Biology subjects

Laporte, F.

Publications and source records attributed to Laporte, F..

10 recordsLinked to original sources

bioRxiv2025

Metabolic resistance of the tiger mosquito to pyrethroid insecticides in La Reunion Island likely results from local adaptation

The resistance of mosquitoes to insecticides is a valuable model system for studying the genetic bases of xenobiotic adaptation in insects. The spread of the Asian tiger mosquito Aedes albopictus combined to the massive use of pyrethroid insecticides to limit arbovirus transmission resulted in the rise of resistance in various continents. Here, we investigated the genetic mechanisms underlying the recent adaptation of this mosquito to deltamethrin in La Reunion island. Bioassays confirmed the presence of resistance alleles in field populations. The resistance phenotype was further enhanced in the laboratory following a few generations of controlled selection. Combining whole genome Pool-seq and RNA-seq revealed no evidence of target-site resistance mutations but the over-expression and variant selection of detoxification enzymes associated with pyrethroid metabolism including cytochrome P450s, transferases and ABC-transporters. Among over-expressed detoxification genes, only one was linked to a gene duplication while polymorphism data suggest most of them being trans-regulated. Genome-wide selection signatures revealed a 9 Mb inverted superlocus responding to insecticide selection whose phenotypical importance remains uncertain. Altogether, this study indicates that the multigenic metabolic resistance phenotype observed in this insular territory mainly results from local adaptation. From an applied perspective, this study provides a set of markers to track pyrethroid resistance in the tiger mosquito in the South-West Indian Ocean. As this region is subjected to recurrent arbovirus outbreaks, the additive resistance phenotype that may arise from the introduction of Kdr mutations from other territories also calls for improving resistance surveillance at the regional scale. Author summaryWhile novel vector control strategies are being developed, chemical insecticides remain widely used to control mosquitoes transmitting human diseases such as the Asian tiger mosquito. However, the recurrent use of insecticides resulted in the emergence of resistance which can ultimately affect vector control efficacy. Here, we investigate the genetic bases underlying the resistance of the Asian tiger mosquito to the pyrethroid insecticide deltamethrin in La Reunion island. By combining two complementary genomic approaches, we showed that resistance is mainly caused by an increased insecticide detoxification while classical Knock down resistance mutations affecting the target of the insecticide were not detected. We also showed that resistance is underlain by multiple genetic changes spread across the genome, supporting the local selection of resistance rather than the introduction of resistance alleles. Furthermore, we identified a large inverted supergene responding to insecticide selection. This study provides valuable insights into the genetic bases of insecticide resistance, enabling the implementation of molecular makers to improve the tracking of insecticide resistance in this major mosquito vector across the Indian Ocean.

genomics↗

bioRxiv2025

Arctic plant species display contrasting levels of chloroplast DNA copy numbers

DNA metabarcoding has revolutionised our ability to characterise biodiversity at unprecedented spatial and temporal scales, outperforming most traditional methods for biodiversity monitoring. However, DNA metabarcoding is not without limitations, in particular regarding the quantitative relationship between sequence read abundances and species numerical abundances or biomass (i.e., quantitative performance). Variation in DNA copy numbers has been often pinpointed as a potentially important factor biasing DNA metabarcoding quantitative performance but empirical comparisons of DNA copy number variation across species remain rare. Here, we identify chloroplast DNA copy number variation (cpDNA CNV) in plants as a potentially important factor that could impact quantitative performance in DNA metabarcoding studies. Using digital droplet PCR, we quantified chloroplast copy number variation in four common high Arctic plant species and between two plant tissue types (green tissues and roots). The amount of cpDNA per unit of dry mass varied by a factor of 3 (for roots) to 7.6 (for green tissues) among species, and up to 67 when comparing cpDNA copy numbers between green and root tissues from the same species. Despite significant differences in cpDNA copy numbers among species for both green tissues and roots, the most pronounced differences in cpDNA copy numbers were clearly between the two tissue types tested. These findings suggest that variation in cpDNA copy numbers among plant species and particularly plant tissue types can be an important but underestimated factor impacting plant sequence reads abundance in DNA metabarcoding datasets. We call for more extensive cpDNA CNV referencing efforts from wild-ranging plants to improve the use of DNA metabarcoding for research and biodiversity monitoring.

ecology↗

bioRxiv2024

A genomic duplication spanning multiple P450s contributes to insecticide resistance in the dengue mosquito Aedes aegypti

Resistance of mosquitoes to insecticides is one example of rapid adaptation to anthropogenic selection pressures having a strong impact on human health and activities. Target-site modification and increased insecticide detoxification are the two main mechanisms underlying insecticide resistance in mosquitoes. While target-sites mutations are well characterised and often used to track resistance in the field, the genomic events associated with insecticide detoxification remain partially characterised. Recent studies evidenced the key role of gene duplications in the over-expression of detoxification enzymes and their potential use to track metabolic resistance alleles in the field. However, such genomic events remain difficult to characterise due to their complex genomic architecture and their co-occurrence with other resistance alleles. In this concern, the present work investigated the role of a large genomic duplication affecting a cluster of detoxification enzymes in conferring resistance to the pyrethroid insecticide deltamethrin in the mosquito Aedes aegypti. Two isofemale lines originating from French Guiana and being deprived from major target-site mutations showed distinct insecticide resistance levels. Combining RNA-seq and whole genome pool-seq identified a 220 Kb genomic duplication enhancing the expression of multiple contiguous cytochrome P450s in the resistant line. The genomic architecture of the duplicated loci was elucidated through long read sequencing, evidencing its transposon-mediated evolutionary origin. The involvement of this P450 duplication in deltamethrin survival was supported by a significant phenotypic response to the P450 inhibitor piperonyl butoxide together with genotype-phenotype association and RNA interference. Experimental evolution suggested that this P450 duplication is associated with a significant fitness cost, potentially affecting its adaptive value in presence of other resistance alleles. Overall, this study supports the importance of genomic duplications affecting detoxification enzymes in the rapid adaptation of mosquitoes to insecticides. Deciphering their genomic architecture provides new insights into the evolutionary processes underlying such rapid adaptation. Such findings provide new tools for the surveillance and management of resistance in the field.

evolutionary biology↗

bioRxiv2023

Towards quantitative DNA Metabarcoding: A method to overcome PCR amplification bias

Metabarcoding analyses have recently undergone significant development due to the power of this technique in biodiversity monitoring. However, it is still difficult to draw accurate quantitative conclusions about the ecosystems studied, mainly because of biases inherent in the environmental DNA or introduced during the experimental process. These biases alter the relationship between the amount of DNA observed and the biomass or number of individuals of the species detected. Two of the biases inherent in metabarcoding have been measured: the ratio between total DNA and target DNA concentrations, and the PCR amplification bias. A method for their correction is proposed. All experimental tests were performed on mock alpine plant communities using the marker Sper01, which is expected to have low amplification bias due to its highly conserved priming sites. Our approach combines standard quantitative PCR techniques (qPCR and digital droplet PCR) with a realistic stochastic model of PCR dynamics that accounts for PCR saturation. The model was used to estimate PCR efficiencies for each species and to infer the true species proportions of the mock communities from the read relative frequencies. The corrections are easy to implement and can be applied to previously generated DNA metabarcoding data. This work demonstrates the relative importance of the two biases considered and is an open door to quantitative metabarcoding data, although many other biases remain to be considered.

ecology↗

bioRxiv2023

ChoruMM: a versatile multi-components mixed model for bacterial-GWAS

Genome-wide Association Studies (GWAS) have been central to studying the genetics of complex human outcomes, and there is now tremendous interest in implementing GWAS-like approaches to study pathogenic bacteria. A variety of methods have been proposed to address the complex linkage structure of bacterial genomes, however, some questions remain about to optimize the genetic modelling of bacteria to decipher causal variations from correlated ones. Here we examined the genetic structure underlying whole-genome sequencing data from 3,824 Listeria monocytogenes strains, and demonstrate that the standard human genetics model, commonly assumed by existing bacterial GWAS methods, is inadequate for studying such highly structured organisms. We leverage these results to develop ChoruMM, a robust and powerful approach that consists of a multi-component linear mixed model, where components are inferred from a hierarchical clustering of the bacteria genetic relatedness matrix. Our ChoruMM approach also includes post-processing and visualization tools that address the pervasive long-range correlation observed in bacteria genome and allow to assess the type I error rate calibration.

genetics↗

bioRxiv2021

De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals

Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.

molecular biology↗

bioRxiv2021

Neonicotinoid and pyrethroid combination: A tool to manage insecticide resistance in malaria vectors? Insights from experimental evolution

BackgroundThe introduction of neonicotinoids for managing insecticide resistance in mosquitoes is of high interest as they interact with a biochemical target not previously used in public health. In this concern, Bayer developed a combination of the neonicotinoid clothianidin and the pyrethroid deltamethrin (brand name Fludora(R) Fusion) as a new vector control tool. Although this combination proved to be efficient against pyrethroid-resistant mosquitoes, its ability to prevent the selection of pyrethroid and neonicotinoid resistance alleles was not investigated. In this context, the objective of this work was to study the dynamics and the molecular mechanisms of resistance of An. gambiae to the separated or combined components of this combination. A field-derived An. gambiae line carrying resistance alleles to multiple insecticides at low frequencies was used as a starting for 33 successive generations of controlled selection. Resistance levels to each insecticide and target site mutation frequencies were monitored throughout the selection process. Cross resistance to other public health insecticides were also investigated. RNA-seq was used to compare gene transcription variations and polymorphisms across all lines. ResultsThis study confirmed the potential of this insecticide combination to impair the selection of resistance as compared to its two separated components. Deltamethrin selection led to the rapid enrichment of the kdr L1014F target-site mutation while clothianidin selection led to the over-transcription of multiple cytochrome P450s including some showing high homology with the ones conferring neonicotinoid resistance in other insects. A strong selection signature associated with clothianidin selection was observed on a cytochrome P450 gene cluster previously associated with resistance. Within this cluster, the gene CYP6M1 showed the highest selection signature together with a transcription profile supporting a role in clothianidin resistance. Modelling the impact of point mutations selected by clothianidin on CYP6M1 protein structure suggested that the selection of variants affecting its active site can enhance clothianidin metabolism. ConclusionsIn the context of the recent deployment of neonicotinoids for mosquito control and their frequent usage in agriculture, the present study highlights the benefit of combining them with other insecticides for preventing the selection of resistance and sustaining vector control activities.

evolutionary biology↗

bioRxiv2020

A novel assay for tracking carboxylesterase gene amplifications conferring organophosphate resistance in the mosquito Aedes aegypti: from experimental evolution to field application

By altering gene expression and creating paralogs, genomic amplifications represent a key component of short-term adaptive processes. In insects, the use of insecticides can select gene amplifications causing an increased expression of detoxification enzymes, supporting the usefulness of these DNA markers for monitoring the dynamics of resistance alleles in the field. In this context, the present study aims to characterise a genomic amplification event associated with resistance to organophosphate insecticides in the mosquito Aedes aegypti and to develop a molecular assay to monitor the associated resistance alleles in the field. An experimental evolution experiment using a composite population from Laos supported the association between the over-transcription of multiple contiguous carboxylesterase genes on chromosome 2 and resistance to multiple organophosphate insecticides. Combining whole genome sequencing and qPCR on specific genes confirmed the presence of a ~100 Kb amplification spanning at least five carboxylesterase genes at this locus with the co-existence of multiple structural duplication haplotypes. Field data confirmed their circulation in South-East Asia and revealed high copy number polymorphism among and within populations suggesting a trade-off between this resistance mechanism and associated fitness costs. A dual-colour multiplex TaqMan assay allowing the rapid detection and copy number quantification of this amplification event in Ae. aegypti was developed and validated on field populations. The routine use of this novel assay will improve the tracking of resistance alleles in this major arbovirus vector.

evolutionary biology↗

bioRxiv2019

Estimating the effective sample size in association studies of quantitative traits

The effective sample size (ESS) is a quantity estimated in genome-wide association studies (GWAS) with related individuals and/or linear mixed models used in analysis. ESS originally measured relative power in family-based GWAS and has recently become important for correcting GWAS summary statistics in post-GWAS analyses. However, existing ESS approaches have been overlooked and based on empirical estimation. This work presents an analytical form of ESS in mixed-model GWAS of quantitative traits, which is derived using the expectation of quadratic form and validated in extensive simulations. We illustrate the performance and relevance of our ESS estimator in common GWAS scenarios and analytically show that (i) family-based studies are consistently underpowered compared to studies of unrelated individuals of the same sample size; (ii) conditioning on polygenic genetic effect by linear mixed models boosts power; and (iii) power of detecting gene-environment interaction can be substantially gained or lost in family-based designs depending on exposure distribution. We further analyze UK Biobank dataset in two samples of 336,347 unrelated and 68,910 related individuals. Analysis in unrelated individuals reveals a high accuracy of our ESS estimator compared to the existing empirical approach; and analysis of related individuals suggests that the loss in effective sample size due to relatedness is at most 0.94x. Overall, we provide an analytical form of ESS for guiding GWAS designs and processing summary statistics in post-GWAS analyses.

genetics↗

bioRxiv2019

Combining genetic crosses and pool targeted DNA-seq for untangling genomic variations associated with resistance to multiple insecticides in the dengue vector Aedes aegypti

In addition to combating vector-borne diseases, studying the adaptation of mosquitoes to insecticides provides a remarkable example of evolution-in-action driving the selection of complex phenotypes. Indeed, most resistant mosquito populations show multi-resistance phenotypes as a consequence of the variety of insecticides employed and of the complexity of selected resistance mechanisms. Such complexity makes challenging the identification of alleles conferring resistance to specific insecticides and prevents the development of molecular assays to track them in the field. Here we showed that combining simple genetic crosses with pool targeted DNA-seq can enhance the specificity of resistance alleles detection while maintaining experimental work and sequencing effort at reasonable levels. A multi-resistant population of the mosquito Aedes aegypti was exposed to three distinct insecticides (deltamethrin, bendiocarb and fenitrothion) and survivors to each insecticide were crossed with a susceptible strain to generate 3 distinct lines. F2 individuals from each line were then segregated with 2 insecticide doses. Bioassays supported the improved segregation of resistance alleles between lines. Hundreds of genes covering all detoxifying enzymes and insecticide targets together with more than 7,000 intergenic regions equally spread over mosquito genome were sequenced from pools of F0 and F2 individuals unexposed or surviving insecticide. Differential coverage analysis identified 39 detoxification enzymes showing an increased gene copy number in association with resistance. Combining an allele frequency filtering approach with a Bayesian FST-based genome scan identified multiple genomic regions showing strong selection signatures together with 50 non-synonymous variations associated with resistance. This study provides a simple and cost-effective approach to improve the segregation of resistant alleles in multi-resistant populations while reducing false positives frequently arising when comparing populations showing divergent genetic backgrounds. The identification of these insecticide resistance markers paves the way for the design of novel DNA-based resistance tracking assays.\n\nAuthor summaryIn addition to combating vector-borne diseases, understanding how mosquitoes adapt to insecticides provides a remarkable example of evolution-in-action. However, the variety of insecticides used and the complexity of adaptive mechanisms make it difficult to identify the genetic changes conferring resistance to each insecticide. Here we combined simple controlled crosses with mass DNA sequencing for enhancing the specificity of resistance gene detection. A multi-resistant mosquito population was exposed to three distinct insecticides and survivors were crossed with a susceptible strain to generate 3 distinct mosquito lines. Individuals from the second generation of each line were then segregated based on their resistance to each insecticide. Bioassays supported the improved segregation of genetic resistance markers between lines. Hundreds of genes potentially involved in resistance together with thousands non-genic regions equally spread over mosquito genome were sequenced from individuals from each line. Genomic analyses identified detoxification enzymes showing an increased gene copy number in association with resistance and multiple genomic regions showing strong selection signatures and carrying point mutations associated with resistance. Such approach improves the specificity of resistance gene detection in field mosquito populations resisting to multiple insecticides and paves the way for the design of novel DNA-based resistance tracking tools.

genomics↗