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

Chromosome-level genome assembly and comparative genomics shed light on Helicoverpa assulta ecology and pest management

BACKGROUND

The Oriental tobacco budworm, Helicoverpa assulta, a specialist herbivorous insect that exclusively feeds on plants of the Solanaceae family, causes considerable damage to crops, such as tobacco and hot pepper. The absence of a genome sequence for this species hinders further research on its pest management and ecological adaptation.

RESULTS

Here, we present a high-quality chromosome-level genome of a Korean strain of H. assulta (Pyeongchang strain, K18). The total assembly spans 424.4 Mb with an N50 length of 14.54 Mb and 37% GC content. The assembled genome (ASM2961881v1) comprises 31 chromosomes, similar to other congeneric generalist species including H. armigera and H. zea. In terms of genomic assembly quality, the complete BUSCOs and repeat content accounted for 98.3% and 33.01% of the genome, respectively. Based on this assembly, 19 485 protein-coding genes were predicted in the genome annotation. A comparative analysis was conducted using the identified number of protein-coding genes in H. armigera (24154) and H. zea (23696). Out of the 19 485 predicted genes, 137 genes in 15 orthogroups were found to have expanded significantly in H. assulta, while 149 genes in 95 orthogroups contracted rapidly.

CONCLUSION

This study revealed specific gene expansions and contractions in H. assulta compared to those in its close relatives, indicating potential adaptations related to its specialized feeding habits. Also, the comparative genome analysis provides valuable insights for the integrated pest management of H. assulta and other globally significant pests in the Heliothinae subfamily. © 2024 Society of Chemical Industry.

A chromosome-level genome assembly of Sesamia inferens

The pink stem borer, Sesamia inferens (Walker), is a significant polyphagous pest historically restricted to regions south of N34° latitude. However, with changes in global climate and farming practices, the distribution of this moth has progressively exceeded its traditional limit of 34° N and encompassed most regions in North China. The genetic adaptations of S. inferens remain incompletely understood due to the lack of high-quality genome resources. Here, we sequenced the genome of S. inferens using PacBio and Hi-C technology, yielding a genome assembly of 865.04 Mb with contig N50 of 1.23 Mb. BUSCO analysis demonstrated this genome assembly has a high-level completeness of 96.1% gene coverage. In total, 459.72 Mb repeat sequences (53.14% of the assembled genome) and 20858 protein-coding genes were identified. We used the Hi-C technique to anchor 1135 contigs to 31 chromosomes, yielding a chromosome-level genome assembly with a scaffold N50 of 29.99 Mb. In conclusion, our high-quality genome assembly provided valuable resource that exploring the genetic characteristics of local adaptation and developing an efficient control strategy.

Reduced expression of the P-glycoprotein gene HaABCB1 is linked to resistance to Bacillus thuringiensis Cry1Ac toxin but not Cry2Ab toxin in Helicoverpa armigera

Rapid evolution of pest resistance to Bt insecticidal proteins presents a serious threat to the sustainable use of Bt crops. The cotton bollworm has been extensively exposed to Bt cotton worldwide and has evolved resistance in laboratory and field. Previous studies have highlighted the significant roles played by the ABC transporter proteins in Bt resistance. In this study, the ORF of HaABCB1 was cloned and analyzed. The expression of HaABCB1 was detected in all developmental stages and tissues, with the highest expression in third instar larvae stage and hindgut tissue. Compared with susceptible strain, a remarkable decrease of HaABCB1 expression in Cry1Ac resistant strain while no significant change in Cry2Ab resistant strain were found. The HaABCB1 expression reduced after susceptible larvae induced by Cry1Ac, but no obvious expression changes after Cry2Ab exposure. RNAi-mediated down-regulation of HaABCB1 could lead to a significant reduction in larval susceptibility to Cry1Ac, but not to Cry2Ab, in susceptible strain. Genetic linkage analysis confirmed that decreased expression of the HaABCB1 mediates resistance to Cry1Ac, but not Cry2Ab resistance. This knowledge contributes to better understanding of the complex molecular mechanisms underlying Bt resistance and provide theoretical foundation for the development of new strategies for pest resistance management.

Overexpression of the F116V allele of CYP9A186 in transgenic Helicoverpa armigera confers high-level resistance to emamectin benzoate

Insect cytochrome P450s play important roles in the detoxification of xenobiotics and the metabolic resistance to insecticides. However, the approach for in vivo validation of the contribution of specific candidate P450s to resistance is still limited in most non-model insect species. Previous studies with heterologous expression and in vitro functional assays have confirmed that a natural substitution (F116V) in the substrate recognition site 1 (SRS1) of the CYP9A186 of Spodoptera exigua is a gain-of-function mutation, which results in detoxification capability of and thus high-level resistance to both emamectin benzoate (EB) and abamectin. In this study, we established an effective piggyBac-based transformation system in the serious agricultural pest Helicoverpa armigera and overexpressed in vivo a resistance P450 allele, CYP9A186-F116V, from another lepidopteran pest Spodoptera exigua. Bioassays showed that transgenic H. armigera larvae expressing CYP9A186-F116V obtained 358-fold and 38.6-fold resistance to EB and abamectin, respectively. In contrast, a transgenic line of Drosophila melanogaster overexpressing this P450 variant only confers ∼20-fold resistance to the two insecticides. This bias towards the resistance level revealed that closely related species might provide a more appropriate cellular environment for gene expression and subsequent toxicokinetics of insecticides. These results not only present an alternative method for in vivo functional characterization of P450s in H. armigera and other phylogenetically close species but also provide a valuable genetic engineering toolkit for the genetic manipulation of H. armigera.

Virulence of Beauveria sp. and Metarhizium sp. fungi towards fall armyworm (Spodoptera frugiperda)

The development of effective pest management strategies for Spodoptera frugiperda is a high priority for crop protection across its invasive ranges. Here, we examined six Beauveria and five Metarhizium fungal isolates against this pest. Two Beauveria isolates (B-0571, B-1311) induced high mortality toward 3rd and 6th instar caterpillars and adults. For B-0571 mortality was 82.81 ± 5.75%, 61.46 ± 6.83%, and 93.75 ± 3.61%, and 73.72 ± 2.51%, 71.88 ± 5.41%, and 97.92 ± 2.08% for B-1311, with deaths in caterpillars largely occurring under 24 h (3rd instar control 0.74 ± 0.33%, B-0571 73.96 ± 7.85% and B-1311 62.08 ± 3.67%; 6th instar control 0%, B-0571 66.67% ± 11.02% and B-1311 62.5% ± 9.55%). Infection from both Beauveria isolates fully prevented reproduction in surviving S. frugiperda females. In contrast, all five Metarhizium isolates tested and the remaining four Beauveria isolates exhibited lower virulence. The discovery of two highly virulent Beauveria fungal isolates to S. frugiperda opens avenues to develop novel biological control tools against this highly invasive pest.

Absence of known knockdown resistance mutations but fixation of CYP337B3 was detected in field populations of Helicoverpa armigera across China

The cotton bollworm (Helicoverpa armigera) is a worldwide agricultural pest that infests many important crops. Pyrethroids targeting the voltage-gated sodium channel (VGSC) have been long used in the control of the cotton bollworm. Two amino acid substitutions (D1561V and E1565G) in H. armigera VGSC (HaVGSC) and the presence of a chimeric P450 gene (CYP337B3) have been documented to be associated with pyrethroid resistance. To understand the current occurrence of kdr mutations and the CYP337B3 gene in Chinese H. armigera populations, high-throughput amplicon sequencing was adopted to detect potential nucleotide variations in three fragments of the VGSC gene that cover 10 reported knockdown resistance (kdr) sites in insects, and gene-specific PCR was performed to examine the presence of CYP337B3 gene in H. armigera samples collected across China. The nucleotide variation analysis revealed a wealth of nucleotide variations in not only exons but also introns in the VGSC gene in Chinese H. armigera populations. However, neither previously reported kdr-conferring amino acid replacements nor other non-synonymous mutations were observed in a total of 1439 examined individuals. Population genetic analysis suggested that the H. armigera population in Nanchang, Jiangxi Province (JNC) had a moderate genetic differentiation from other populations, while no significant divergence was observed in other populations in northern and northwestern China. The CYP337B3 was present in all the examined individuals, indicating that CYP337B3 is extensively fixed in H. armigera populations across China. These results support that point mutations in VGSC are not a major factor involved in the current pyrethroid resistance in H. armigera. Instead, CYP337B3 plays a prevalent role in the development of resistance to pyrethroids in H. armigera.

Population Genomics of Nonrecessive Resistance to Bt Toxin Cry1Ac in Helicoverpa armigera From Northern China

Transgenic crops that produce insecticidal proteins from Bacillus thuringiensis (Bt) have provided control of some key pests since 1996. However, the evolution of resistance by pests reduces the benefits of Bt crops. Resistance to Bt crops that is not recessively inherited is especially challenging to manage. Here we analyzed nonrecessive resistance to Bt toxin Cry1Ac in eight field populations of Helicoverpa armigera sampled in 2018 from northern China, where this global pest has been exposed to Cry1Ac in Bt cotton since 1997. Bioassays revealed 7.5% of field-derived larvae were resistant to Cry1Ac of which 87% had at least one allele conferring nonrecessive resistance. To analyze this nonrecessive resistance, we developed and applied a variant of a genomic mapping approach called quantitative trait locus (QTL)-seq. This analysis identified a region on chromosome 10 associated with nonrecessive resistance to Cry1Ac in all 21 backcross families derived from field-collected moths. Individual sequencing revealed that all 21 field-collected resistant grandparents of the backcross families had a previously identified dominant point mutation in the tetraspanin gene HaTSPAN1 that occurs in the region of chromosome 10 identified by QTL-seq. QTL-seq also revealed a region on chromosome 26 associated with nonrecessive resistance in at most 14% of the backcross families. Overall, the results imply the point mutation in HaTSPAN1 is the primary genetic basis of nonrecessive resistance to Cry1Ac in field populations of H. armigera from northern China. Moreover, because nonrecessive resistance is predominant, tracking the frequency of this point mutation could facilitate resistance monitoring in the region.

Novel insights into plant defensin ingestion induced metabolic responses in the polyphagous insect pest Helicoverpa armigera

Lepidopteran insect pest Helicoverpa armigera is one of the most destructive pests of crop plants and several biotechnological approaches are being developed for its control. Plant defensins are small cationic and cysteine-rich peptides that play a role in plant defense. Ingestion of a defensin from Capsicum annuum (CanDef-20) induced a dose-dependent reduction in larval and pupal mass, delayed metamorphosis and also severely reduced fecundity and fertility in H. armigera. To understand the molecular mechanisms of CanDef-20 ingestion-mediated antibiosis in H. armigera larvae, a comparative transcriptomics analysis was carried out. Predominant downregulation of GOs represents serine-type endopeptidases, structural constituents of ribosomes and integral membrane components and differential upregulation of ATP binding, nucleus and translation, while up-regulation of nucleic acid binding represented by transposable elements, were detected. Different isoforms of lipase, serine endopeptidase, glutathione S-transferase, cadherin, alkaline phosphatase and aminopeptidases were found to be upregulated as a compensatory response to CanDef-20 ingestion. In vitro enzyme assays and qPCR analysis of some representative genes associated with vital cellular processes like metamorphosis, food digestion and gut membrane indicated adaptive differential regulations in CanDef-20 fed H. armigera larvae. We conclude that CanDef-20 ingestion affects insect metabolism in a number of ways through its interaction with cell membrane, enzymes, cytoplasmic proteins and triggering transposon mobilization which are linked to growth retardation and adaptive strategies in H. armigera.

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.

Genome-Wide Identification and Expression Profiling of Candidate Sex Pheromone Biosynthesis Genes in the Fall Armyworm (Spodoptera frugiperda)

Spodoptera frugiperda is an agricultural pest causing substantial damage and losses to commercial crops. Sex pheromones are critical for successful mating in Lepidoptera and have been used for monitoring and control of many pest species. The sex pheromone of S. frugiperda is known, but the genes involved in its biosynthesis have not been identified. We systematically studied 99 candidate sex pheromone genes in the genome of S. frugiperda including 1 acetyl-CoA carboxylase (ACC), 11 fatty acid synthases (FASs), 17 desaturases (DESs), 4 fatty acid transport proteins (FATPs), 29 fatty acyl-CoA reductases (FARs), 17 acetyl-CoA acetyltransferases (ACTs), 5 acyl-CoA dehydrogenase (ACDs), 3 enoyl-CoA hydratases (ECHs), 3 hydroxyacyl-CoA dehydrogenases (HCDs), 6 ethyl-CoA thiolases (KCTs), and 3 acyl-CoA-binding proteins (ACBPs). Based on the comparative transcriptome results, we found 22 candidate sex pheromone biosynthesis genes predominately expressed in pheromone glands (PGs) than abdomens without PGs including SfruFAS4, SfruFATP3, SfruACD5, SfruKCT3, SfruDES2, SfruDES5, SfruDES11, SfruDES13, SfruFAR1, SfruFAR2, SfruFAR3, SfruFAR6, SfruFAR7, SfruFAR8, SfruFAR9, SfruFAR10, SfruFAR11, SfruFAR14, SfruFAR16, SfruFAR29, SfruACT6, and SfruACT10. A combination of phylogenetic and tissue-specific transcriptomic analyses indicated that SfruDES5, SfruDES11, SfruFAR2, SfruFAR3, and SfruFAR9 may be key genes involved in the sex pheromone synthesis of S. frugiperda. Our results could provide a theoretical basis for understanding the molecular mechanisms of sex pheromone biosynthesis in S. frugiperda, and also provide new targets for developing novel pest control methods based on disrupting sexual communication.

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).

Intestinal Bacterial Diversity and Functional Analysis of Three Lepidopteran Corn Ear Worm Larvae

Insects, as the most abundant animal group on earth, and their symbionts help their hosts to adapt to various environments. Conogethes punctiferalis, Ostrinia furnacalis and Helicoverpa armigera are three main pests co-occurring in the ear stage of corn, which significantly affect the yield and quality of corn. The purpose of this study was to compare the diversity and function of the intestinal bacteria of the three co-occurring lepidopteran pests, C. punctiferalis, O. furnacalis and H. armigera, and to explore the reason of their prevalence from the microbiota's view. Our results showed the difference of diversity and abundance of the gut bacteria of three co-occurring lepidopteran pests at the ear stage. Proteobacteria and Firmicutes were the dominant phyla, and the Enterobacteriaceae and Enterococcaceae were the dominant families in the three pests. Compared with the other two pests, Bacteroidetes was found much more in C. punctiferalis. In addition, C. punctiferalis showed more correlation and similarity in bacteria composition with corn endophytic bacteria, as well as had obvious advantages in metabolic, environmental information processing, cellular processes and organic systems function pathways. Our findings may provide insight into the prevalence of corn earworm larvae from the perspective of gut microbiota and function prediction.