Biology subjects

Tay, W. T.

Publications and source records attributed to Tay, W. T..

13 recordsLinked to original sources

bioRxiv2026

Transposable element disruption of a second thyroglobulin-like gene confers Vip3Aa resistance in Helicoverpa armigera

BackgroundThe cotton bollworm Helicoverpa armigera is a major global pest controlled by genetically engineered crops expressing Bacillus thuringiensis (Bt) toxins, including Vip3Aa. While Vip3Aa is widely deployed, the genetic basis of resistance remains poorly understood. Previous work identified disruption of a thyroglobulin-like gene (HaVipR1) as one mechanism of resistance, suggesting additional loci may be involved. ResultsUsing linkage analysis, transcriptomics, long-read sequencing, and CRISPR-Cas9 gene editing, we identify a second thyroglobulin-like gene, HaVipR2, as a novel mediator of Vip3Aa resistance. Resistance in a field-derived H. armigera line was shown to be monogenic, recessive, and autosomal, mapping to chromosome 29. Long-read sequencing revealed a [~]16 kb transposable element insertion disrupting HaVipR2, which was undetectable using standard short-read approaches. CRISPR-Cas9 knockout of HaVipR2 conferred >900-fold resistance, confirming its causal role. Comparative analyses show that HaVipR1 and HaVipR2 share conserved domain architecture, indicating that thyroglobulin-domain proteins represent a recurrent target of resistance evolution. ConclusionsOur findings establish thyroglobulin-domain proteins as a new class of Bt resistance genes in Lepidoptera and demonstrate that transposable element insertions can drive adaptive resistance while evading detection by conventional methods. These results highlight the importance of long-read sequencing and accurate genome annotation for resistance monitoring and provide new insights into the molecular basis and evolution of Vip3Aa resistance.

genomics↗

bioRxiv2025

Molecular resources for the stored grain Cryptolestes cryptic pest species (Coleoptera: Laemophloeidae)

Recent research activities relating to evolutionary genetics and molecular characterisation of the stored grain Cryptolestes (Ganglbauer) beetle pest species have revealed gaps in public DNA databases, and resulted in molecular diagnostic inconsistencies. This study reports on characterisation of the mitochondrial DNA cytochrome oxidase I (mtCOI) gene from specimens detected during biosecurity inspections at Australias border, and surveys of publicly available mtCOI gene sequences, for re-assessment of Cryptolestes species status. The results enabled clarification of a new putative C. sp. WTT-2016 species, and supported the close evolutionary relationships between C. ferrugineus (Stephens)/C. pusilloides (Steel and Howe), and between C. pusillus (Schonherr) and the previously identified C. sp. WTT-2013 cryptic species. Widespread confusion between C. ferrugineus, C. pusiolloides, C. pusillus and the two putative novel C. sp. WTT-2013 and C. sp. WTT-2016, highlighted the taxonomic challenge surrounding this beetle genus, while inter-specific genetic distances between C. spartii (Curtis)/C. corticinus (Reitter) suggested they belonged to the same species. Assembled and annotated mitochondrial DNA genomes (mitogenomes) of six Cryptolestes species via high throughput sequencing identified assembly errors associated with published mitogenomes of C. ferrugineus and C. turcicus (Grouvelle), and misidentification of C. pusillus. Based on re-evaluation of intra- and inter-specific genetic distances and congruence from phylogenetic inferences, we proposed a Cryptolestes species genetic gap at approximately 5% that could help with defining species boundaries. By reconciling these molecular incongruences, this study will contribute to improving agricultural biosecurity preparedness associated with the economically important Cryptolestes flat grain beetle species.

evolutionary biology↗

bioRxiv2024

Knockout of the SfVipR1 gene confers high-level resistance to Bacillus thuringiensis Vip3Aa toxin in Spodoptera frugiperda

BackgroundBacillus thuringiensis (Bt) insecticidal proteins, including Cry proteins and vegetative insecticidal proteins (Vips), are extensively utilized in transgenic crops due to their efficacy and safety. The fall armyworm, Spodoptera frugiperda, has evolved practical resistance to Cry1Fa, yet no practical resistance to Vip3Aa has been documented. However, both laboratory selection and field screen studies indicate a high potential for this pest to evolve resistance to Vip3Aa, making it crucial to evaluate potential resistance genes. HaVipR1 has recently been identified as a key determinant of Vip3Aa resistance in the cotton bollworm, Helicoverpa armigera. This study investigated whether the HaVipR1-homologous gene in S. frugiperda (SfVipR1) is similarly involved in Vip3Aa resistance. ResultsWe employed CRISPR/Cas9 technology to generate a homozygous knockout strain of SfVipR1. In comparison with the parent susceptible YJ-19 strain, the knockout strain (Sfru-KO) exhibited high-level resistance to Vip3Aa (>1875-fold) but showed no resistance to Cry1Fa. This acquired resistance to Vip3Aa is autosomal, recessive, and genetically linked to the deletion mutation in SfVipR1 within the Sfru-KO strain of S. frugiperda. ConclusionDisruption of SfVipR1 results in high-level resistance to Vip3Aa, highlighting SfVipR1 has a critical role in Vip3Aa toxicity in S. frugiperda, despite the exact mechanism remaining unclear. Early detection of SfVipR1 mutant alleles in the field is essential for developing adaptive resistance management strategies against S. frugiperda.

genetics↗

bioRxiv2024

Identification of a novel resistance gene which provides insight into Vip3Aa mode of action in Helicoverpa armigera

The global reliance on Bacillus thuringiensis (Bt) proteins for controlling lepidopteran pests in cotton, corn, and soybean crops underscores the critical need to understand resistance mechanisms. Vip3Aa, one of the most widely deployed and currently effective Bt proteins in genetically modified crops, plays a pivotal role in pest management. This study identifies the molecular basis of Vip3Aa resistance in Australian Helicoverpa armigera through genetic crosses, and integrated genomic and transcriptomic analyses. We identified a previously uncharacterized gene, LOC110373801 (designated HaVipR1), as a crucial determinant of Vip3Aa resistance in two field-derived resistant lines. Functional validation using CRISPR-Cas9 knockout in susceptible lines confirmed the genes role in conferring resistance. Despite extensive laboratory selection of Vip3Aa-resistant colonies in Lepidoptera, the biochemical mechanisms underlying resistance have remained elusive. Our research demonstrates that HaVipR1-mediated resistance operates independently of known resistance genes, including midgut-specific chitin synthase and the transcription factor SfMyb. The identification of HaVipR1 offers further insights into the Vip3Aa mechanism of action. This discovery is vital for devising strategies to counteract resistance and sustain the efficacy of Bt crops. Future research should focus on elucidating the biochemical pathways involving HaVipR1 and investigating its interactions with other resistance mechanisms. Our findings underscore the utility of analysing field-derived resistant lines in providing biologically relevant insights and stress the necessity for comprehensive management strategies to maintain agricultural productivity. Significance StatementThis is the first identification of a specific gene in Helicoverpa armigera which mediates resistance to the Bacillus thuringiensis (Bt) protein Vip3Aa. We identify that this gene is disrupted in two different ways in separate field-derived resistant lines, one being a large transposable element insertion in the first intron of the HaVipR1 gene, confirmed using long-read sequencing. Disruption of this gene using CRISPR-Cas9 knockout in a susceptible H. armigera line confers Vip3A resistance. The identification of a specific gene is important for molecular monitoring and management of H. armigera as well as other global pests of concern like Spodoptera frugiperda. These findings also offer insights for researchers aiming to understand how Vip3Aa functions, as the action pathway remains unclear.

genomics↗

bioRxiv2022

Genome-wide SNPs reveal the social structure and invasion pathways of the invasive tropical fire ant (Solenopsis geminata)

Elucidating invasion pathways of invasive species is often challenging because invasive populations frequently have low genetic diversity caused by genetic bottlenecks during introduction events. Genome-wide sequencing such as Restriction Site-Associated DNA Sequencing (RADseq) can overcome these challenges by generating thousands of genome-wide single nucleotide polymorphic (SNP) markers. The tropical fire ant, Solenopsis geminata, is a global invader with low genetic diversity in its introduced range, making RADseq one of the best available methods to investigate its population genetics. We used double digest RADseq to generate 3,834 SNPs to compare the genetic diversity of S. geminata in its introduced range to its most likely source of introduction, determined the invasion pathways among populations at an unprecedented level of detail for this species, and determined the social structure of S. geminata workers collected in 13 locations worldwide. We found that introduced S. geminata went through a strong genetic bottleneck. We also identified multiple secondary introduction events among S. geminata populations, indicating that the bridgehead effect is an important driver in the global spread of this species. We found that all colonies in the introduced range were polygyne (i.e., with more than one queen) which may increase their invasion success and potential to cause adverse effects.

genetics↗

bioRxiv2022

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 also 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 were overwhelmingly C- and R-strain hybrids. 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.

evolutionary biology↗

bioRxiv2022

Resistance bioassays and allele characterisation inform Spodoptera frugiperda (Lepidoptera: Noctuidae) management and introduction pathways in Asia and Australia

The fall armyworm (FAW) Spodoptera frugiperda 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 and Spodoptera litura, were concurrently screened to obtain larval LC50 estimates against various insecticides. We characterised 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 10x LC50 difference for indoxacarb was detected between Australian populations, which was approximately 28x higher than that reported from an Indian population. Characterisation of ACE-1 and VGSC alleles provided further evidence of multiple introductions in Asia, and multiple pathways involving genetically distinct individuals into Australia. The preliminary bioassay results and resistance allele patterns from invasive S. frugiperda populations suggest multiple introductions have contributed to the pests spread and challenge the axiom of its rapid west-to-east spread.

evolutionary biology↗

bioRxiv2020

A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey

Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multi-primer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the tabaci species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multi-primer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field-testing our redesigned Bemisia metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multi-primer HTS metabarcoding method incorporated two over-lapping amplicons of 472bp and 518bp that spanned the entire 657bp 3 barcoding region for Bemisia, and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving trans-boundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.

evolutionary biology↗

bioRxiv2020

Genomic balancing selection is key to the invasive success of the fall armyworm

A successful biological invasion involves survival in a newly occupied environment. If a population bottleneck occurs during an invasion, the resulting depletion of genetic variants could cause increased inbreeding depression and decreased adaptive potential, which may result in a fitness reduction. How invasive populations survive in the newly occupied environment despite reduced heterozygosity and how, in many cases, they maintain moderate levels of heterozygosity are still contentious issues1. The Fall armyworm (FAW; Lepidoptera: Spodoptera frugiperda), a polyphagous pest, is native to the Western hemisphere. Its invasion in the Old World was first reported from West Africa in early 2016, and in less than four years, it swept sub-Saharan Africa and Asia, finally reaching Australia. We used population genomics approaches to investigate the factors that may explain the invasive success of the FAW. Here we show that genomic balancing selection played a key role in invasive success by restoring heterozygosity before the global invasion. We observe a drastic loss of mitochondrial polymorphism in invasive populations, whereas nuclear heterozygosity exhibits a mild reduction. The population from Benin in West Africa has the lowest length of linkage disequilibrium amongst all invasive and native populations despite its reduced population size. This result indicates that balancing selection increased heterozygosity by facilitating the admixture of invasive populations from distinct origins and that, once heterozygosity was sufficiently high, FAW started spreading globally in the Old World. As comparable heterozygosity levels between invasive and native populations are commonly observed1, we postulate that the restoration of heterozygosity through balancing selection could be widespread among successful cases of biological invasions.

evolutionary biology↗

bioRxiv2020

Whole genome sequencing of global Spodoptera frugiperda populations: evidence for complex, multiple introductions across the Old World

Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by chronological order of detections 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, while from 870 high-quality nuclear single nucleotide polymorphic DNA markers five distinct New World population clusters were identified, broadly reflected their native geographical ranges and 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 underpinned the pests 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 population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

genomics↗

bioRxiv2019

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 climate change, development of suitable agroecosystems, and 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 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 more recent populations from 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, admixture proportions were reduced between 2013 and 2017, indicating a decline in hybridization rates. Recent populations also showed shorter introgressed tracks suggesting selection against admixture. In contrast to the genome-wide pattern, there was striking evidence for introgression of a single region including an insecticide-resistance allele from the invasive H. armigera into local H. zea, which increased in frequency over time but was localized within the genome. 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 and hybridization, with significant implications for pest management in future population expansions and introductions of novel resistance genes from new invasive H. armigera populations. Author summarySecondary contact occurs when related species with non-overlapping ranges are geographically reunited. Scenarios of secondary contact have increased due to anthropogenic movement of species outside of their native range, often resulting in invasive species that successfully spread and stabilised in the new environment. This is the case for Helicoverpa armigera, a major agricultural pest in the Old World that has recently invaded the Americas, where it reunited with its closest relative, H. zea. While some authors reported hybridisation, and hypothesised about the potential emergence of novel ecotypes and the exchange of pesticide-resistant genes, these outcomes have not been tested yet. We examine these outcomes by sequencing individuals from both species in Brazil, collected in 2013 after outbreaks of H. armigera were reported, and individuals collected during 2017. We discovered that despite hybridisation, these moths have not collapsed into a single species nor formed new ecotypes, and that the species distinctiveness is maintained through selection against most of the foreign genotypes that cross species boundaries. However, we found that hybridisation mediated the rapid acquisition of a H. armigera gene conferring resistance to pyrethroids by H. zea. The overall decline in populations of both species during the interval covered by this study means that our results are likely to reflect the consequences of hybridization events early after invasion, despite the likely ongoing introduction of H. armigera genetic diversity through trade across the South American continent. Our results provide a rare example of adaptive transferral of variation right after invasion and elucidate the dynamics of insecticide resistance evolution in H. zea.

evolutionary biology↗

bioRxiv2019

Multiple incursion pathways for Helicoverpa armigera in Brazil show its genetic diversity spreading in a connected world

The Old World cotton bollworm Helicoverpa armigera was first detected in Brazil with subsequent reports from Paraguay, Argentina, Bolivia, and Uruguay. This pattern suggests that the H. armigera spread across the South American continent following incursions into northern/central Brazil, however, this hypothesis has not been tested. Here we compare northern and central Brazilian H. armigera mtDNA COI haplotypes with those from southern Brazil, Uruguay, Argentina, and Paraguay. We infer spatial genetic and gene flow patterns of this dispersive pest in the agricultural landscape of South America. We show that the spatial distribution of H. armigera mtDNA haplotypes and its inferred gene flow patterns in the southwestern region of South America exhibited signatures inconsistent with a single incursion hypothesis. Simulations on spatial distribution patterns show that the detection of rare and/or the absence of dominant mtDNA haplotypes in southern H. armigera populations are inconsistent with genetic signatures observed in northern and central Brazil. Incursions of H. armigera into the New World are therefore likely to have involved independent events in northern/central Brazil, and southern Brazil/Uruguay-Argentina-Paraguay. This study demonstrates the significant biosecurity challenges facing the South American continent, and highlights alternate pathways for introductions of alien species into the New World.

evolutionary biology↗

bioRxiv2019

Take out the rubbish - Removing NUMTs and pseudogenes from the Bemisia tabaci cryptic species mtCOI database

Identification of Bemisia tabaci cryptic whitefly species complex currently relies on molecular characterisation of the mitochondrial DNA cytochrome oxidase subunit I (mtCOI) partial gene, however, nuclear mitochondrial sequences (NUMTs), PCR-derived pseudogenes and/or poor sequence editing have hindered this effort. To-date, ca. 5,175 partial ([≥] 300bp) mtCOI sequences for species identification purposes have been reported. We reviewed ca. 10% of sequences representing the standard B. tabaci species complex mtCOI dataset. We found that 333 sequences (64.9%) were NUMTs, pseudogenes and/or affected by poor sequence quality. Amino acid pattern analyses of high throughput sequencing-derived mtCOI gene from 24 tabaci and non-tabaci species enabled differentiation between NUMTs/pseudogene-affected and likely real mtCOI sequences, and that the SSA4, SSA5/SSA8, AsiaII-2 and AsiaII_4 species were NUMTs/pseudogenes artefacts. Intra-specific uncorrected nucleotide distances (p-dist) from our up-dated dataset ranged from 0-1.98%, inter-specific p-dist within phylogenetic clades ranged between ca. 2.5 and 8%, and 8 and >19% for species between phylogenetic clades. Differentiating between closely related species could therefore utilise an average p-dist of 2.5%. Despite the smaller B. tabaci mtCOI dataset, six putative new species were identified. Adoption of our standardised workflow and up-dated mtCOI clean dataset could facilitate better diagnostics of B. tabaci and non-tabaci cryptic species.

evolutionary biology↗