Comparative transcriptome profiling reveals candidate genes related to insecticide resistance of Glyphodes pyloalis

Binding characteristics and structural dynamics of two general odorant-binding proteins with plant volatiles in the olfactory recognition of Glyphodes pyloalis

Glyphodes pyloalis Walker (Lepidoptera: Pyralidae) is the most destructive pest, causing severe damage to mulberry production in China's sericulture industry. The insecticide application in mulberry orchards poses a significant risk of poisoning to Bombyx mori. Shifting from insecticides to odor attractants is a beneficial alternative, but not much data is available on the olfactory system of G. pyloalis. We identified 114 chemosensory genes from the antennal transcriptome database of G. pyloalis, with 18 odorant-binding protein (OBP) and 17 chemosensory protein (CSP) genes significantly expressed in the antennae. Ligand-binding assays for two antennae-biased expressed general odorant-binding proteins (GOBPs) showed high binding affinities of GOBP1 to hexadecanal, β-ionone, and 2-ethylhexyl acrylate, while GOBP2 exhibited binding to 4-tert-octylphenol, benzyl benzoate, β-ionone, and farnesol. Computational simulations indicated that van der Waal forces predominantly contributed to the binding free energy in the binding processes of complexes. Among them, Phe12 of GOBP1 and Phe19 of GOBP2 were demonstrated to play crucial roles in their bindings to plant volatiles using site-directed mutagenesis experiments. Moreover, hexadecanal and β-ionone attracted G. pyloalis male moths in the behavioral assays, while none of the candidate plant volatiles significantly affected female moths. Our findings provide a comprehensive understanding of the molecular mechanisms underlying olfactory recognition in G. pyloalis, setting the groundwork for novel mulberry pests control strategies based on insect olfaction.

Integrated de novo transcriptome of Culex pipiens mosquito larvae as a resource for genetic control strategies

We present a de novo transcriptome of the mosquito vector Culex pipiens, assembled by sequences of susceptible and insecticide resistant larvae. The high quality of the assembly was confirmed by TransRate and BUSCO. A mapping percentage until 94.8% was obtained by aligning contigs to Nr, SwissProt, and TrEMBL, with 27,281 sequences that simultaneously mapped on the three databases. A total of 14,966 ORFs were also functionally annotated by using the eggNOG database. Among them, we identified ORF sequences of the main gene families involved in insecticide resistance. Therefore, this resource stands as a valuable reference for further studies of differential gene expression as well as to identify genes of interest for genetic-based control tools.

Binding characteristics of pheromone-binding protein 1 in Glyphodes pyloalis to organophosphorus insecticides: Insights from computational and experimental approaches

Glyphodes pyloalis (Lepidoptera: Pyralidae) is one of the major pests in mulberry production in China, which has developed resistance to various insecticides. Chemoreception is one of the most crucial physiological tactics in insects, playing a pivotal role in recognizing chemical stimuli in the environment, including noxious stimuli such as insecticides. Herein, we obtained recombinant pheromone-binding protein 1 (GpylPBP1) that exhibited antennae-biased expression in G. pyloalis. Ligand-binding assays indicated that GpylPBP1 had the binding affinities to two organophosphorus insecticides, with a higher binding affinity to chlorpyrifos than to phoxim. Computational simulations showed that a mass of nonpolar amino acid residues formed the binding pocket of GpylPBP1 and contributed to the hydrophobic interactions in the bindings of GpylPBP1 to both insecticides. Furthermore, the binding affinities of three GpylPBP1 mutants (F12A, I52A, and F118A) to both insecticides were all significantly reduced compared to those of the GpylPBP1-wild type, suggesting that Phe12, Ile52, and Phe118 residues were crucial binding sites and played crucial roles in the bindings of GpylPBP1 to both insecticides. Our findings can be instrumental in elucidating the effects of insecticides on olfactory recognition in moths and facilitating the development of novel pest management strategies using PBPs as targets based on insect olfaction.

Identification and functional study of detoxification-related genes in response to tolfenpyrad stress in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae)

Glyphodes pyloalis Walker (G. pyloalis) is a common destructive mulberry pest. Due to the long-term and frequent use of insecticides, it has developed tolerance to commonly used insecticides. Tolfenpyrad (TFP) is a novel pyrazole heterocyclic insecticide. In order to understand the TFP detoxification mechanism of G. pyloalis larvae, we first estimated the LC30 dose of TFP for 3rd instar G. pyloalis larvae. Next, we identified genes that were differentially expressed in 3rd instar G. pyloalis larvae treated with TFP compared to the control group by transcriptome sequencing. In total, 86,949,569 and 67,442,028 clean reads were obtained from TFP-treated and control G. pyloalis larvae, respectively. A total of 5588 differentially expressed genes (DEGs) were identified in TFP-treated and control G. pyloalis larvae, of which 3084 genes were upregulated and 2504 genes were downregulated. We analyzed the expression of 43 candidate detoxification enzyme genes associated with insecticide tolerance using qPCR. According to the spatiotemporal expression pattern of DEGs, we found that CYP6ABE1, CYP333A36 and GST-epsilon8 were highly expressed in the midgut, while CarEs14 was strongly expressed in haemolymph. Furthermore, we successfully knocked down these genes by RNA interference. After silencing CYP6ABE1 and CYP333A36, bioassay showed that the mortality rate of TFP-treated G. pyloalis larvae was significantly higher compared to the control group. This study provides a theoretical foundation for understanding the sensitivity of G. pyloalis to TFP and establish the basis for the effective and green management of this pest.

Biochemical and Molecular Analysis of Field Resistance to Spirodiclofen in Panonychus citri (McGregor)

Spirodiclofen is one of the most widely used acaricides in China. The citrus red mite, Panonychus citri (McGregor) (Acari: Tetranychidae), is one of the most destructive citrus pests worldwide and has developed a high resistance to spirodiclofen. However, the molecular mechanism of spirodiclofen resistance in P. citri is still unknown. In this study, we identified a field spirodiclofen-resistant strain (DL-SC) that showed 712-fold resistance to spirodiclofen by egg bioassay compared to the susceptible strain. Target-site resistance was not detected as non-synonymous mutations were not found by amplification and sequencing of the ACCase gene of resistant and susceptible strains; in addition, the mRNA expression levels of ACCase were similar in both resistant and susceptible strains. The activity of detoxifying enzymes P450s and CCEs in the resistant strain was significantly higher than in the susceptible strain. The transcriptome expression data showed 19 xenobiotic metabolisms genes that were upregulated. Stage-specific expression profiling revealed that the most prominent upregulated gene, CYP385C10, in transcriptome data was significantly higher in resistant strains in all stages. Furthermore, functional analysis by RNAi indicated that the mortality caused by spirodiclofen was significantly increased by silencing the P450 gene CYP385C10. The current results suggest that overexpression of the P450 gene, CYP385C10, may be involved in spirodiclofen resistance in P. citri.

A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae

Chlorops oryzae is a pest of rice that has caused severe damage to crops in major rice-growing areas in recent years. We generated a 447.60 Mb high-quality chromosome-level genome with contig and scaffold N50 values of 1.17 Mb and 117.57 Mb, respectively. Hi-C analysis anchored 93.22% scaffolds to 4 chromosomes. The relatively high expression level of Heat Shock Proteins (HSPs) and antioxidant genes in response to thermal stress suggests these genes may play a role in the environmental adaptability of C. oryzae. The identification of multiple pathways that regulate reproductive development (juvenile hormone, 20-hydroxyecdsone, and insulin signaling pathways) provides evidence that these pathways also play an important role in vitellogenesis and thus insect population maintenance. These findings identify possible reasons for the increased frequency of outbreaks of C. oryzae in recent years. Our chromosome-level genome assembly may provide a basis for further genetic studies of C. oryzae, and promote the development of novel, sustainable strategies to control this pest.

A chromosome-level genome assembly for the rice pest, Chlorops oryzae, pinpoints molecular pathways that might contribute toward increased outbreaks for this important crop pest.

The role of Glutathione-S-transferases in phoxim and chlorfenapyr tolerance in a major mulberry pest, Glyphodes pyloalis walker (Lepidoptera: Pyralidae)

Glyphodes pyloalis Walker is a destructive pest on mulberry trees and poses a significant threat to the sericultural industry in China. Phoxim and chlorfenapyr are two commonly used insecticides in mulberry fields. Glutathione-S-transferases (GSTs) comprise a multifunctional protein superfamily that plays important roles in the detoxification of insecticides and xenobiotic compounds in insects. However, whether GSTs participate in the tolerance of phoxim and chlorfenapyr in G. pyloalis is still unknown. To better understand the mechanism of insecticide tolerance in G. pyloalis, the enzymatic activity of GSTs was evaluated under phoxim and chlorfenapyr exposure, respectively. GST enzyme activity was significantly increased after 12, 36 and 48 h of phoxim treatment and 12, 24, 36 and 48 h of chlorfenapyr treatment. Subsequently, eighteen GST genes were identified from the larvae transcriptome of G. pyloalis. Among these, ten GpGSTs had GSH-binding sites and fifteen GpGSTs had variable hydrophobic substrate-binding sites. The expression levels of Delta-GpGST and Epsilon-GpGST genes were significantly influenced by phoxim and chlorfenapyr treatment, and by the time post insecticide application. Furthermore, after silencing GpGST-E4, the mortality rate of G. pyloalis larvae was increased when they were exposed to chlorfenapyr, but it did not significantly alter when the larvae were exposed to phoxim. Our results indicated the vital roles of GpGSTs in the tolerance of insecticides and this action depends on the categories of insecticides. The present study provides a theoretical basis for elucidating insecticide susceptibility and promotes functional research on GST genes in G. pyloalis.

Transcriptional response of detoxifying enzyme genes in Bombyx mori under chlorfenapyr exposure

The silkworm, Bombyx mori (B. mori) is an important economic insect which ingests mulberry leaves and products the silk in industry. Chlorfenapyr is a new halogenated pyrrole insecticide which has been promoted for the control of mulberry insect pests in China. However, the detoxification mechanism of the silkworm to chlorfenapyr has not been investigated yet. In the present study, we first estimated the LC₃₀ dose of chlorfenapyr for 3rd instar B. mori larvae, and then, in order to characterise the chlorfenapyr detoxification mechanism, the transcriptomes of chlorfenapyr-treated and untreated 3rd instar B. mori larvae were compared using RNA-sequencing. In total, 146, 533, 126 and 148, 957, 676 clean reads were obtained from insecticide-treated and control silkworm larvae, respectively, and these reads generated 10, 954 genes. The transcriptional profile of silkworm larvae was significantly influenced by chlorfenapyr treatment. A total of 1196 differentially expressed genes (DEGs) were identified in insecticide-treated and control B. mori larvae, in which 644 genes were upregulated and 552 genes were downregulated. Results showed that multiple DEGs were enriched in detoxication-related gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Eleven detoxifying enzyme genes which differentially expressed were screened, and their expression patterns were validated by qRT-PCR. Furthermore, we successfully knocked down all differentially upregulated detoxifying enzyme genes, and a bioassay showed that the mortality of chlorfenapyr-treated silkworm larvae was significantly higher after silencing these genes than in groups injected with dsGFP. The present study reveals the molecular basis of silkworm detoxification to chlorfenapyr exposure, and provides new insights into the management of insecticide damage in the silkworm.

Characterization and Functional Analysis of trehalase Related to Chitin Metabolism in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae)

Simple Summary

Sericulture has always been threatened by Glyphodes pyloalis Walker (G. pyloalis). Trehalase is an essential enzyme in chitin metabolism and energy supply. In this study, two trehalase genes in G. pyloalis (GpTre1 and GpTre2) were identified and functionally analyzed. Knockdown of the two genes led to the significant downregulation of chitin metabolism pathway-related genes, the difficulty in molting of larvae, and the deformation of adult wings. Moreover, the trehalase inhibitor, Validamycin A, treatment increased GpTre1 and GpTre2 expression and affected the expressions of chitin metabolism pathway-related genes. The inhibitor also caused a significantly increased cumulative mortality of larvae. The results suggested that GpTre1 and GpTre2 played a vital role on G. pyloalis development, which could be useful for providing information for insect pest control in the future.

Abstract

Glyphodes pyloalis Walker (G. pyloalis) is a serious pest on mulberry. Due to the increasing pesticide resistance, the development of new and effective environmental methods to control G. pyloalis is needed. Trehalase is an essential enzyme in trehalose hydrolysis and energy supply, and it has been considered a promising target for insect pest control. However, the specific function of trehalase in G. pyloalis has not been reported. In this study, two trehalase genes (GpTre1 and GpTre2) were identified from our previous transcriptome database. The functions of the trehalase in chitin metabolism were studied by injecting larvae with dsRNAs and trehalase inhibitor, Validamycin A. The open reading frames (ORFs) of GpTre1 and GpTre2 were 1,704 bp and 1,869 bp, which encoded 567 and 622 amino acid residues, respectively. Both of GpTre1 and GpTre2 were mainly expressed in the head and midgut. The highest expression levels of them were in 5th instar during different development stages. Moreover, knockdown both of GpTre1 and GpTre2 by the dsRNAs led to significantly decreased expression of chitin metabolism pathway-related genes, including GpCHSA, GpCDA1, GpCDA2, GpCHT3a, GpCHT7, GpCHSB, GpCHT-h, GpCHT3b, GpPAGM, and GpUAP, and abnormal phenotypes. Furthermore, the trehalase inhibitor, Validamycin A, treatment increased the expressions of GpTre1 and GpTre2, increased content of trehalose, and decreased the levels of glycogen and glucose. Additionally, the inhibitor caused a significantly increased cumulative mortality of G. pyloalis larvae on the 2nd (16%) to 6th (41.3%) day, and decreased the rate of cumulative pupation (72.3%) compared with the control group (95.6%). After the activities of trehalase were suppressed, the expressions of 6 integument chitin metabolism-related genes decreased significantly at 24 h and increased at 48 h. The expressions of GpCHSB and GpCHT-h, involved in chitin metabolism pathway of peritrophic membrane in the midgut, increased at 24 h and 48 h, and there were no changes to GpCHT3b and GpPAGM. These results reveal that GpTre1 and GpTre2 play an essential role in the growth of G. pyloalis by affecting chitin metabolism, and this provides useful information for insect pest control in the future.

Dynamic changes of transcriptome of fifth-instar spodoptera litura larvae in response to insecticide

Spodoptera litura is a major insect with a cosmopolitan distribution and strong resistance to multiple insecticides. Determining the molecular basis and key candidate genes of the insecticide resistance of S. litura may help in managing this insect. In this study, fifth-instar S. litura larvae were subjected to transcriptome analysis at 6, 12, 24, 48, and 72 h after feeding on an LC20 dose of avermectin. The result showed that genes responding to avermectin changed dynamically with different gene counts and resistance mechanisms at the fifth instar based on a metabolic pathway map. These responses included degrading the insecticide by a series of P450 and glutathione-S-transferase enzymes starting at the 12 h time point, with subsequent increases in the number of genes involved and shifts to TOLL and immune deficiency (IMD) pathways at 48 h after feeding the insecticide. Weighted correlation network analysis (WGCNA) determined a co-expression module related to the avermectin response at 12 and 24 h (r = 0.403, p = 0.0371; r = 0.436, p = 0.023), in which a hub gene (LOC111358940) related to metalloproteinase activity was identified. In addition, Analysis of the genes in the co-expression module further revealed that eight genes encoding UDP-glucuronosyltransferases were directly associated with insecticide response in S. litura. These results provide better understanding of the avermectin response mechanism of S. litura and may be useful in developing improved control strategies for this species.

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The online version of this article (10.1007/s13205-021-02651-9) contains supplementary material, which is available to authorized users.

Screening of Helicoverpa armigera Mobilome Revealed Transposable Element Insertions in Insecticide Resistance Genes

Simple Summary

Transposable elements (TEs) are mobile DNA sequences that can copy themselves within a host genome. TE-mediated changes in regulation can lead to massive and rapid changes in expression, responses that are potentially highly adaptive when an organism is faced with a mortality agent in the environment, such as an insecticide. Helicoverpa armigera shows a hight number of reported cases of insecticide resistance worldwide, having evolved resistance against pyrethroids, organophosphates, carbamates, organochlorines, and recently to macrocyclic lactone spinosad and several Bacillus thuringiensis toxins. In the present study, we conducted a TE annotation using combined approaches, and the results revealed a total of 8521 TEs, representing 236,132 copies, covering 12.86% of the H. armigera genome. In addition, we underlined TE insertions in defensome genes and we successfully identified nine TE insertions belonging to the RTE, R2, CACTA, Mariner and hAT superfamilies.

Abstract

The cotton bollworm Helicoverpa armigera Hübner (Lepidoptera: Noctuidae) is an important pest of many crops that has developed resistance to almost all groups of insecticides used for its management. Insecticide resistance was often related to Transposable Element (TE) insertions near specific genes. In the present study, we deeply retrieve and annotate TEs in the H. armigera genome using the Pipeline to Retrieve and Annotate Transposable Elements, PiRATE. The results have shown that the TE library consists of 8521 sequences representing 236,132 TE copies, including 3133 Full-Length Copies (FLC), covering 12.86% of the H. armigera genome. These TEs were classified as 46.71% Class I and 53.29% Class II elements. Among Class I elements, Short and Long Interspersed Nuclear Elements (SINEs and LINEs) are the main families, representing 21.13% and 19.49% of the total TEs, respectively. Long Terminal Repeat (LTR) and Dictyostelium transposable element (DIRS) are less represented, with 5.55% and 0.53%, respectively. Class II elements are mainly Miniature Inverted Transposable Elements (MITEs) (49.11%), then Terminal Inverted Repeats (TIRs) (4.09%). Superfamilies of Class II elements, i.e., Transib, P elements, CACTA, Mutator, PIF-harbinger, Helitron, Maverick, Crypton and Merlin, were less represented, accounting for only 1.96% of total TEs. In addition, we highlighted TE insertions in insecticide resistance genes and we successfully identified nine TE insertions belonging to RTE, R2, CACTA, Mariner and hAT superfamilies. These insertions are hosted in genes encoding cytochrome P450 (CyP450), glutathione S-transferase (GST), and ATP-binding cassette (ABC) transporter belonging to the G and C1 family members. These insertions could therefore be involved in insecticide resistance observed in this pest.

Comparative Transcriptome Analysis Reveals the Mechanism Related to Fluazinam Stress of Panonychus citri (Acarina: Tetranychidae)

Simple Summary

The citrus red mite, Panonychus citri, is an important pest that causes serious citrus production losses in China. The insecticide fluazinam has a good control effect on the pest mites; however, its mechanism of action on mites remains unclear. In this study, we analyzed the transcriptomic sequencing and differential expression genes in P. citri treated with fluazinam, and identified some of the genes potential involved in detoxification metabolism related with the fluazinam exposure. Evaluating the efficacy of fluazinam, and analyzing the transcriptome data of P. citri under fluazinam stress, potentially provide a new agent for prevention and control of P. citri, and also preliminary research results for exploring the mechanism of action of fluazinam on P. citri. Given the up-regulated expression levels of genes for Mn-superoxide dismutase and catalase, we speculate that they play an important role in fluazinam-stress action on P. citri.

Abstract

The use of a large number of chemical acaricides to control these pest mites has led to an increasing problem of pesticide resistance, which has always been the difficulty in integrated pest management (IPM). Fluazinam has a good control effect on Panonychus citri, the serious pest on citrus; however, we only know the mechanism of action of fluazinam as a fungicide and its mechanism of action on mites remains unclear. Through analysis using Illumina high-throughput transcriptomic sequencing and differential expression genes in P. citri treated with fluazinam, 59 cytochrome P450 genes, 23 glutathione s-transferase genes, five carboxylate esterase genes, 11 superoxide dismutase genes and 15 catalase genes were identified. The Gene Ontology enrichment and the enrichment of KEGG results showed that the treatment were enrichment for redox enzyme pathways. Evaluating the efficacy of fluazinam, and analyzing the transcriptome data of P. citri under fluazinam stress, potentially provide a new agent for prevention and control of P. citri, and also preliminary research results for exploring the mechanism of action of fluazinam on P. citri. Given the up-regulated expression levels of genes for Mn-superoxide dismutase and catalase, we speculate that they play an important role in fluazinam-stress action on P. citri.

Identification, Characterization, and Functional Analysis of Chitin Synthase Genes in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae)

Glyphodes pyloalis Walker (G. pyloalis) causes significant damage to mulberry every year, and we currently lack effective and environmentally friendly ways to control the pest. Chitin synthase (CHS) is a critical regulatory enzyme related to chitin biosynthesis, which plays a vital role in the growth and development of insects. The function of CHS in G. pyloalis, however, has not been studied. In this study, two chitin synthase genes (GpCHSA and GpCHSB) were screened from our previously created transcriptome database. The complete coding sequences of the two genes are 5,955 bp and 5,896 bp, respectively. Expression of GpCHSA and GpCHSB could be detected throughout all developmental stages. Relatively high expression levels of GpCHSA occurred in the head and integument and GpCHSB was most highly expressed in the midgut. Moreover, silencing of GpCHSA and GpCHSB using dsRNA reduced expression of downstream chitin metabolism pathway genes and resulted in abnormal development and wings stretching, but did not affect normal pupating of larvae. Furthermore, the inhibitor of chitin synthesis diflubenzuron (DFB) was used to further validate the RNAi result. DFB treatment significantly improved expression of GpCHSA, except GpCHSB, and their downstream genes, and also effected G. Pyloali molting at 48 h (62% mortality rate) and 72 h (90% mortality rate), respectively. These results show that GpCHSA and GpCHSB play critical roles in the development and wing stretching in G. pyloalis adults, indicating that the genes are attractive potential pest control targets.

Identification and Functional Study of Chitin Metabolism and Detoxification-Related Genes in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae) Based on Transcriptome Analysis

Glyphodes pyloalis Walker (Lepidoptera: Pyralididae) is a serious pest in the sericulture industry, which has caused damage and losses in recent years. With the widespread use of insecticides, the insecticide resistance of G. pyloalis has becomes increasingly apparent. In order to find other effective methods to control G. pyloalis, this study performed a transcriptome analysis of the midgut, integument, and whole larvae. Transcriptome data were annotated with KEGG and GO, and they have been shown to be of high quality by RT-qPCR. The different significant categories of differentially expressed genes between the midgut and the integument suggested that the transcriptome data could be used for next analysis. With the exception of Dda9 (GpCDA5), 19 genes were involved in chitin metabolism, most of which had close protein–protein interactions. Among them, the expression levels of 11 genes, including GpCHSA, GpCDA1, GpCDA2, GpCDA4, GPCHT1, GPCHT2a, GPCHT3a, GPCHT7, GpTre1, GpTre2, and GpRtv were higher in the integument than in the midgut, while the expression levels of the last eight genes, including GpCHSB, GpCDA5, GpCHT2b, GpCHT3b, GpCHT-h, GpPAGM, GpNAGK, and GpUAP, were higher in the midgut than in the integument. Moreover, 282 detoxification-related genes were identified and can be divided into 10 categories, including cytochrome P450, glutathione S-transferase, carboxylesterase, nicotinic acetylcholine receptor, aquaporin, chloride channel, methoprene-tolerant, serine protease inhibitor, sodium channel, and calcium channel. In order to further study the function of chitin metabolism-related genes, dsRNA injection knocked down the expression of GpCDA1 and GpCHT3a, resulting in the significant downregulation of its downstream genes. These results provide an overview of chitin metabolism and detoxification of G. pyloalis and lay the foundation for the effective control of this pest in the sericulture industry.