination of polysaccharides, salts, phenols, proteins and other cellular by-products that can interfere with subsequent reactions. DNA purity estimates reveal A260: A280 ratios greater than 1.9, which were evidenced by quality test on agarose gel, observing complete integrity and high purity of the resulting samples, and yielded 30–99 µg/g of total DNA. Therefore, the quality of the DNA produced from this extraction is suitable for subsequent molecular applications: (i) next generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes and (iv) gene cloning. In addition, to become an anticipating diagnostic tool for invasive lepidopteran larval stages:•

The resulting protocol is an easy-to-use time-saving method.

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This new extraction method prevents contamination from polysaccharides, salts, phenols, proteins, and other cellular sub-products.

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DNA purity estimations reveal A260:A280 ratios above 1.9.

Pyrethroid metabolism by eleven Helicoverpa armigera P450s from the CYP6B and CYP9A subfamilies

Lepidopteran P450s of the CYP6B and CYP9A subfamilies are thought to play important roles in host plant adaptation and insecticide resistance. An increasing number of paralogs and orthologs with high levels of sequence identity have been found in these subfamilies by mining recent genome projects. However, the biochemical function of most of them remains unknown. A better understanding of the evolution of P450 genes and of the catalytic competence of the enzymes they encode is needed to facilitate studies of host plant use and insecticide resistance. Here, we focused on the full complement of CYP6B (4 genes) and CYP9A (7 genes) in the generalist herbivore, Helicoverpa armigera. These P450s were heterologously expressed in Sf9 cells and compared functionally. In vitro assays showed that all CYP6B and CYP9A P450s can metabolize esfenvalerate efficiently, except for the evolutionarily divergent CYP6B43. A new 2'-hydroxy-metabolite of esfenvalerate was identified and found to be the main metabolite produced by CYP9A12. All tested P450s showed only low induction responses to esfenvalerate. To put these results from H. armigera P450s in perspective, 158 complete CYP6B and 100 complete CYP9A genes from 34 ditrysian species were manually curated. The CYP9A subfamily was more widespread than the CYP6B subfamily and the latter showed dramatic gains and losses, with ten species lacking CYP6B genes. Two adjacent CYP6B loci were found on chromosome 21, with different fates during the evolution of Lepidoptera. The diversity and functional redundancy of CYP6B and CYP9A genes challenge resistance management and pest control strategies as many P450s are available to insects to cope with chemical stresses they encounter.

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.

Saltational evolution of a pesticide-metabolizing cytochrome P450 in a global crop pest

BACKGROUND

The cotton bollworm, Helicoverpa armigera (Hübner), is a damaging insect pest threatening agricultural crops worldwide as a result of its resistance to insecticides. Metabolic resistance to pyrethroid insecticides is conferred by the chimeric P450 enzyme CYP337B3, produced by unequal crossing-over between CYP337B1 and CYP337B2. CYP337B3 is 99.7% similar to CYP337B1 except for the 177 N-terminal amino acids (AAs) containing the substrate recognition site 1 from CYP337B2. Here, we studied the structure-function relationship of CYP337B3 and CYP337B1 to determine the AAs that enable CYP337B3 to efficiently hydroxylate the 4'-carbon position of fenvalerate, which neither CYP337B1 nor CYP337B2 can do.

RESULTS

Site-directed mutagenesis showed that the L114F substitution in CYP337B3 reduced its 4'-hydroxylation activity by 89%, but the reciprocal F114L substitution in CYP337B1 increased its 4'-hydroxylation activity to only 49% of the level of CYP337B3. Docking models showed that AA 114 seems to have different functions in CYP337B1 and CYP337B3. Antibodies detected two- to three-fold more CYP337B1 than CYP337B3 in larval cuticle, which along with a 49% 4'-hydroxylation activity increase due to a F114L substitution in vivo might be expected to provide as much protection for the larva against exposure to fenvalerate as CYP337B3. However, CYP337B3 is present at much higher frequencies than CYP337B1-CYP337B2 in most populations, including those recently invading South America.

CONCLUSION

The metabolic resistance to pyrethroids in H. armigera has evolved by saltational evolution - by a single mutation, an unequal crossing-over, producing a larger selective advantage than could be attained gradually by stepwise improvement of the parental enzyme. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Evaluating Cross-Resistance to Cry and Vip Toxins in Four Strains of Helicoverpa armigera With Different Genetic Mechanisms of Resistance to Bt Toxin Cry1Ac

Evolution of resistance by pests has diminished the efficacy of transgenic crops producing insecticidal proteins from Bacillus thuringiensis (Bt). In China, where transgenic cotton producing Bt toxin Cry1Ac has been planted since 1997, field control failures have not been reported but the frequency of resistance to Cry1Ac has increased in the cotton bollworm, Helicoverpa armigera. This provides incentive to switch to multi-toxin Bt cotton, which is grown in many other countries. Previous work created four laboratory strains of H. armigera with >100-fold resistance to Cry1Ac, with the genetic basis of resistance known in all but the LF256 strain. Here, we analyzed the genetic basis of resistance in Cry1Ac in LF256 and evaluated cross-resistance of all four strains to three toxins produced by widely planted multi-toxin Bt cotton: Cry1Fa, Cry2Ab, and Vip3Aa. DNA sequencing revealed that LF256 lacked the mutations in three genes (HaTSPAN1, HaABCC2, and HaABCC3) that confer resistance to Cry1Ac in two other strains of H. armigera we analyzed. Together with previous results, the data reported here show that each of the four strains examined has a different genetic basis of resistance to Cry1Ac. Significant positive cross-resistance occurred to Cry1Fa in three of the four strains tested but not to Cry2Ab or Vip3Aa in any strain. Thus, Cry2Ab and Vip3Aa are likely to be especially valuable for increasing the efficacy and durability of Bt cotton against H. armigera populations that have some resistance to Cry1Ac.

Whole-genome sequencing to detect mutations associated with resistance to insecticides and Bt proteins in Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a major pest native to the Americas that has recently invaded the Old World. Point mutations in the target-site proteins acetylcholinesterase-1 (ace-1), voltage-gated sodium channel (VGSC) and ryanodine receptor (RyR) have been identified in S. frugiperda as major resistance mechanisms to organophosphate, pyrethroid and diamide insecticides respectively. Mutations in the adenosine triphosphate-binding cassette transporter C2 gene (ABCC2) have also been identified to confer resistance to Cry1F protein. In this study, we applied a whole-genome sequencing (WGS) approach to identify point mutations in the target-site genes in 150 FAW individuals collected from China, Malawi, Uganda and Brazil. This approach revealed three amino acid substitutions (A201S, G227A and F290V) of S. frugiperda ace-1, which are known to be associated with organophosphate resistance. The Brazilian population had all three ace-1 point mutations and the 227A allele (mean frequency = 0.54) was the most common. Populations from China, Malawi and Uganda harbored two of the three ace-1 point mutations (A201S and F290V) with the 290V allele (0.47-0.58) as the dominant allele. Point mutations in VGSC (T929I, L932F and L1014F) and RyR (I4790M and G4946E) were not detected in any of the 150 individuals. A novel 12-bp insertion mutation in exon 15 of the ABCC2 gene was identified in some of the Brazilian individuals but absent in the invasive populations. Our results not only demonstrate robustness of the WGS-based genomic approach for detection of resistance mutations, but also provide insights for improvement of resistance management tactics in S. frugiperda.

On species delimitation, hybridization and population structure of cassava whitefly in Africa

The Bemisia cassava whitefly complex includes species that cause severe crop damage through vectoring cassava viruses in eastern Africa. Currently, this whitefly complex is divided into species and subgroups (SG) based on very limited molecular markers that do not allow clear definition of species and population structure. Based on 14,358 genome-wide SNPs from 62 Bemisia cassava whitefly individuals belonging to sub-Saharan African species (SSA1, SSA2 and SSA4), and using a well-curated mtCOI gene database, we show clear incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. We show that the SSA4 species is nested within SSA2, and that populations of the SSA1 species comprise well-defined south-eastern (Madagascar, Tanzania) and north-western (Nigeria, Democratic Republic of Congo, Burundi) putative sub-species. Signatures of allopatric incipient speciation, and the presence of a 'hybrid zone' separating the two putative sub-species were also detected. These findings provide insights into the evolution and molecular ecology of a highly cryptic hemipteran insect complex in African, and allow the systematic use of genomic data to be incorporated in the development of management strategies for this cassava pest.

Helicoverpa armigera Harm 1 Haplotype Predominates in the Heliothinae (Lepidoptera: Noctuidae) Complex Infesting Tomato Crops in Brazil

Tomato (Solanum lycopersicum L.) is a natural host for the Helicoverpa-Chloridea (Lepidoptera: Noctuidae: Heliothinae) pest complex. The species Helicoverpa armigera (Hübner) was responsible for significant yield losses in several crops after its detection in Brazil. The morphology of its larval stage resembles common Heliothinae species, making pest control decisions difficult. The overall lack of studies on the Heliothinae associated with tomatoes in Brazil and the establishment of H. armigera in the country plus their recent outbreaks supported our investigation about the relative importance of the insects from the Helicoverpa-Chloridea complex in this vegetable crop. A nationwide survey was carried out across fresh-market and processing tomato fields. Molecular analyses targeting a segment of the mitochondrial cytochrome oxidase subunit I (mtCOI) gene and their sequence analyses indicated the presence of a pest complex, comprising the introduced species H. armigera and the indigenous species, Helicoverpa zea (Boddie), and Chloridea virescens (Fabricius). The Harm 1 haplotype of H. armigera was identified as the predominant Heliothinae pest infesting fresh-market tomatoes. The New World species Chloridea subflexa (Guenée) as well as the exotic Solanaceae-specific species Helicoverpa assulta (Guenée) were not found in our survey. Additional larvae surveys in processing tomato fields during 2013/2014 in Central Brazil also indicated H. armigera as the most abundant Heliothinae species (95%) together with H. zea (4.75%) and C. virescens (0.25%). The occurrence of distinct Helicoverpa species (which are potentially capable of interbreeding) indicates that novel crop management strategies will be necessary in order to minimize damages caused by this pest complex in tomatoes.

Host plant use of Helicoverpa spp. (Lepidoptera: Noctuidae) in the Brazilian agricultural landscape

BACKGROUND

The Old-World bollworm, Helicoverpa armigera (Hübner), was recently documented attacking cotton and soybean plants in Brazil; however, restricted basic knowledge on host plant interactions and landscape use in Brazil have limited the effectiveness of control measures. In this study, we evaluated the suitability of different crops commonly cultivated in Brazil as hosts for H. armigera and H. zea, and examined their contribution to the establishment and size of H. armigera and H. zea field populations. We also estimated the proportions of H. armigera and H. zea moths that used cotton, noncotton C₃ plants, and C₄ plants as hosts in four regions in Brazil through the length of the cropping season.

RESULTS

Viability of H. armigera larvae was highest on cotton (46.1%), followed by millet (39.5%), sorghum (31.2%), soybean (24.2%), and maize (21.1%). Noncotton C₃ hosts served as the major source of H. armigera moths in all regions evaluated, and C₄ hosts were a source of H. armigera mainly in regions where winter maize is typically cultivated. H. armigera moths that used cotton plants as natal hosts were observed during the reproductive stage of the crop mainly in the state of Bahia. Only C₄ host plants were a consistent source of H. zea moths, primarily when maize was in the reproductive stage. H. armigera individuals were the main species infesting cotton and soybean fields while H. zea individuals were the main species infesting maize ears.

CONCLUSIONS

Regional differences in the host use and population dynamics of H. armigera among the regions evaluated may be attributed to variation in alternative host utilization (crops, noncrops, and weeds) and the possible occurrence of facultative diapause and or migration.

Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in Brazil: the Big Outbreak Monitored by Light Traps

The first detection of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) in Brazil pointed to a gloomy future for South American agriculture in the 2012/2013 harvest, and insecticide sales increased exponentially during 2013 and 2014. However, after this outbreak, the population of this insect returned to manageable levels. This study documents data on H. armigera moth collection using light traps during the outbreak in two locations: (a) western region of the state of Bahia, including population levels of H. armigera and main noctuid pests during the big outbreak (February and March 2013); (b) Federal District, including monthly data for five growing seasons (July 2012-June 2017). During the outbreak, an average of 527.3 moths were collected per trap (cotton crop, March) in the western region of Bahia each night, while the maximum average in the Federal District was 75.4 moths (January). The number of moths decreased in the following growing seasons, and in October 2016, the maximum number was 2.8 moths per trap. Aspects related to the variations of H. armigera and Helicoverpa zea (Boddie) populations, including the study of phenology and relationship with climatic factors and Oceanic Niño Index, were analyzed and discussed. All aspects are approached to contribute to the management of lepidopteran pests, especially H. armigera, in the productive systems of the Brazilian Cerrado.

Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm

BACKGROUND

The process of speciation involves differentiation of whole genome sequences between a pair of diverging taxa. In the absence of a geographic barrier and in the presence of gene flow, genomic differentiation may occur when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host-plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that genomic differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for genomic differentiation in the fall armyworm.

RESULTS

These two strains exhibit a low level of genomic differentiation (FST = 0.0174), while 99.2% of 200 kb windows have genetically differentiated sequences (FST > 0). We found that the combined effect of mild positive selection and genetic linkage to selectively targeted loci are responsible for the genomic differentiation. However, a single event of very strong positive selection appears not to be responsible for genomic differentiation. The contribution of chromosomal inversions or tight genetic linkage among positively selected loci causing reproductive barriers is not supported by our data. Phylogenetic analysis shows that the genomic differentiation occurred by sub-setting of genetic variants in one strain from the other.

CONCLUSIONS

From these results, we concluded that genomic differentiation may occur at the early stage of a speciation process in the fall armyworm and that mild positive selection targeting many loci alone is sufficient evolutionary force for generating the pattern of genomic differentiation. This genomic differentiation may provide a condition for accelerated genomic differentiation by synergistic effects among linkage disequilibrium generated by following events of positive selection. Our study highlights genomic differentiation as a key evolutionary factor connecting positive selection to divergent selection.

Increased insect herbivore performance under elevated CO2 is associated with lower plant defence signalling and minimal declines in nutritional quality

Changes in insect herbivore performance under elevated atmosphere carbon dioxide concentrations e[CO₂] are often driven by changes in the nutritional and defensive chemistry of their host plants. Studies addressing how the prolific pest cotton bollworm (Helicoverpa armigera) responds to e[CO₂] show that performance usually declines, often associated with lower nutritional (e.g. nitrogen (N) concentrations) quality of host plants under e[CO₂]. We investigated the impacts of e[CO₂] on nutritional quality and anti-herbivore (jasmonate) defensive signalling in lucerne (Medicago sativa) when challenged by H. armigera. While foliar N decreased under e[CO₂], other aspects of nutritional quality (soluble protein, amino acids, foliar C:N) were largely unaffected, potentially due to increased root nodulation under e[CO₂]. In contrast, e[CO₂] greatly reduced jasmonate signalling in M. sativa following H. armigera attack; jasmonic acid concentrations were ca. 56% lower in attacked plants grown under e[CO₂]. Concurrent with this, relative growth rates of H. armigera were ca. 66% higher when feeding on e[CO₂]-grown plants. In contrast with previous reports, which we meta-analytically summarise, we provide the first evidence that H. armigera performance can increase under e[CO₂]. This may occur in plants, such as M. sativa, where e[CO₂] has limited impacts on nutritional quality yet reduces jasmonate defence signalling.

Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Invasive Helicoverpa armigera Moths

Hybridization between invasive and native species has raised global concern, given the dramatic increase in species range shifts and pest outbreaks due to anthropogenic dispersal. Nevertheless, secondary contact between sister lineages of local and invasive species provides a natural laboratory to understand the factors that determine introgression and the maintenance or loss of species barriers. Here, we characterize the early evolutionary outcomes following secondary contact between invasive Helicoverpa armigera and native H. zea in Brazil. We carried out whole-genome resequencing of Helicoverpa moths from Brazil in two temporal samples: during the outbreak of H. armigera in 2013 and 2017. There is evidence for a burst of hybridization and widespread introgression from local H. zea into invasive H. armigera coinciding with H. armigera expansion in 2013. However, in H. armigera, the admixture proportion and the length of introgressed blocks were significantly reduced between 2013 and 2017, suggesting selection against admixture. In contrast to the genome-wide pattern, there was striking evidence for adaptive introgression of a single region from the invasive H. armigera into local H. zea, including an insecticide resistance allele that increased in frequency over time. In summary, despite extensive gene flow after secondary contact, the species boundaries are largely maintained except for the single introgressed region containing the insecticide-resistant locus. We document the worst-case scenario for an invasive species, in which there are now two pest species instead of one, and the native species has acquired resistance to pyrethroid insecticides through introgression.

CRISPR-mediated gene knockout reveals nicotinic acetylcholine receptor (nAChR) subunit α6 as a target of spinosyns in Helicoverpa armigera

BACKGROUND

The spinosyn insecticides (spinosad and spinetoram) have been intensively used to control a wide range of agricultural pests. However, resistance to spinosyns has evolved in several agricultural pests. Disruption of the nicotinic acetylcholine receptor subunit α6 (nAChRα6) has been associated with high levels of resistance to spinosyns in both field and laboratory-selected strains of several insect pests. Among the 12 nAChR subunits of Helicoverpa armigera, Haα6 has the closest sequence similarity (66.02%) to Haα7. Here we used CRISPR-mediated knockouts to evaluate the role of two nAChR subunits (Haα6 and Haα7) of H. armigera in toxicity of spinosyns.

RESULTS

Individual knockouts of Haα6 and Haα7 were created utilizing CRISPR/Cas9 system in H. armigera. The Haα6 knockout (Haα6-KO) strain exhibited high levels of resistance to spinosad (531-fold) and spinetoram (1105-fold) compared with the wild-type parent SCD strain, whereas the Haα7 knockout (Haα7-KO) strain showed no significant susceptibility changes to both spinosyns. Genetic analyses demonstrated that resistance to spinosad conferred by knockout of Haα6 was autosomal, incompletely recessive and tightly linked to the disruption mutation of Haα6. Both Haα6-KO and Haα7-KO strains had no significant effects on susceptibility to other four insecticides including emamectin benzoate, beta-cypermethrin, chlorantraniliprole and indoxacarb.

CONCLUSION

Our results provide in vivo functional evidence for Haα6 as a target of spinosyns in H. armigera, and little or no role of Haα7 in mediating toxicity of spinosyns. The results are valuable to the development of resistance monitoring and management methods for spinosyn resistance in H. armigera. © 2020 Society of Chemical Industry.

Arthropod Invasions Versus Soybean Production in Brazil: A Review

Soybean production in Brazil has been markedly affected by invasions of non-native arthropod species that feed on the crop, severely impacting biodiversity, food security, health, and economic development. Data on soybean production losses and increase in insecticide usage over the last two decades have not been explored in association with past invasion events, and the dynamics underlying the recent blitz of invasive species into Brazil remain largely unclear. We provide a review of arthropod invasions in the Brazilian soybean agroecosystem since 1990, indicating that the introductions of Bemisia tabaci (Gennadius) MEAM1 (Hemiptera: Aleyrodidae), Tetranychus urticae (Koch) (Acari: Tetranychidae), and Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) are likely correlated with periods of increase in insecticide usage for soybean production. Using these three cases as examples, we review factors that could lead to increased likelihood of future invasions by particular pests, outlining four possible criteria to evaluate potential invasiveness of non-native arthropods: likelihood of entry, likelihood of establishment, biological features of the species, and availability of control measures. Spodoptera litura (F.) (Lepidoptera: Noctuidae) and Aphis glycines (Matsumura) (Hemiptera: Sternorrhynca) are examples of highly damaging soybean pests, related to one or more of these factors, that could be introduced into Brazil over the next years and which could lead to problematic scenarios. Melanagromyza sojae (Zehnter) (Diptera: Agromyzidae) also meets these criteria and has successfully invaded and colonized Brazilian soybean fields in recent years. Our review identifies current issues within soybean pest management in Brazil and highlights the need to adopt management measures to offset future costs and minimize lost revenue.