Using genomic data to study insecticide resistance in the house fly, Musca domestica

New insights into immune genes and other expanded gene families of the house fly, Musca domestica, from an improved whole genome sequence

The house fly, Musca domestica, is a pest of livestock, transmits pathogens of human diseases, and is a model organism in multiple biological research areas. The first house fly genome assembly was published in 2014 and has been of tremendous use to the community of house fly biologists, but that genome is discontiguous and incomplete by contemporary standards. To improve the house fly reference genome, we sequenced, assembled, and annotated the house fly genome using improved techniques and technologies that were not available at the time of the original genome sequencing project. The new genome assembly is substantially more contiguous and complete than the previous genome. The new genome assembly has a scaffold N50 of 12.46 Mb, which is a 50-fold improvement over the previous assembly. In addition, the new genome assembly is within 1% of the estimated genome size based on flow cytometry, whereas the previous assembly was missing nearly one-third of the predicted genome sequence. The improved genome assembly has much more contiguous scaffolds containing large gene families. To provide an example of the benefit of the new genome, we used it to investigate tandemly arrayed immune gene families. The new contiguous assembly of these loci provides a clearer picture of the regulation of the expression of immune genes, and it leads to new insights into the selection pressures that shape their evolution.

Photorhabdus and Xenorhabdus as Symbiotic Bacteria for Bio-Control Housefly (Musca domestica L.)

<b>Background and Objective:</b> The housefly poses a threat to the public health of humans and domestic animals since it can carry and transmit pathogens. Despite there are many attempts to control this insect, most of them depend on conventional pesticides. Thus, the current study aimed to evaluate the efficacy of whole-cell suspension, cell-free supernatant and crude cells of the symbiotic bacteria <i>Photorhabdus</i> sp. and <i>Xenorhabdus</i> sp., as bio-control agents for housefly stages. <b>Materials and Methods:</b> The <i>Photorhabdus</i> sp. and <i>Xenorhabdus</i> sp., were isolated from the entomopathogenic nematodes, <i>Heterorhabditis indica</i> and <i>Steinernema feltiae</i>, respectively. The phenotypic, as well as the enzymatic characterizations of both bacteria, were determined. In addition, histopathological changes of the alimentary canal of <i>M. domestica</i> adults treated with whole-cell suspensions (at 3×10<sup>8 </sup>cells mL<sup></sup><sup>1</sup>) of both bacteria were carefully examined using transmission electron microscopy. <b>Results:</b> The results showed that both symbiotic bacteria significantly suppressed larvae, pupae and adults of <i>M. domestica</i>, particularly when they were applied as whole-cell suspensions. For example, the highest concentration of whole-cell suspension, cell-free supernatant and crude cells of <i>Photorhabdus</i> sp., induced larval mortalities by 94.7, 64.0 and 45.3%, while those of <i>Xenorhabdus</i> sp., induced larval mortalities by 58.7, 46.7 and 30.7% at 96 hrs, respectively. The results also showed that whole-cell suspensions of both symbiotic bacteria caused severe histopathological changes in the ultrastructure of the treated adults' alimentary canal. <b>Conclusion:</b> Both symbiotic bacteria can be effectively used, particularly the whole-cell suspension, as bio-control agents against the housefly either in the larval or adult stage.

Role of the Housefly as a Biological Vector for Bacteria and Fungi at Some Slaughterhouses

<b>Background and Objective:</b> The housefly, <i>Musca domestica</i> L. is the most widespread species of fly in the world. It is in close association with many human pathogens that which can cause serious and life-threatening diseases are known to be carried by house flies, including bacteria, viruses, fungi and parasites, Therefore, this study came intending to determine the role of house flies isolated from some slaughterhouses in the city of Al-Diwaniyah/Iraq in the spread of bacterial and fungal pathogens to humans. <b>Materials and Methods:</b> The 120 insects of house flies were collected randomly from some slaughterhouses for the period September to November, 2021 by special networks prepared for this purpose and transferred to the laboratory and then the bacteria and fungi were isolated and identified from the external surface of house flies by using appropriate culture media. <b>Results:</b> In this study, 148 bacterial isolates belonging to 15 species of bacteria were isolated and diagnosed from the external body of house flies that isolated, 91 samples had given positive growth of bacteria and <i>Escherichia coli</i> was the most occurrence and frequent from the other bacterial isolates, the occurrence rate of it was 16/91 (17.582%) with a frequency rate of 27/148 (18.243%). The 154 fungal isolates belonging to 16 species of fungi were isolated and diagnosed from the external body of house flies, 87 samples had given a positive growth of fungi and <i>Aspergillus niger</i> was the most occurrence and frequent from the other fungal isolates, as its occurrence rate reached 14/87 (16.091%) and the frequency rate of 21/154 (13.636%). <b>Conclusion:</b> House flies transmit many pathological microorganisms such as bacteria, fungi, viruses, etc., which causes various diseases for humans and animals and it may help the spread of antibiotic-resistant species and there is an urgent need to conduct many studies to know the new types of microorganisms that house flies can transmit.

Temperature-dependent effects of house fly proto-Y chromosomes on gene expression could be responsible for fitness differences that maintain polygenic sex determination

Sex determination, the developmental process by which sexually dimorphic phenotypes are established, evolves fast. Evolutionary turnover in a sex determination pathway may occur via selection on alleles that are genetically linked to a new master sex determining locus on a newly formed proto-sex chromosome. Species with polygenic sex determination, in which master regulatory genes are found on multiple different proto-sex chromosomes, are informative models to study the evolution of sex determination and sex chromosomes. House flies are such a model system, with male determining loci possible on all six chromosomes and a female-determiner on one of the chromosomes as well. The two most common male-determining proto-Y chromosomes form latitudinal clines on multiple continents, suggesting that temperature variation is an important selection pressure responsible for maintaining polygenic sex determination in this species. Temperature-dependent fitness effects could be manifested through temperature-dependent gene expression differences across proto-Y chromosome genotypes. These gene expression differences may be the result of cis regulatory variants that affect the expression of genes on the proto-sex chromosomes, or trans effects of the proto-Y chromosomes on genes elswhere in the genome. We used RNA-seq to identify genes whose expression depends on proto-Y chromosome genotype and temperature in adult male house flies. We found no evidence for ecologically meaningful temperature-dependent expression differences of sex determining genes between male genotypes, but we were probably not sampling an appropriate developmental time-point to identify such effects. In contrast, we identified many other genes whose expression depends on the interaction between proto-Y chromosome genotype and temperature, including genes that encode proteins involved in reproduction, metabolism, lifespan, stress response, and immunity. Notably, genes with genotype-by-temperature interactions on expression were not enriched on the proto-sex chromosomes. Moreover, there was no evidence that temperature-dependent expression is driven by chromosome-wide cis-regulatory divergence between the proto-Y and proto-X alleles. Therefore, if temperature-dependent gene expression is responsible for differences in phenotypes and fitness of proto-Y genotypes across house fly populations, these effects are driven by a small number of temperature-dependent alleles on the proto-Y chromosomes that may have trans effects on the expression of genes on other chromosomes.

Gene-Level, but Not Chromosome-Wide, Divergence between a Very Young House Fly Proto-Y Chromosome and Its Homologous Proto-X Chromosome

X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via chromosome-scale divergence from the X. To address this question, we quantified divergence between young proto-X and proto-Y chromosomes in the house fly, Musca domestica. We compared proto-sex chromosome sequence and gene expression between genotypic (XY) and sex-reversed (XX) males. We find evidence for sequence divergence between genes on the proto-X and proto-Y, including five genes with mitochondrial functions. There is also an excess of genes with divergent expression between the proto-X and proto-Y, but the number of genes is small. This suggests that individual proto-Y genes, but not the entire proto-Y chromosome, have diverged from the proto-X. We identified one gene, encoding an axonemal dynein assembly factor (which functions in sperm motility), that has higher expression in XY males than XX males because of a disproportionate contribution of the proto-Y allele to gene expression. The upregulation of the proto-Y allele may be favored in males because of this gene's function in spermatogenesis. The evolutionary divergence between proto-X and proto-Y copies of this gene, as well as the mitochondrial genes, is consistent with selection in males affecting the evolution of individual genes during early Y chromosome evolution.

Toxicity, behavioural and biochemical effect of Piper betle L. essential oil and its constituents against housefly, Musca domestica L

Housefly, Musca domestica L. is a pest of public health importance and is responsible for spreading diseases like typhoid, diarrhoea, plague etc. Indiscriminate reliance on synthetic insecticides has led to development of insecticide resistance and ill effect to humans and nontarget animals. This demands an alternative and safer pest control option. This study evaluates the biological effect of Piper betle L essential oil and its constituent eugenol, eugenol acetate, and β - caryophyllene on the housefly. The major components present in P. betel EO were safrole (44.25%), eugenol (5.16%), β -caryophyllene (5.98%), β -selinene (5.93%), α-selinene (5.27%) and eugenol acetate (9.77%). Eugenol caused 4.5fold higher ovicidal activity (EC₅₀ 86.99 μg/ml) than P. betle EO (EC₅₀ 390.37 μg/ml). Eugenol caused fumigant toxicity to adults (LC₅₀ 88.38 mg/dm³). On contact toxicity by topical application, eugenol acetate, eugenol and β-caryophyllene caused higher mortality to larval and adult stages than EO. FESEM (Field Emission Scanning Electron Microscope) images reveal that exposure to P. betle EO causes the shrinkage of the larval cuticle. Both EO and eugenol induced the detoxifying enzymes Carboxyl esterase (Car E) and Glutathione S - transferases (GST) in larvae and adults. EO and eugenol at 0.2% caused effective repellence and oviposition deterrence to M. domestica adults and this merits their use as alternative strategy to manage M. domestica.

Genome Mining and Expression Analysis of Carboxylesterase and Glutathione S-Transferase Genes Involved in Insecticide Resistance in Eggplant Shoot and Fruit Borer, Leucinodes orbonalis (Lepidoptera: Crambidae)

The shoot and fruit borer, Leucinodes orbonalis (Lepidoptera: Crambidae) is the major cause of low productivity in eggplant and insecticides being the mainstay of management of L. orbonalis. However, field control failures are widespread due to the evolution of insecticide resistance. Taking advantage of the whole genome sequence information, the present study investigated the level of insecticide resistance and the expression pattern of individual carboxylesterase (CE) and glutathione S-transferases (GSTs) genes in various field collected populations of L. orbonalis. Dose-mortality bioassays revealed a very high level of resistance development against fenvalerate (48.2–160-fold), phosalone (94-534.6-fold), emamectin benzoate (7.2–55-fold), thiodicarb (9.64–22.7-fold), flubendiamide (187.4–303.0-fold), and chlorantraniliprole (1.6–8.6-fold) in field populations as compared to laboratory-reared susceptible iso-female colony (Lo-S). Over-production of detoxification enzymes viz., CE and GST were evident upon enzyme assays. Mining of the draft genome of L. orbonalis yielded large number of genes potentially belonging to the CE and GST gene families with known history of insecticide resistance in other insects. Subsequent RT-qPCR studies on relative contribution of individual genes revealed over-expression of numerous GSTs and few CEs in field populations, indicating their possible involvement of metabolic enzymes in insecticide resistance. The genomic information will facilitate the development of novel resistance management strategies against this pest.

Sex Chromosome Evolution in Muscid Flies

Sex chromosomes and sex determining genes can evolve fast, with the sex-linked chromosomes often differing between closely related species. Population genetics theory has been developed and tested to explain the rapid evolution of sex chromosomes and sex determination. However, we do not know why the sex chromosomes are divergent in some taxa and conserved in others. Addressing this question requires comparing closely related taxa with conserved and divergent sex chromosomes to identify biological features that could explain these differences. Cytological karyotypes suggest that muscid flies (e.g., house fly) and blow flies are such a taxonomic pair. The sex chromosomes appear to differ across muscid species, whereas they are conserved across blow flies. Despite the cytological evidence, we do not know the extent to which muscid sex chromosomes are independently derived along different evolutionary lineages. To address that question, we used genomic and transcriptomic sequence data to identify young sex chromosomes in two closely related muscid species, horn fly (Haematobia irritans) and stable fly (Stomoxys calcitrans). We provide evidence that the nascent sex chromosomes of horn fly and stable fly were derived independently from each other and from the young sex chromosomes of the closely related house fly (Musca domestica). We present three different scenarios that could have given rise to the sex chromosomes of horn fly and stable fly, and we describe how the scenarios could be distinguished. Distinguishing between these scenarios in future work could identify features of muscid genomes that promote sex chromosome divergence.

Detoxification enzymes associated with butene-fipronil resistance in Epacromius coerulipes

BACKGROUND

Epacromius coerulipes is a widely distributed locust pest species. Chemical control is the main method used to kill locusts; however, this can result in the selection of locusts with resistance to chemical pesticides. Therefore, the study of resistance is of great significance for the sustainable management of locusts.

RESULTS

In this study, to investigate the relationship between detoxification enzymes and butene-fipronil resistance in E. coerulipes, resistant strains of the locust were compared with sensitive strains. The synergism of synergistic agents was significantly enhanced, and the activities of multifunctional oxidase, carboxylesterase, and glutathione sulfur transferase were significantly increased. Transcriptome sequencing revealed 226 detoxification enzyme genes and 23 upregulated genes. Neighbor-joining was used to construct a phylogenetic tree of related gene families, which included 59 P450 genes, 52 carboxylesterases (CarE) genes, and 25 glutathione S-transferase (GST) genes. Reverse transcription polymerase chain reaction (RT-PCR) analysis results of overexpressed genes in the resistant population combined with a phylogenetic tree showed that four P450 genes belonged to the CYP6, CYP4, CYP18 and CYP302 families, two CarE genes belonged to Clade A families, and one GST gene belonged to the Sigma family. These family members were annotated as detoxification enzyme genes of metabolic insecticide in the transcriptome databases.

CONCLUSIONS

This study showed that P450, CarE and GST together resulted in moderate resistance to butene-fipronil in locusts. The analysis revealed several overexpressed detoxification enzyme genes that will be the focus of future studies on the mechanism of resistance to butene-fipronil. © 2019 Society of Chemical Industry.

Efficacy and repellency of some essential oils and their blends against larval and adult house flies, Musca domestica L. (Diptera: Muscidae)

House flies are global pests and notoriously difficult to control. Essential oils of vetiver, cinnamon, and lavender and their blends were tested for toxic and repellent effects against larval and adult flies. All of the oils had moderate toxicity for eggs. Mortality of 2^nd instar larvae was 57-78% in dipping assays, 38-100% in contact assays, and 94-100% in treated media. Lavender was less effective (38% mortality) than the others (91-100%) in contact bioassays. Oil blends were not more effective against larvae than individual oils. Vetiver and cinnamon oils were strongly repellent (84 and 78%, respectively) for larvae in treated media. None of the oils were repellent for adult house flies in olfactometer assays, but testing of additional products demonstrated significant repellency for neem oil, p-menthane-3,8-diol (PMD), and vanillin. Contact/fumigant toxicity of vetiver, cinnamon, and lavender oils was 100%, significantly higher than mortality from sunflower oil (67%). Blends of oils were not more effective against adults than the individual oils, but blends diluted with sunflower oil were as effective as the individual oils. Essentials oils of vetiver and cinnamon may have potential for fly management in situations where conventional insecticides cannot be used.

Perspectives on new strategies for the identification and development of insecticide targets

The discovery and development of new active ingredients to control arthropod populations and circumvent the inevitable evolution of insecticide resistance has been of consistent interest to the field of insecticide science. This interest has resulted in a slow, but steady increase in the diversity of chemical scaffolds and biochemical target sites within the insecticide arsenal over the past 70 years with growth from three biochemical target sites in the 1950s to 22 distinct biochemical targets in 2018. Despite this growth, the number of biochemical target sites for insecticides remains relatively limited when compared to human pharmaceuticals, which has approximately 700 distinct biochemical targets that are targeted by FDA approved drugs. Potential reasons for this large discrepancy between two closely related fields and putative mechanisms to enhance the identification of tractable biochemical targets for insecticides are discussed. Next, this perspective discusses the movement of insecticide science into the "genomic era" and for comparative purposes, I provide a retrospective analysis of the impact the release of the human genome had to human pharmaceutical development. Based on this analysis and because the fields of insecticide science and human pharmaceuticals mirror each other, researchers in the field of insecticide science would do well to heed the lessons learned by the human pharmaceutical industry and to carefully consider the challenges that arise from genomic approaches for chemical development. Lastly, I pose the question if the field of insecticide science would benefit from adapting an industry-academia model through the generation of industry-sponsored centers of excellence. The goal of this article is not to definitively describe strategies to enhance insecticide development, but rather present different thoughts on agrochemical development that will foster discussions among academic, government, and industry scientists to address current and future problems in the field of insecticide science.

Minimal Effects of Proto-Y Chromosomes on House Fly Gene Expression in Spite of Evidence that Selection Maintains Stable Polygenic Sex Determination

Sex determination, the developmental process by which organismal sex is established, evolves fast, often due to changes in the master regulators at the top of the pathway. Additionally, in species with polygenic sex determination, multiple different master regulators segregate as polymorphisms. Understanding the forces that maintain polygenic sex determination can be informative of the factors that drive the evolution of sex determination. The house fly, Musca domestica, is a well-suited model to those ends because natural populations harbor male-determining loci on each of the six chromosomes and a biallelic female determiner. To investigate how natural selection maintains polygenic sex determination in the house fly, we assayed the phenotypic effects of proto-Y chromosomes by performing mRNA-sequencing experiments to measure gene expression in house fly males carrying different proto-Y chromosomes. We find that the proto-Y chromosomes have similar effects as a nonsex-determining autosome. In addition, we created sex-reversed males without any proto-Y chromosomes and they had nearly identical gene expression profiles as genotypic males. Therefore, the proto-Y chromosomes have a minor effect on male gene expression, consistent with previously described minimal X-Y sequence differences. Despite these minimal differences, we find evidence for a disproportionate effect of one proto-Y chromosome on male-biased expression, which could be partially responsible for fitness differences between males with different proto-Y chromosome genotypes. Therefore our results suggest that, if natural selection maintains polygenic sex determination in house fly via gene expression differences, the phenotypes under selection likely depend on a small number of genetic targets.