Transcriptome analysis of the citrus red mite, Panonychus citri, and its gene expression by exposure to insecticide/acaricide

Plant Essential Oils: Dual Action of Toxicity and Egg-Laying Inhibition on Tetranychus urticae (Acari: Tetranychidae), Unveiling Their Potential as Botanical Pesticides

Tetranychus urticae, a prominent pest mite in strawberry and vegetable cultivation in China, has developed escalating resistance due to extensive chemical pesticide application. Consequently, there is an urgent need to identify safe and efficacious methods to reduce resistance development. In this study, 38 commercially available plant essential oils (EOs) were screened for their acaricidal potential and ability to inhibit oviposition. The findings revealed that 13 EOs exhibited notable acaricidal activity, with lemon EO demonstrating the highest toxicity, followed by sage, patchouli, frankincense, lemongrass, palmarosa, and oregano EOs. In addition, 18 EOs displayed significant inhibitory effects on oviposition, with lemon EO exhibiting the highest inhibition rate (99.15%) and inhibition index (0.98). Subsequently, sage, frankincense, clove, lemongrass, oregano, patchouli, myrrh, black pepper, palmarosa, and geranium EOs also showed inhibition rates exceeding 50%. Despite black pepper, clove, myrrh, and oregano EOs demonstrating relatively low toxicity against T. urticae, they exhibited heightened efficacy in inhibiting oviposition and suppressing population expansion. This study conducted a comparative assessment of the acaricidal and oviposition inhibition activities of EOs and their principal constituents, thus providing a theoretical basis for the development of botanical acaricides against T. urticae.

Transcriptome Profiling of Rhipicephalus annulatus Reveals Differential Gene Expression of Metabolic Detoxifying Enzymes in Response to Acaricide Treatment

Ticks are hematophagous ectoparasites of economic consequence by virtue of being carriers of infectious diseases that affect livestock and other sectors of the agricultural industry. A widely prevalent tick species, Rhipicephalus (Boophilus) annulatus, has been recognized as a prime vector of tick-borne diseases in South Indian regions. Over time, the use of chemical acaricides for tick control has promoted the evolution of resistance to these widely used compounds through metabolic detoxification. Identifying the genes related to this detoxification is extremely important, as it could help detect valid insecticide targets and develop novel strategies for effective insect control. We performed an RNA-sequencing analysis of acaricide-treated and untreated R. (B.) annulatus and mapped the detoxification genes expressed due to acaricide exposure. Our results provided high-quality RNA-sequenced data of untreated and amitraz-treated R. (B.) annulatus, and then the data were assembled into contigs and clustered into 50,591 and 71,711 uni-gene sequences, respectively. The expression levels of the detoxification genes across different developmental stages of R. (B.) annulatu identified 16,635 transcripts as upregulated and 15,539 transcripts as downregulated. The annotations of the differentially expressed genes (DEGs) revealed the significant expression of 70 detoxification genes in response to the amitraz treatment. The qRT-PCR revealed significant differences in the gene expression levels across different life stages of R. (B.) annulatus.

Transcriptome analysis revealed detoxification gene expression changes in Tetranychus cinnabarinus challenged with ethyl oleate

Natural acaricides are potential biorational mite control alternatives to conventional chemical acaricides. However, little is known about the molecular mechanism of defense response to natural acaricides in mites. We previously reported significant acaricidal properties of ethyl oleate (EO) against Tetranychus cinnabarinus (here referred to as a sibling species of two-spotted spider mite, Tetranychus urticae), a highly polyphagous pest devastating crops in fields and greenhouses worldwide. In this study, we explored the molecular responses of T. cinnabarinus exposed to EO using RNA-Seq and differentially expressed gene (DEG) analysis. A total of 131, 185, and 154 DEGs were identified in T. cinnabarinus after 1, 6, and 24 h of EO treatment. In addition, 36 putative detoxification-related DEGs, including 10 cytochrome P450s (P450s), three glutathione S-transferases (GSTs), nine UDP-glycosyltransferases (UGTs), eight esterases (ESTs), and six ATP-binding cassette transporters (ABC transporters), were identified. Interestingly, the upregulation of these detoxification-related genes might be the main defense response of T. cinnabarinus exposed to EO. A quantitative real-time PCR analysis indicated that the expression profiles of 19 random DEGs were consistent with the RNA-Seq results. These findings serve as valuable information for a better understanding of the acaricide-mite interaction and molecular mechanisms involved in the defense response of T. cinnabarinus against EO.

Transcription factors CncC and Maf connect the molecular network between pesticide resistance and resurgence of pest mites

Pesticide resistance and resurgence are serious problems often occurring simultaneously in the field. In our long-term study of a fenpropathrin-resistant strain of Tetranychus cinnabaribus, enhancement of detoxification and modified fecundity mechanisms were both observed. Here we investigate the network across these two mechanisms and find a key node between resistance and resurgence. We show that the ecdysone pathway is involved in regulating the fecundity of T. cinnabaribus. The concentration change of ecdysone is consistent with the fecundity curve; the concentration of ecdysone is higher in the fenpropathrin-resistant strain which has stronger fecundity. The enhancement of ecdysone is due to overexpression of two P450 genes (CYP314A1 and CYP315A1) in the ecdysone synthesis pathway. Silencing expression of these CYP genes resulted in lower concentration of ecdysone, reduced expression of vitellogenin, and reduced fecundity of T. cinnabaribus. The expression of CYP315A1 is regulated by transcription factors Cap-n-collar isoform C (CncC) and Musculoaponeurotic fibrosarcoma protein (Maf), which are involved in regulating other P450 genes functioning in detoxification of fenpropathrin in T. cinnabaribus. A similar regulation is established in citrus pest mite Panonychus citri showing that the CncC pathway regulates expression of PcCYP315A1, which affects mite fecundity. Transcription factors are activated to upregulate detoxification genes facilitating pesticide resistance, while the "one to multiple" regulation mode of transcription factors simultaneously increases expression of metabolic enzyme genes in hormone pathways and alters the physiology of pests. This is an important response of arthropods to pesticides which leads to resistance and population resurgence.

Transcriptomic profile of the predatory mite Amblyseius swirskii (Acari: Phytoseiidae) on different host plants

Amblyseius swirskii Athias-Henriot (Acari: Phytoseiidae) is a predatory mite, effective at controlling whiteflies and thrips in protected crops. However, on tomato its efficacy as a biocontrol agent is hindered, most probably by the plant trichomes and their exudates. Our aim was to characterize the response of A. swirskii to the tomato trichome exudates and identify three major detoxification gene sets in this species: cytochromes P450 (CYPs), glutathione S-transferases (GSTs) and carboxyl/cholinesterases (CCEs). Mites were exposed separately to tomato and pepper, a favourable host plant for A. swirskii, after which their transcriptional responses were analysed and compared. The de novo transcriptome assembly resulted in 71,336 unigenes with 66.1% of them annotated. Thirty-nine A. swirskii genes were differentially expressed after transfer on tomato leaves when compared to pepper leaves; some of the expressed genes were associated with the metabolism of tomato exudates. Our results illustrate that the detoxification gene sets CYPs, GSTs and CCEs are abundant in A. swirskii, but do not play a significant role when in contact with the tomato exudates.

A De Novo Transcriptomics Approach Reveals Genes Involved in Thrips Tabaci Resistance to Spinosad

The onion thrip, Thrips tabaci (Thysanoptera: Thripidae) is a major polyphagous pest that attacks a wide range of economically important crops, especially Allium species. The thrip's damage can result in yield loss of up to 60% in onions (Allium cepa). In the past few decades, thrip resistance to insecticides with various modes of actions have been documented. These include resistance to spinosad, a major active compound used against thrips, which was reported from Israel. Little is known about the molecular mechanisms underlying spinosad resistance in T. tabaci. We attempted to characterize the mechanisms involved in resistance to spinosad using quantitative transcriptomics. Susceptible (LC50 = 0.6 ppm) and resistant (LC50 = 23,258 ppm) thrip populations were collected from Israel. An additional resistant population (LC50 = 117 ppm) was selected in the laboratory from the susceptible population. De novo transcriptome analysis on the resistant and susceptible population was conducted to identify differently expressed genes (DGEs) that might be involved in the resistance against spinosad. In this analysis, 25,552 unigenes were sequenced, assembled, and functionally annotated, and more than 1500 DGEs were identified. The expression levels of candidate genes, which included cytochrome P450 and vittelogenin, were validated using quantitative RT-PCR. The cytochrome P450 expression gradually increased with the increase of the resistance. Higher expression levels of vitellogenin in the resistant populations were correlated with higher fecundity, suggesting a positive effect of the resistance on resistant populations. This research provides a novel genetic resource for onion thrips and a comprehensive molecular examination of resistant populations to spinosad. Those resources are important for future studies concerning thrips and resistance in insect pests regarding agriculture.

A Gene Family Coding for Salivary Proteins (SHOT) of the Polyphagous Spider Mite Tetranychus urticae Exhibits Fast Host-Dependent Transcriptional Plasticity

The salivary protein repertoire released by the herbivorous pest Tetranychus urticae is assumed to hold keys to its success on diverse crops. We report on a spider mite-specific protein family that is expanded in T. urticae. The encoding genes have an expression pattern restricted to the anterior podocephalic glands, while peptide fragments were found in the T. urticae secretome, supporting the salivary nature of these proteins. As peptide fragments were identified in a host-dependent manner, we designated this family as the SHOT (secreted host-responsive protein of Tetranychidae) family. The proteins were divided in three groups based on sequence similarity. Unlike TuSHOT3 genes, TuSHOT1 and TuSHOT2 genes were highly expressed when feeding on a subset of family Fabaceae, while expression was depleted on other hosts. TuSHOT1 and TuSHOT2 expression was induced within 24 h after certain host transfers, pointing toward transcriptional plasticity rather than selection as the cause. Transfer from an 'inducer' to a 'noninducer' plant was associated with slow yet strong downregulation of TuSHOT1 and TuSHOT2, occurring over generations rather than hours. This asymmetric on and off regulation points toward host-specific effects of SHOT proteins, which is further supported by the diversity of SHOT genes identified in Tetranychidae with a distinct host repertoire.

Abamectin treatment affects glutamate decarboxylase expression and induces higher GABA levels in the citrus red mite, Panonychus citri

The citrus red mite, Panonychus citri, is one of the most economically and globally destructive mite pests of citrus. Acaricide resistance has been a growing problem in controlling this pest. As the main inhibitory neurotransmitter in organisms, γ-aminobutyric acid (GABA) is synthesized from the amino acid glutamate by the action of glutamate decarboxylases (GADs). In the present study, one novel GAD gene, PcGAD, was identified and characterized from P. citri. The opening reading frame of PcGAD contained 1548 nucleotides that encode 515 amino acids. The subsequent spatiotemporal expression pattern by RT-qPCR revealed that the expression levels of PcGAD were significantly higher in larvae than in adults. Challenging with various concentrations of abamectin resulted in the upregulation of PcGAD transcript levels. Furthermore, biochemical characterization indicated that changes in GAD activity coincided with its mRNA levels. High-performance liquid chromatography confirmed that the GABA contents of P. citri increased upon abamectin treatment. The application of abamectin induces PcGAD expression and activates GAD activity, thereby resulting in an increase in GABA content in P. citri, which contributes to the adaptability of the mite to abamectin challenge.

Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes

Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.

The choreography of the chemical defensome response to insecticide stress: insights into the Anopheles stephensi transcriptome using RNA-Seq

Animals respond to chemical stress with an array of gene families and pathways termed “chemical defensome”. In arthropods, despite many defensome genes have been detected, how their activation is arranged during toxic exposure remains poorly understood. Here, we sequenced the transcriptome of Anopheles stephensi larvae exposed for six, 24 and 48 hours to the LD₅₀ dose of the insecticide permethrin to monitor transcriptional changes of defensome genes across time. A total of 177 genes involved in insecticide defense were differentially expressed (DE) in at least one time-point, including genes encoding for Phase 0, I, II, III and antioxidant enzymes and for Heat Shock and Cuticular Proteins. Three major patterns emerged throughout time. First, most of DE genes were down-regulated at all time-points, suggesting a reallocation of energetic resources during insecticide stress. Second, single genes and clusters of genes turn off and on from six to 48 hours of treatment, showing a modulated response across time. Third, the number of up-regulated genes peaked at six hours and then decreased during exposure. Our results give a first picture of how defensome gene families respond against toxicants and provide a valuable resource for understanding how defensome genes work together during insecticide stress.

Functional analysis of a chitinase gene during the larval-nymph transition in Panonychus citri by RNA interference

Chitinases are hydrolytic enzymes that are required for chitin degradation and reconstruction in arthropods. In this study, we report a cDNA sequence encoding a putative chitinase (PcCht1) from the citrus red mite, Panonychus citri. The PcCht1 (564 aa) possessed a signal peptide, a conserver domain, and a chitin-binding domain. Structural and phylogenetic analyses found that PcCht1 had high sequence similarity to chitinases in Tetranychus urticae. Real-time quantitative PCR analyses showed that the transcript levels of PcCht1 peaked periodically in larval and nymph stages. Moreover, significant increase of PcCht1 transcript level in the larvae was observed upon the exposure of diflubenzuron. In contrast, exposures of the larvae to diflubenzuron resulted in the decreased chitin content. Furthermore, through a feeding-based RNA interference approach, we were able to reduce the PcCht1 transcript level by 59.7 % in the larvae, and consequently the treated larvae showed a very low molting rate compared with the control. Our results expanded the understanding of the important role of PcCht1 in the growth and development of P. citri.

Characterization and functional analysis of a novel glutathione S-transferase gene potentially associated with the abamectin resistance in Panonychus citri (McGregor)

The citrus red mite, Panonychus citri (McGregor), a major citrus pest distributed worldwide, has been found to be resistant to various insecticides and acaricides used in China. However, the molecular mechanisms associated with the abamectin resistance in this species have not yet been reported. In this study, results showed over-expression of a novel glutathione S-transferases (GSTs) gene (PcGSTm5) in abamectin-resistant P. citri. Quantitative real-time PCR analysis showed that the transcripts of PcGSTm5 were also significantly up-regulated after exposure to abamectin and the maximum mRNA expression level at nymphal stage. The recombinant protein of PcGSTm5-pET-28a produced by Escherichia coli showed a pronounced activity toward the conjugates of 1-chloro-2,4 dinitrobenzene (CDNB) and glutathione (GSH). The kinetics of CDNB and GSH and its optimal pH and thermal stability were also determined. Reverse genetic study through a new method of leaf-mediated dsRNA feeding further support a link between the expression of PcGSTm5 and abamectin resistance. However, no direct evidence was found in metabolism or inhibition assays to confirm the hypothesis that PcGSTm5 can metabolize abamectin. Finally, it is here speculated that PcGSTm5 may play a role in abamectin detoxification through other pathway such as the antioxidant protection.

Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq

BACKGROUND

The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resistance, and the elucidation of resistance mechanisms for P. ulmi has not kept pace with insects or with the closely related spider mite Tetranychus urticae. The main reason for this lack of knowledge has been the absence of genomic resources needed to investigate the molecular biology of resistance mechanisms.

RESULTS

Here, we provide a comprehensive strand-specific RNA-seq based transcriptome resource for P. ulmi derived from strains susceptible and resistant to the widely used acaricide spirodiclofen. From a de novo assembly of the P. ulmi transcriptome, we manually annotated detoxification enzyme families, target-sites of commonly used acaricides, and horizontally transferred genes implicated in plant-mite interactions and pesticide resistance. In a comparative analysis that incorporated sequences available for Panonychus citri, T. urticae, and insects, we identified radiations for detoxification gene families following the divergence of Panonychus and Tetranychus genera. Finally, we used the replicated RNA-seq data from the spirodiclofen susceptible and resistant strains to describe gene expression changes associated with resistance. A cytochrome P450 monooxygenase, as well as multiple carboxylcholinesterases, were differentially expressed between the susceptible and resistant strains, and provide a molecular entry point for understanding resistance to spirodiclofen, widely used to control P. ulmi populations.

CONCLUSIONS

The new genomic resources and data that we present in this study for P. ulmi will substantially facilitate molecular studies of underlying mechanisms involved in acaricide resistance.

Transcriptome Analysis of the Carmine Spider Mite, Tetranychus cinnabarinus (Boisduval, 1867) (Acari: Tetranychidae), and Its Response to β-Sitosterol

Tetranychus cinnabarinus (Acari: Tetranychidae) is a worldwide polyphagous agricultural pest that has the title of resistance champion among arthropods. We reported previously the identification of the acaricidal compound β-sitosterol from Mentha piperita and Inula japonica. However, the acaricidal mechanism of β-sitosterol is unclear. Due to the limited genetic research carried out, we de novo assembled the transcriptome of T. cinnabarinus using Illumina sequencing and conducted a differential expression analysis of control and β-sitosterol-treated mites. In total, we obtained >5.4 G high-quality bases for each sample with unprecedented sequencing depth and assembled them into 22,941 unigenes. We identified 617 xenobiotic metabolism-related genes involved in detoxification, binding, and transporting of xenobiotics. A highly expanded xenobiotic metabolic system was found in mites. T. cinnabarinus detoxification genes-including carboxyl/cholinesterase and ABC transporter class C-were upregulated after β-sitosterol treatment. Defense-related proteins, such as Toll-like receptor, legumain, and serine proteases, were also activated. Furthermore, other important genes-such as the chloride channel protein, cytochrome b, carboxypeptidase, peritrophic membrane chitin binding protein, and calphostin-may also play important roles in mites' response to β-sitosterol. Our results demonstrate that high-throughput-omics tool facilitates identification of xenobiotic metabolism-related genes and illustration of the acaricidal mechanisms of β-sitosterol.

Cloning and Characterization of the Acetylcholinesterase1 Gene of Tetranychus cinnabarinus (Acari: Tetranychidae)

The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is a major agriculture pest. It can be found worldwide, has an extensive host plant range, and has shown resistance to pesticides. Organophosphate and carbamate insecticides account for more than one-third of all insecticide sales. Insecticide resistance and the toxicity of organophosphate and carbamate insecticides to mammals have become a growing concern. Acetylcholinesterase (AChE) is the major targeted enzyme of organophosphate and carbamate insecticides. In this study, we fully cloned, sequenced and characterized the ace1 gene of T. cinnabarinus, and identified the differences between T. cinnabarinus AChE1, Tetranychus urticae Koch AChE1, and human AChE1. Resistance-associated target-site mutations were displayed by comparing the AChE amino acid sequences and their AChE three-dimensional (3D) structures of the insecticide-susceptible strains of T. cinnabarinus and T. urticae to that of a T. urticae-resistant strain. We identified variation in the active-site gorge and the sites interacting with gorge residues by comparing AChE1 3D structures of T. cinnabarinus, T. urticae, and humans, though their 3D structures were similar. Furthermore, the expression profile of T. cinnabarinus AChE, at the different developmental stages, was determined by quantitative real-time polymerase chain reaction; the transcript levels of AChE were higher in the larvae stage than in other stages. The changes in AChE expression between different developmental stages may be related to their growth habits and metabolism characteristics. This study may offer new insights into the problems of insecticide resistance and insecticide toxicity of nontarget species.

Molecular characterization of vitellogenin and its receptor genes from citrus red mite, Panonychus citri (McGregor)

The production and uptake of yolk protein play an important role in the reproduction of all oviparous organisms. Vitellogenin (Vg) is the precursor of vitellin (Vn), which is the major egg storage protein, and vitellogenin receptor (VgR) is a necessary protein for the uptake of Vg into developing oocytes. In this paper, we characterize the full-length Vg and VgR, PcVg1 and PcVgR, respectively, of the citrus red mite Panonychus citri (McGregor). The PcVg1 cDNA is 5748 nucleotides (nt) with a 5553-nt open reading frame (ORF) coding for 1851 amino acids (aa), and the PcVgR is 6090 nt, containing an intact ORF of 5673 nt coding an expected protein of 1891 aa. The PcVg1 aa sequence shows a typical GLCG domain and several K/RXXR cleavage sites, and PcVgR comprises two ligand-binding domains, two epidermal growth factor (EGF)-like regions containing YWTD motifs, a transmembrane domain, and a cytoplasmic domain. An analysis of the aa sequences and phylogenetics implied that both genes were genetically distinct from those of ticks and insects. The transcriptional profiles determined by real-time quantitative PCR in different developmental stages showed that both genes present the same expressional tendencies in eggs, larvae, nymphs, and adults. This suggested that the biosynthesis and uptake of PcVg occurs coordinately. The strong reproductive capacity of P. citri has been hypothesized as an important factor in its resistance; consequently, understanding the molecular mechanisms regulating Vg and VgR are fundamental for mite control.

Molecular characterisation of a sodium channel gene and identification of a Phe1538 to Ile mutation in citrus red mite, Panonychus citri

BACKGROUND

The citrus red mite, Panonychus citri (McGregor), is regarded as one of the most serious citrus pests in many countries and has developed high resistance to pyrethroids as a result of the intensive use of these acaricides.

RESULTS

The para sodium channel gene of P. citri (named PcNav ), containing an entire coding region of 6729 bp, was cloned in this study. Three alternative splicing sites and 12 potential RNA editing sites were identified in PcNav . Thus, exons alt 1 and alt 3-v3 were found to be unique to PcNav . Comparison of field fenpropathrin-resistant (WZ) and susceptible (LS) strains identified the point mutation F1538I in IIIS6 of the sodium channel, which is known to confer strong resistance to pyrethroids in mites. Moreover, it was also found that the PcNav mRNA was present during all life stages, and the transcript seems to be more abundant in larvae than in other developmental stages.

CONCLUSION

These results suggest that the F1538I mutation plays an important role in fenpropathrin resistance in citrus red mites. This is the first study of the sodium channel in P. citri and provides abundant information for further research on the mechanism of pyrethroid resistance.

De novo transcriptome of the Hemimetabolous German cockroach (Blattella germanica)

Background

The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica.

Methodology/Principal Findings

A total of 1,365,609 raw reads with an average length of 529 bp were generated via pyrosequencing the mixed cDNA library from different life stages of German cockroach including maturing oothecae, nymphs, adult females and males. The raw reads were de novo assembled to 48,800 contigs and 3,961 singletons with high-quality unique sequences. These sequences were annotated and classified functionally in terms of BLAST, GO and KEGG, and the genes putatively coding detoxification enzyme systems, insecticide targets, key components in systematic RNA interference, immunity and chemoreception pathways were identified. A total of 3,601 SSRs (Simple Sequence Repeats) loci were also predicted.

Conclusions/Significance

The whole transcriptome pyrosequencing data from this study provides a usable genetic resource for future identification of potential functional genes involved in various biological processes.

Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit

Background

Spiders (Order Araneae) are essential predators in every terrestrial ecosystem largely because they have evolved potent arsenals of silk and venom. Spider silks are high performance materials made almost entirely of proteins, and thus represent an ideal system for investigating genome level evolution of novel protein functions. However, genomic level resources remain limited for spiders.

Results

We de novo assembled a transcriptome for the Western black widow (Latrodectus hesperus) from deeply sequenced cDNAs of three tissue types. Our multi-tissue assembly contained ~100,000 unique transcripts, of which > 27,000 were annotated by homology. Comparing transcript abundance among the different tissues, we identified 647 silk gland-specific transcripts, including the few known silk fiber components (e.g. six spider fibroins, spidroins). Silk gland specific transcripts are enriched compared to the entire transcriptome in several functions, including protein degradation, inhibition of protein degradation, and oxidation-reduction. Phylogenetic analyses of 37 gene families containing silk gland specific transcripts demonstrated novel gene expansions within silk glands, and multiple co-options of silk specific expression from paralogs expressed in other tissues.

Conclusions

We propose a transcriptional program for the silk glands that involves regulating gland specific synthesis of silk fiber and glue components followed by protecting and processing these components into functional fibers and glues. Our black widow silk gland gene repertoire provides extensive expansion of resources for biomimetic applications of silk in industry and medicine. Furthermore, our multi-tissue transcriptome facilitates evolutionary analysis of arachnid genomes and adaptive protein systems.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-365) contains supplementary material, which is available to authorized users.

An analysis of the small RNA transcriptome of four developmental stages of the citrus red mite (Panonychus citri)

The citrus red mite (Panonychus citri) can feed on more than 112 plant species around the world. Endogenous small RNAs (sRNAs) have proved to be important components of gene regulation in many eukaryotes. Recently, many sRNAs have been shown to be involved in various biological processes, such as development in many animals, including insects; however, to date, no sRNAs have been reported in the citrus red mite. Using Illumina sequencing, several categories of sRNAs were identified, including 594 known microRNAs (miRNAs) grouped into 206 families and 31 novel miRNAs in the four developmental stages of citrus red mite. In addition, according to bioinformatics analysis and S-Poly(T) miRNA assays, the expression level of many miRNAs varied among the developmental stages. Furthermore, the prediction of miRNAs target genes and their functional annotation indicated that miRNAs are involved in the regulation of multiple pathways in the citrus red mite. As the first report of the sRNA world in citrus red mite, the present study furthers our understanding of the roles played by sRNAs in the development of citrus red mite and the data may help to develop methods of controlling the pests in the field.

Exposure to diflubenzuron results in an up-regulation of a chitin synthase 1 gene in citrus red mite, Panonychus citri (Acari: Tetranychidae)

Chitin synthase synthesizes chitin, which is critical for the arthropod exoskeleton. In this study, we cloned the cDNA sequences of a chitin synthase 1 gene, PcCHS1, in the citrus red mite, Panonychus citri (McGregor), which is one of the most economically important pests of citrus worldwide. The full-length cDNA of PcCHS1 contains an open reading frame of 4605 bp of nucleotides, which encodes a protein of 1535 amino acid residues with a predicted molecular mass of 175.0 kDa. A phylogenetic analysis showed that PcCHS1 was most closely related to CHS1 from Tetranychus urticae. During P. citri development, PcCHS1 was constantly expressed in all stages but highly expressed in the egg stage (114.8-fold higher than in the adult). When larvae were exposed to diflubenzuron (DFB) for 6 h, the mite had a significantly high mortality rate, and the mRNA expression levels of PcCHS1 were significantly enhanced. These results indicate a promising use of DFB to control P. citri, by possibly acting as an inhibitor in chitin synthesis as indicated by the up-regulation of PcCHS1 after exposure to DFB.

Identification and characterization of seven glutathione S-transferase genes from citrus red mite, Panonychus citri (McGregor)

The citrus red mite, Panonychus citri (McGregor), is a global citrus pest, and has developed severe resistance to several types of acaricides. However, the molecular mechanisms of resistance in this mite remain unknown. In this study, seven full-length cDNAs encoding glutathione S-transferases (GSTs) genes were identified and characterized in P. citri. The effects of pyridaben and fenpropathrin exposure on the expression of these genes were also investigated. Phylogenetic analysis revealed that the seven GSTs genes in P. citri cloned in this study belong to three different cytosolic classes, including four in mu, two in delta and one in zeta. Among these seven GSTs genes, the relative expression level of PcGSTm1 was significantly higher in adult than in the other life stages (egg, larvae and nymph). Compared with the control, the mRNA levels of the seven GST genes did not change significantly following exposure to pyridaben at LC10. However, RT-qPCR results showed that, when exposed to LC10 of fenpropathrin, six GSTs gene (PcGSTm1, PcGSTm3, PcGSTm4, PcGSTd1, PcGSTd2 and PcGSTz1) transcripts increased in a time-dependent manner. This is the first insight into the molecular characteristics of GSTs gene cDNAs in P. citri. The elevated GSTs gene transcripts following exposure to fenpropathrin might be one of the mechanisms involved in detoxification of this acaricide.

Mining genes involved in insecticide resistance of Liposcelis bostrychophila Badonnel by transcriptome and expression profile analysis

BACKGROUND

Recent studies indicate that infestations of psocids pose a new risk for global food security. Among the psocids species, Liposcelis bostrychophila Badonnel has gained recognition in importance because of its parthenogenic reproduction, rapid adaptation, and increased worldwide distribution. To date, the molecular data available for L. bostrychophila is largely limited to genes identified through homology. Also, no transcriptome data relevant to psocids infection is available.

METHODOLOGY AND PRINCIPAL FINDINGS

In this study, we generated de novo assembly of L. bostrychophila transcriptome performed through the short read sequencing technology (Illumina). In a single run, we obtained more than 51 million sequencing reads that were assembled into 60,012 unigenes (mean size = 711 bp) by Trinity. The transcriptome sequences from different developmental stages of L. bostrychophila including egg, nymph and adult were annotated with non-redundant (Nr) protein database, gene ontology (GO), cluster of orthologous groups of proteins (COG), and KEGG orthology (KO). The analysis revealed three major enzyme families involved in insecticide metabolism as differentially expressed in the L. bostrychophila transcriptome. A total of 49 P450-, 31 GST- and 21 CES-specific genes representing the three enzyme families were identified. Besides, 16 transcripts were identified to contain target site sequences of resistance genes. Furthermore, we profiled gene expression patterns upon insecticide (malathion and deltamethrin) exposure using the tag-based digital gene expression (DGE) method.

CONCLUSION

The L. bostrychophila transcriptome and DGE data provide gene expression data that would further our understanding of molecular mechanisms in psocids. In particular, the findings of this investigation will facilitate identification of genes involved in insecticide resistance and designing of new compounds for control of psocids.

Whole transcriptome analysis of the poultry red mite Dermanyssus gallinae (De Geer, 1778)

SUMMARY Although the poultry red mite Dermanyssus gallinae (De Geer, 1778) is the major parasitic pest in poultry farming causing substantial economic losses every year, nucleotide data are rare in the public databases. Therefore, de novo sequencing covering the transcriptome of D. gallinae was carried out resulting in a dataset of 232 097 singletons and 42 130 contiguous sequences (contigs) which were subsequently clustered into 24 140 isogroups consisting of 35 788 isotigs. After removal of sequences possibly originating from bacteria or the chicken host, 267 464 sequences (231 657 singletons, 56 contigs and 35 751 isotigs) remained, of which 10·3% showed homology to proteins derived from other organisms. The most significant Blast top-hit species was the mite Metaseiulus occidentalis followed by the tick Ixodes scapularis. To gain functional knowledge of D. gallinae transcripts, sequences were mapped to Gene Ontology terms, Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways and parsed to InterProScan. The transcriptome dataset provides new insights in general mite genetics and lays a foundation for future studies on stage-specific transcriptomics as well as genomic, proteomic, and metabolomic explorations and might provide new perspectives to control this parasitic mite by identifying possible drug targets or vaccine candidates. It is also worth noting that in different tested species of the class Arachnida no 28S rRNA was detectable in the rRNA profile, indicating that 28S rRNA might consists of two separate, hydrogen-bonded fragments, whose (heat-induced) disruption may led to co-migration with 18S rRNA.