Genome-wide and expression-profiling analyses of the cytochrome P450 genes in Bactrocera dorsalis (Hendel) and screening of candidate P450 genes associated with malathion resistance

Mitochondrial coding genes mediate insecticide tolerance in the oriental fruit fly, Bactrocera dorsalis (Hendel)

The oriental fruit fly, Bactrocera dorsalis (Hendel), an invasive insect pest infesting fruits and vegetables, possesses a remarkable capacity for environmental adaptation. The investigation of behind mechanisms of the stress adaptability in B. dorsalis holds significantly practical relevance. Previous studies on the molecular mechanism underlying stress resistance in B. dorsalis have predominantly focused on nuclear-coding genes, with limited exploration on organelle-coding genes. In this study, we assessed alterations in the mitochondrial physiological parameters of B. dorsalis under exposure to malathion, avermectin, and beta-cypermethrin at LD50 dosages. The results showed that all three insecticides were capable of reducing mitochondrial complex IV activity and ATP content. Expression patterns of mitochondrial coding genes across different developmental stages, tissues and insecticide exposures were analyzed by RT-qPCR. The results revealed that these mitochondrial coding genes were expressed in various tissues and at different developmental stages. Particularly noteworthy, atp6, cox2, and cytb exhibited substantial up-regulation in response to malathion and avermectin treatment. Furthermore, RNAi-mediated knockdown of atp6 and cox2 resulted in the increased toxicity of malathion and avermectin against B. dorsalis, and cox2 silencing was also associated with the decreased complex IV activity. These findings suggest that atp6 and cox2 most likely play pivotal roles in mediating tolerance or resistance to malathion and avermectin in B. dorsalis. Our results provide novel insights into the role of mitochondrial coding genes in conferring tolerance to insecticides in B. dorsalis, with practical implications for controlling this pest in the field.

Cuticular competing endogenous RNAs regulate insecticide penetration and resistance in a major agricultural pest

BACKGROUND

The continuously developing pesticide resistance is a great threat to agriculture and human health. Understanding the mechanisms of insecticide resistance is a key step in dealing with the phenomenon. Insect cuticle is recently documented to delay xenobiotic penetration which breaks the previous stereotype that cuticle is useless in insecticide resistance, while the underlying mechanism remains scarce.

RESULTS

Here, we find the integument contributes over 40.0% to insecticide resistance via different insecticide delivery strategies in oriental fruit fly. A negative relationship exists between cuticle thickening and insecticide penetration in resistant/susceptible, also in field strains of oriental fruit fly which is a reason for integument-mediated resistance. Our investigations uncover a regulator of insecticide penetration that miR-994 mimic treatment causes cuticle thinning and increases susceptibility to malathion, whereas miR-994 inhibitor results in opposite phenotypes. The target of miR-994 is a most abundant cuticle protein (CPCFC) in resistant/susceptible integument expression profile, which possesses capability of chitin-binding and influences the cuticle thickness-mediated insecticide penetration. Our analyses find an upstream transcriptional regulatory signal of miR-994 cascade, long noncoding RNA (lnc19419), that indirectly upregulates CPCFC in cuticle of the resistant strain by sponging miR-994. Thus, we elucidate the mechanism of cuticular competing endogenous RNAs for regulating insecticide penetration and demonstrate it also exists in field strain of oriental fruit fly.

CONCLUSIONS

We unveil a regulatory axis of lnc19419 ~ miR-994 ~ CPCFC on the cuticle thickness that leads to insecticide penetration resistance. These findings indicate that competing endogenous RNAs regulate insecticide resistance by modulating the cuticle thickness and provide insight into the resistance mechanism in insects.

Functional characterization of cytochrome P450s associated with pyrethroid resistance in the olive fruit fly Bactrocera oleae

Resistance to pyrethroid insecticides has evolved in Bactrocera oleae populations in Greece, threatening the efficacy of control interventions based on this insecticide class. Here we report the collection of populations from Crete, with resistance levels reaching up to 132-folds, compared to susceptible laboratory strains and show that pyrethroid resistance is substantially suppressed by the PBO synergist, suggesting the involvement of detoxification enzymes. To identify specific candidate genes implicated in resistance, we performed comparative transcriptomic analysis, between the pyrethroid resistant populations from Crete and the susceptible laboratory strains, using both whole bodies and Malpighian tubules. Several genes were found differentially transcribed between resistant and susceptible flies in each comparison, with P450s being among the most highly over-expressed detoxification genes in pyrethroid resistant populations. Four of the over-expressed P450s (Cyp6A61, Cyp6G6, Cyp4P6 and Cyp6G28) were recombinantly expressed in Escherichia coli and in vitro metabolism assays revealed that CYP6A61 is capable of metabolizing alpha-cypermethrin, while CYP6G6, CYP4P6 and CYP6G28 are capable of metabolizing deltamethrin. No metabolism of neonicotinoid insecticides was recorded. We further silenced CYP6G6 in vivo, via RNAi, which led to a small, but significant increase in deltamethrin toxicity. The study provides valuable information towards the development of molecular diagnostics and evidence-based insecticide resistance management strategies.

Genome-Wide Identification and Expression Pattern of Cytochrome P450 Genes in the Social Aphid Pseudoregma bambucicola

Cytochrome P450 monooxygenases (P450s) have a variety of functions, including involvement in the metabolism of exogenous substances and the synthesis and degradation of endogenous substances, which are important for the growth and development of insects. Pseudoregma bambucicola is a social aphid that produces genetically identical but morphologically and behaviorally distinct first-instar soldiers and normal nymphs within colonies. In this study, we identified 43 P450 genes based on P. bambucicola genome data. Phylogenetic analysis showed that these genes were classified into 4 clans, 13 families, and 23 subfamilies. The CYP3 and CYP4 clans had a somewhat decreased number of genes. In addition, differential gene expression analysis based on transcriptome data showed that several P450 genes, including CYP18A1, CYP4G332, and CYP4G333, showed higher expression levels in soldiers compared to normal nymphs and adult aphids. These genes may be candidates for causing epidermal hardening and developmental arrest in soldiers. This study provides valuable data and lays the foundation for the study of functions of P450 genes in the social aphid P. bambucicola.

Chromosome-level genome assembly reveals potential epigenetic mechanisms of the thermal tolerance in the oriental fruit fly, Bactrocera dorsalis

The oriental fruit fly, Bactrocera dorsalis (Hendel), has very strong ecological adaptability and phenotypic plasticity. Here, the genome of B. dorsalis was assembled into 549.45 Mb sequences with a contig N50 length of 12.81 Mb. Among, 95.67 % assembled genome sequences were anchored on six chromosomes with an N50 length of 94.63 Mb. According to the basic characteristics of the sex chromosomes of Tephritidae, the X chromosome of B. dorsalis was identified. Significant gene expansions were detected in several important gene families related to adaptability. In particular, we annotated 50 histone modification enzymes (HMEs) in this genome. A comparative transcriptome analysis indicated that 12 HME genes were differentially expressed in two thermo-tolerant strains (heat and cold). Interestingly, four and seven of the 12 HME genes responded to heat shock or cold hardening, respectively. These evidences suggested that the histone modification as an epigenetic modification may be involved in the thermal tolerance of B. dorsalis, but with different regulation mechanisms in thermal acclimation and hardening. The high quality genome of B. dorsalis provides an invaluable resource for further functional genomic study. Moreover, comparative genomic analysis will shed insights on revealing the mechanisms of adaptive evolution in this fly.

CYP4G100 contributes to desiccation resistance by mediating cuticular hydrocarbon synthesis in Bactrocera dorsalis

The oriental fruit fly Bactrocera dorsalis (Hendel) is expanding its distribution to higher latitudes. Our goal in this study was to understand how B. dorsalis adapts to higher latitude environments that are more arid than tropical regions. Cuticular hydrocarbons (CHCs) on the surface of the epicuticle in insects act as a hydrophobic barrier against water loss. The essential decarbonylation reaction in CHC synthesis is catalysed by CYP4G, a cytochrome P450 subfamily protein. Hence, in B. dorsalis it is necessary to clarify the function of the CYP4G gene and its role in desiccation resistance. CYP4G100 was identified in the B. dorsalis genome. The complete open reading frame (ORF) encodes a CYP4 family protein (552 amino acid residues) that has the CYP4G-specific insertion. This CYP4G gene was highly expressed in adults, especially in the oenocyte-rich peripheral fat body. The gene can be induced by desiccation treatment, suggesting its role in CHC synthesis and waterproofing. Silencing of CYP4G100 resulted in a decrease of CHC levels and the accumulation of triglycerides. It also increased water loss and resulted in higher desiccation susceptibility. CYP4G100 is involved in hydrocarbon synthesis and contributes to cuticle waterproofing to help B. dorsalis resist desiccation in arid environments.

Genome-wide and expression-profiling analyses of the cytochrome P450 genes in Tenebrionidea

Cytochrome P450 monooxygenases (CYPs) are present in almost all areas of the tree of life. As one of the largest and most diverse superfamilies of multifunctional enzymes, they play important roles in the metabolism of xenobiotics and biosynthesis of endogenous compounds, shaping the success of insects. In this study, the CYPome (an omics term for all the CYP genes in a genome) diversification was examined in the four Tenebrionidea species through genome-wide analysis. A total of 483 CYP genes were identified, of which 103, 157, 122, and 101 were respectively deciphered from the genomes of Tebebrio molitor, Asbolus verucosus, Hycleus cichorii and Hycleus phaleratus. These CYPs were classified into four major clans (mitochondrial, CYP2, CYP3, and CYP4), and clans CYP3 and CYP4 are most diverse. Phylogenetic analysis showed that most CYPs of these Tenebrionidea beetles from each clan had a very close 1:1 orthology to each other, suggesting that they originate closely and have evolutionally conserved function. Expression analysis at different developmental stages and in various tissues showed the life stage-, gut-, salivary gland-, fat body-, Malpighian tubule-, antennae-, ovary- and testis-specific expression patterns of T. molitor CYP genes, implying their various potential roles in development, detoxification, immune response, digestion, olfaction, and reproduction. Our studies provide a platform to understand the evolution of Tenebrionidea CYP gene superfamily, and a basis for further functional investigation of the T. molitor CYPs involved in various biological processes.

Monitoring the Methyl Eugenol Response and Non-Responsiveness Mechanisms in Oriental Fruit Fly Bactrocera dorsalis in China

Bactrocera dorsalis is a notorious polyphagous pest in China, and its management strategies largely depend on methyl eugenol (ME), which has been widely used as an attractant to monitor and eradicate B. dorsalis populations for seven decades. However, the non-responsiveness levels in field B. dorsalis populations to ME is unknown. In this study, we monitored the response to ME in field populations from the four most heavily infested provinces in China, and the results showed that the populations had lower sensitivity to ME relative to GZS susceptible strain. The percent responsiveness of the lowest sensitivity population was 5.88-, 3.47-, and 1.47-fold lower relative to the susceptible strain at doses of 1, 10, and 100 µL of ME, respectively. Gene expression analysis and inhibitor assays further revealed that odorant binding protein (BdorOBP2, BdorOBP83b) and the P450 enzyme system may be associated with the lower response to ME. To our knowledge, this work is the first to report that the P450 enzyme system confers a lower responsiveness to lure insects. These findings provided valuable insights for exploiting ME non-responsiveness to protect sterile males from ME-based control strategies and the use of lures combined with insecticides.

Transcriptome Analysis to Identify Responsive Genes under Sublethal Concentration of Bifenazate in the Diamondback Moth, Plutella xylostella (Linnaeus, 1758) (Lepidoptera: Plutellidae)

Bifenazate is a novel acaricide that has been widely used to control spider mites. Interestingly, we found bifenazate had a biological activity against the diamondback moth (Plutella xylostella), one of the most economically important pests on crucifer crops around the world. However, the molecular mechanisms underlying the response of P. xylostella to bifenazate treatment are not clear. In this study, we first estimated the LC₃₀ dose of bifenazate for third-instar P. xylostella larvae. Then, in order to identify genes that respond to the treatment of this insecticide, the comparative transcriptome profiles were used to analyze the gene expression changes in P. xylostella larvae after exposure to LC₃₀ of bifenazate. In total, 757 differentially expressed genes (DEGs) between bifenazate-treated and control P. xylostella larvae were identified, in which 526 and 231 genes were up-regulated and down-regulated, respectively. The further Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the xenobiotics metabolisms pathway was significantly enriched, with ten detoxifying enzyme genes (four P450s, five glutathione S-transferases (GSTs), and one UDP-Glucuronosyltransferase (UGT)) were up-regulated, and their expression patterns were validated by qRT-PCR as well. Interestingly, the present results showed that 17 cuticular protein (CP) genes were also remarkably up-regulated, including 15 CPR family genes. Additionally, the oxidative phosphorylation pathway was found to be activated with eight mitochondrial genes up-regulated in bifenazate-treated larvae. In contrast, we found some genes that were involved in tyrosine metabolism and purine pathways were down-regulated, indicating these two pathways of bifenazate-exposed larvae were significantly inhibited. In conclusion, the present study would help us to better understand the molecular mechanisms of sublethal doses of bifenazate detoxification and action in P. xylostella.

Integrated miRNA and transcriptome profiling to explore the molecular mechanism of Spodoptera frugiperda larval midgut in response to azadirachtin exposure

As a destructive agricultural pest, Spodoptera frugiperda has spread worldwide in the past few years. Azadirachtin, an environmentally friendly and most promising compound, showed adverse effects, including mortality and growth inhibition, against S. frugiperda. While the effects of azadirachtin on the midgut of this pest remain to be determined. In this study, structural damage was observed in the larval midguts of S. frugiperda with azadirachtin exposure. RNA-seq on the larval midguts with different azadirachtin treatments was performed. Compared to the control group, a total of 3344 and 4759 differentially expressed genes (DEGs) were identified in the midguts with 0.1 and 0.5 μg/g azadirachtin exposure, respectively. Among them, the DEGs encoding detoxification enzymes/proteins, immune-related proteins, digestion and absorption-related proteins, and transcript factors were further analyzed. High-throughput sequencing was also used for the identification of differentially expressed microRNAs in different treatments. A total of 153 conserved miRNAs and 147 novel miRNAs were identified, of which 11 and 29 miRNAs were affected by 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The integrated analysis found that 13 and 178 miRNA versus mRNA pairs were acquired in the samples with 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The results of high-throughput sequencing were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). These results provide useful information for revealing the molecular mechanism of S. frugiperda larval midgut in response to azadirachtin.

Genome-Wide Identification of P450 Genes in Chironomid Propsilocerus akamusi Reveals Candidate Genes Involved in Gut Microbiota-Mediated Detoxification of Chlorpyrifos

Chironomids commonly dominate macroinvertebrate assemblages in aquatic habitats and these non-biting midges are known for their ability to tolerate contaminants. Studies regarding the interplay between gut microbiota and host detoxification ability is currently a point of interest. Cytochrome P450s (P450s) are critical metabolic enzymes in which a subset is involved in xenobiotic detoxification. In this study, we first conducted an integrated global investigation of P450s based on the whole genomic sequence of Propsilocerus akamusi and retrieved a series of 64 P450 genes which were further classified into 4 clans and 25 families on the basis of phylogenetic relationships. With assistance of RNA-Seq and RT-qPCR validation, the expression profile of screened PaP450s in guts was compared between chlorpyrifos-challenged larvae with deficient gut microbiota (GD) and those with a conventional gut community (CV). An increasing prevalence of chlorpyrifos from sublethal to lethal dosages induced a greater mortality rate of individuals coupled with remarkable downregulation of 14 P450s in GD larval guts when compared to CV ones. Moreover, it turned out that the decreased level of PaCYP3998B1 and PaCYP3987D1 might imply impaired host endogenous detoxification capability potentiated by gut dysbiosis, reflected by a remarkably severe mortality in GD larvae treated with lethal chlorpyrifos. Collectively, our study unveiled candidate P450 genes that might be mediated by gut symbionts in chlorpyrifos-challenged P. akamusi larvae, possibly facilitating further understanding of the detoxified mechanism that chironomids might employ to alleviate poisonousness.

Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato

Fruit production is negatively affected by a wide range of frugivorous insects, among them tephritid fruit flies are one of the most important. As a replacement for pesticide-based controls, enhancing natural fruit resistance through biotechnology approaches is a poorly researched but promising alternative. The use of quantitative reverse transcription PCR (RT-qPCR) is an approach to studying gene expression which has been widely used in studying plant resistance to pathogens and non-frugivorous insect herbivores, and offers a starting point for fruit fly studies. In this paper, we develop a gene selection pipe-line for known induced-defense genes in tomato fruit, Solanum lycopersicum, and putative detoxification genes in Queensland fruit fly, Bactrocera tryoni, as a basis for future RT-qPCR research. The pipeline started with a literature review on plant/herbivore and plant/pathogen molecular interactions. With respect to the fly, this was then followed by the identification of gene families known to be associated with insect resistance to toxins, and then individual genes through reference to annotated B. tryoni transcriptomes and gene identity matching with related species. In contrast for tomato, a much better studied species, individual defense genes could be identified directly through literature research. For B. tryoni, gene selection was then further refined through gene expression studies. Ultimately 28 putative detoxification genes from cytochrome P450 (P450), carboxylesterase (CarE), glutathione S-transferases (GST), and ATP binding cassette transporters (ABC) gene families were identified for B. tryoni, and 15 induced defense genes from receptor-like kinase (RLK), D-mannose/L-galactose, mitogen-activated protein kinase (MAPK), lipoxygenase (LOX), gamma-aminobutyric acid (GABA) pathways and polyphenol oxidase (PPO), proteinase inhibitors (PI) and resistance (R) gene families were identified from tomato fruit. The developed gene selection process for B. tryoni can be applied to other herbivorous and frugivorous insect pests so long as the minimum necessary genomic information, an annotated transcriptome, is available.