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

In vivo functional analysis of the cotton bollworm Helicoverpa armigera 24-dehydrocholesterol reductase (HaDHCR24) in phytosterol metabolism

Insects have to obtain sterols from food due to the inability to synthesize this essential nutrient de novo. For lepidopteran insects, they can convert a variety of phytosterols into cholesterol to meet their growth needs. The final step of the cholesterol biosynthesis is the metabolism of desmosterol catalyzed by 24-dehydrocholesterol reductase (DHCR24). In this study, we identified a DHCR24 homolog in the cotton bollworm Helicoverpa armigera, designated as H. armigera 24-dehydrocholesterol reductase (HaDHCR24)-1. The quantitative expression analyses indicated that HaDHCR24-1 was highly enriched in the midgut where dietary sterol uptake occurs. Compared to the control, the DHCR24-1 mutant larvae generated by clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated nuclease 9 technology accumulated more desmosterol in the gut, while the content of cholesterol was significantly reduced. A similar phenomenon was observed when the DHCR24 inhibitor, amiodarone, was applied to the insects. Moreover, DHCR24-1 played an important role for the usage of β-sitosterol, a major sterol in plants, in H. armigera, and loss of function of DHCR24-1 resulted in higher mortality on β-sitosterol. However, the DHCR24 homolog does not necessarily exist in the genomes of all insects. The loss of this gene occurred more frequently in the insects feeding on animals, which further support the role of DHCR24-1 in using phytosterols. This gene may have important potential in developing new strategies to control herbivory pests in Lepidoptera and other insect orders.

Extreme genetic signatures of local adaptation in a notorious rice pest, Chilo suppressalis

Climatic variation stands as a significant driving force behind genetic differentiation and the evolution of adaptive traits. Chilo (C.) suppressalis, commonly known as the rice stem borer, is a highly destructive pest that crucially harms rice production. The lack of natural population genomics data has hindered a more thorough understanding of its climate adaptation, particularly the genetic basis underlying adaptive traits. To overcome this obstacle, our study employed completely resequenced genomes of 384 individuals to explore the population structure, demographic history, and gene flow of C. suppressalis in China. This study observed that its gene flow occurred asymmetrically, moving from central populations to peripheral populations. Using genome-wide selection scans and genotype-environment association studies, we identified potential loci that may be associated with climatic adaptation. The most robust signal was found to be associated with cold tolerance, linked to a homeobox gene, goosecoid (GSC), whose expression level was significantly different in low and high latitudes. Moreover, downregulating the expression of this gene by RNAi enhances its cold tolerance phenotypes. Our findings have uncovered and delved into the genetic foundation of the ability of C. suppressalis to adapt to its environment. This is essential in ensuring the continued effectiveness and sustainability of novel control techniques.

Genomic predictions of invasiveness and adaptability of the cotton bollworm in response to climate change

Agricultural pests cause enormous losses in annual agricultural production. Understanding the evolutionary responses and adaptive capacity of agricultural pests under climate change is crucial for establishing sustainable and environmentally friendly agricultural pest management. In this study, we integrate climate modeling and landscape genomics to investigate the distributional dynamics of the cotton bollworm (Helicoverpa armigera) in the adaptation to local environments and resilience to future climate change. Notably, the predicted inhabitable areas with higher suitability for the cotton bollworm could be eight times larger in the coming decades. Climate change is one of the factors driving the dynamics of distribution and population differentiation of the cotton bollworm. Approximately 19,000 years ago, the cotton bollworm expanded from its ancestral African population, followed by gradual occupations of the European, Asian, Oceanian, and American continents. Furthermore, we identify seven subpopulations with high dispersal and adaptability which may have an increased risk of invasion potential. Additionally, a large number of candidate genes and SNPs linked to climatic adaptation were mapped. These findings could inform sustainable pest management strategies in the face of climate change, aiding future pest forecasting and management planning.

The genetic architecture of resistance to flubendiamide insecticide in Helicoverpa armigera (Hübner)

Insecticide resistance is a major problem in food production, environmental sustainability, and human health. The cotton bollworm Helicoverpa armigera is a globally distributed crop pest affecting over 300 crop species. H. armigera has rapidly evolved insecticide resistance, making it one of the most damaging pests worldwide. Understanding the genetic basis of insecticide resistance provides insights to develop tools, such as molecular markers, that can be used to slow or prevent the evolution of resistance. We explore the genetic architecture of H. armigera resistance to a widely used insecticide, flubendiamide, using two complementary approaches: genome-wide association studies (GWAS) in wild-caught samples and quantitative trait locus (QTL) mapping in a controlled cross of susceptible and resistant laboratory strains. Both approaches identified one locus on chromosome 2, revealing two SNPs within 976 bp that can be used to monitor field resistance to flubendiamide. This was the only region identified using linkage mapping, though GWAS revealed additional sites associated with resistance. Other loci identified by GWAS in field populations contained known insecticide detoxification genes from the ATP-binding cassette family, ABCA1, ABCA3, ABCF2 and MDR1. Our findings revealed an oligogenic genetic architecture, contrasting previous reports of monogenic resistance associated with the ryanodine receptor. This work elucidates the genetic basis of rapidly evolving insecticide resistance and will contribute to developing effective insecticide resistance management strategies.

A midgut transcriptional regulatory loop favors an insect host to withstand a bacterial pathogen

Mounting evidence suggests that insect hormones associated with growth and development also participate in pathogen defense. We have discovered a previously undescribed midgut transcriptional control pathway that modulates the availability of 20-hydroxyecdysone (20E) in a worldwide insect pest (Plutella xylostella), allowing it to defeat the major virulence factor of an insect pathogen Bacillus thuringiensis (Bt). A reduction of the transcriptional inhibitor (PxDfd) increases the expression of a midgut microRNA (miR-8545), which in turn represses the expression of a newly identified ecdysteroid-degrading glucose dehydrogenase (PxGLD). Downregulation of PxGLD reduces 20E degradation to increase 20E titer and concurrently triggers a transcriptional negative feedback loop to mitigate 20E overproduction. The moderately elevated 20E titer in the midgut activates a MAPK signaling pathway to increase Bt tolerance/resistance. These findings deepen our understanding of the functions attributed to these classical insect hormones and help inform potential future strategies that can be employed to control insect pests.

The genome sequence of the Cotton Bollworm moth, Helicoverpa armigera (Hübner, 1808)

We present a genome assembly from an adult female Cotton Bollworm moth, Helicoverpa armigera (Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 362.20 megabases. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.

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.

The novel function of an orphan pheromone receptor reveals the sensory specializations of two potential distinct types of sex pheromones in noctuid moth

Sex pheromones play crucial role in mating behavior of moths, involving intricate recognition mechanisms. While insect chemical biology has extensively studied type I pheromones, type II pheromones remain largely unexplored. This study focused on Helicoverpa armigera, a representative species of noctuid moth, aiming to reassess its sex pheromone composition. Our research unveiled two previously unidentified candidate type II sex pheromones-3Z,6Z,9Z-21:H and 3Z,6Z,9Z-23:H-in H. armigera. Furthermore, we identified HarmOR11 as an orphan pheromone receptor of 3Z,6Z,9Z-21:H. Through AlphaFold2 structural prediction, molecular docking, and molecular dynamics simulations, we elucidated the structural basis and key residues governing the sensory nuances of both type I and type II pheromone receptors, particularly HarmOR11 and HarmOR13. This study not only reveals the presence and recognition of candidate type II pheromones in a noctuid moth, but also establishes a comprehensive structural framework for PRs, contributing to the understanding of connections between evolutionary adaptations and the emergence of new pheromone types.

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.

Population genomics of Agrotis segetum provide insights into the local adaptive evolution of agricultural pests

BACKGROUND

The adaptive mechanisms of agricultural pests are the key to understanding the evolution of the pests and to developing new control strategies. However, there are few studies on the genetic basis of adaptations of agricultural pests. The turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) is an important underground pest that affects a wide range of host plants and has a strong capacity to adapt to new environments. It is thus a good model for studying the adaptive evolution of pest species.

RESULTS

We assembled a high-quality reference genome of A. segetum using PacBio reads. Then, we constructed a variation map of A. segetum by resequencing 98 individuals collected from six natural populations in China. The analysis of the population structure showed that all individuals were divided into four well-differentiated populations, corresponding to their geographical distribution. Selective sweep analysis and environmental association studies showed that candidate genes associated with local adaptation were functionally correlated with detoxification metabolism and glucose metabolism.

CONCLUSIONS

Our study of A. segetum has provided insights into the genetic mechanisms of local adaptation and evolution; it has also produced genetic resources for developing new pest management strategies.

Genome-Wide Scanning Loci and Differentially Expressed Gene Analysis Unveils the Molecular Mechanism of Chlorantraniliprole Resistance in Spodoptera frugiperda

Chlorantraniliprole has been widely used to controlSpodoptera frugiperda, but it has led to the development of chlorantraniliprole resistance. Multiomics analysis of strains with two extreme traits helps to elucidate the complex mechanisms involved. Herein, following genome resequencing and application of the Euclidean distance algorithm, 550 genes within a 16.20-Mb-linked region were identified from chlorantraniliprole-resistant (Ch-R) and chlorantraniliprole-susceptible (Ch-Sus) strains. Using transcriptome sequencing, 2066 differentially expressed genes were identified between Ch-R and Ch-Sus strains. Through association analysis, three glutathione S-transferase family genes and four trehalose transporter genes were selected for functional verification. Notably, SfGSTD1 had the strongest binding ability with chlorantraniliprole and is responsible for chlorantraniliprole tolerance. The Ch-R strain also increased the intracellular trehalose content by upregulating the transcription of SfTret1, thereby contributing to chlorantraniliprole resistance. These findings provide a new perspective to reveal the mechanism of resistance of agricultural pests to insecticides.