Acetylcholine esterase of Drosophila melanogaster: a laboratory model to explore insecticide susceptibility gene drives.

Background: One of the proposed applications of gene drives has been to revert pesticide resistant mutations back to the ancestral susceptible state. Insecticides that have become ineffective because of the rise of resistance could have reinvigorated utility and be used to suppress pest populations again, perhaps at lower application doses.

Results: We have created a laboratory model for susceptibility gene drives that replaces field-selected resistant variants of the acetylcholine esterase (Ace) locus of Drosophila melanogaster with ancestral susceptible variants.

The haplolethal gene wupA of Drosophila exhibits potential as a target for an X-poisoning gene drive.

A synthetic gene drive that targets haplolethal genes on the X chromosome can skew the sex ratio toward males. Like an "X-shredder," it does not involve "homing," and that has advantages including the reduction of gene drive resistance allele formation. We examine this "X-poisoning" strategy by targeting 4 of the 11 known X-linked haplolethal/haplosterile genes of Drosophila melanogaster with CRISPR/Cas9.

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.

Rethinking the ecdysteroid source during Drosophila pupal-adult development.

Ecdysteroids, typified by 20-hydroxyecdysone (20E), are essential hormones for the development, reproduction and physiology of insects and other arthropods. For over half a century, the vinegar fly Drosophila melanogaster (Ephydroidea: Diptera) has been used as a model of ecdysteroid biology. Many aspects of the biosynthesis and regulation of ecdysteroids in this species are understood at the molecular level, particularly with respect to their secretion from the prothoracic gland (PG) cells of the ring gland, widely considered the dominant biosynthetic tissue during development.

Ecdysteroid kinase-like (EcKL) paralogs confer developmental tolerance to caffeine in .

A unique aspect of metabolic detoxification in insects compared to other animals is the presence of xenobiotic phosphorylation, about which little is currently understood. Our previous work raised the hypothesis that members of the taxonomically restricted ecdysteroid kinase-like (EcKL) gene family encode the enzymes responsible for xenobiotic phosphorylation in the model insect (Diptera: Ephydroidea)-however, candidate detoxification genes identified in the EcKL family have yet to be functionally validated. Here, we test the hypothesis that EcKL genes in the rapidly evolving Dro5 clade are involved in the detoxification of plant and fungal toxins in .

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.

Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the 'detoxification-by-phosphorylation' enzymes of insects.

Phosphorylation is a phase II detoxification reaction that, among animals, occurs near exclusively in insects, but the enzymes responsible have never been cloned or otherwise identified. We propose the hypothesis that members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene family in 12 species of Drosophila and explored their evolution within the genus.

Sublethal larval exposure to imidacloprid impacts adult behaviour in Drosophila melanogaster.

Pesticides are now chronically found in numerous ecosystems incurring widespread toxic effects on multiple organisms. For insects, the larvae are very exposed to pesticide pollution and the acute effect of insecticides on larvae has been characterized in a range of species. However, the carry-on effects in adults of sublethal exposure occurring in larvae are not well characterized.

Extracellular endonucleases in the midgut of Myzus persicae may limit the efficacy of orally delivered RNAi.

Myzus persicae is a major pest of many crops including canola and Brassica vegetables, partly because it vectors plant viruses. Previously it has been reported that double-stranded RNA delivered to aphids by injection, artificial diet or transgenic plants has knocked down target genes and caused phenotypic effects. While these studies suggest that RNA interference (RNAi) might be used to suppress aphid populations, none have shown effects sufficient for field control.

Mining insect genomes for functionally affiliated genes.

Several hundred insect genome assemblies are already publicly available, and this total grows on a weekly basis. A major challenge now confronting insect science is how best to use genomic data to improve our understanding of insect biology. We consider a framework for genome analysis based on functional affiliation, that is, groups of genes involved in the same biological process or pathway, and explore how such an approach furthers our understanding of several aspects of insect phenotype.

- and -acting variants contribute to survivorship in a naïve population exposed to ryanoid insecticides.

Insecticide resistance is a paradigm of microevolution, and insecticides are responsible for the strongest cases of recent selection in the genome of Here we use a naïve population and a novel insecticide class to examine the ab initio genetic architecture of a potential selective response. Genome-wide association studies (GWAS) of chlorantraniliprole susceptibility reveal variation in a gene of major effect, (), which we validate with linkage mapping and transgenic manipulation of gene expression. We propose that allelic variation in alters sensitivity to the calcium depletion attributable to chlorantraniliprole's mode of action.

Reconciliation of a gene network and species tree.

The phylogenetic trees of genes and the species which they belong to are similar, but distinct due to various evolutionary processes which affect genes but do not create new species. Reconciliations map the gene tree into the species tree, explaining the discrepancies by events including gene duplications and losses. However, when duplicate genes undergo recombination (a phenomenon known as paralog exchange, or non-allelic homologous recombination), the phylogeny of the genes becomes a network, not a tree.

The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster.

Imidacloprid, the world's most used insecticide, has caused considerable controversy due to harmful effects on non-pest species and increasing evidence showing that insecticides have become the primary selective force in many insect species. The genetic response to insecticides is heterogeneous across populations and environments, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations of Drosophila melanogaster originating from four climate extremes replicated across two continents.

Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in the Genetic Reference Panel.

Patterns of nucleotide polymorphism within populations of suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweeps to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid).

Adaptation and conservation insights from the koala genome.

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors.

Insights into DDT Resistance from the Genetic Reference Panel.

Insecticide resistance is considered a classic model of microevolution, where a strong selective agent is applied to a large natural population, resulting in a change in frequency of alleles that confer resistance. While many insecticide resistance variants have been characterized at the gene level, they are typically single genes of large effect identified in highly resistant pest species. In contrast, multiple variants have been implicated in DDT resistance in ; however, only the locus has previously been shown to be relevant to field populations.

GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments.

Motivation: Sequencing pools of individuals (Pool-Seq) is a cost-effective way to gain insight into the genetics of complex traits, but as yet no parametric method has been developed to both test for genetic effects and estimate their magnitude. Here, we propose GWAlpha, a flexible method to obtain parametric estimates of genetic effects genome-wide from Pool-Seq experiments.

Results: We showed that GWAlpha powerfully replicates the results of Genome-Wide Association Studies (GWAS) from model organisms.

Transcriptome Analysis of Third Instar Larval Ring Glands Points to Novel Functions and Uncovers a Cytochrome p450 Required for Development.

In larvae, the ring gland (RG) is a control center that orchestrates major developmental transitions. It is a composite organ, consisting of the prothoracic gland, the corpus allatum, and the corpora cardiaca, each of which synthesizes and secretes a different hormone. Until now, the RG's broader developmental roles beyond endocrine secretion have not been explored.

Genomic and Transcriptomic Associations Identify a New Insecticide Resistance Phenotype for the Selective Sweep at the Cyp6g1 Locus of Drosophila melanogaster.

Scans of the Drosophila melanogaster genome have identified organophosphate resistance loci among those with the most pronounced signature of positive selection. In this study, the molecular basis of resistance to the organophosphate insecticide azinphos-methyl was investigated using the Drosophila Genetic Reference Panel, and genome-wide association. Recently released full transcriptome data were used to extend the utility of the Drosophila Genetic Reference Panel resource beyond traditional genome-wide association studies to allow systems genetics analyses of phenotypes.

The molecular evolution of cytochrome P450 genes within and between drosophila species.

We map 114 gene gains and 74 gene losses in the P450 gene family across the phylogeny of 12 Drosophila species by examining the congruence of gene trees and species trees. Although the number of P450 genes varies from 74 to 94 in the species examined, we infer that there were at least 77 P450 genes in the ancestral Drosophila genome. One of the most striking observations in the data set is the elevated loss of P450 genes in the Drosophila sechellia lineage.