Guang-Mao Shen

Transcriptome Analysis of the Oriental Fruit Fly (Bactrocera dorsalis)

Background The oriental fruit fly, Bactrocera dorsalis (Hendel), is one of the most economically important pests in the world, causing serious damage to fruit production. However, lack of genetic information on this organism is an obstacle to understanding the mechanisms behind its development and its ability to resist insecticides. Analysis of the B. dorsalis transcriptome and its expression profile data is essential to extending the genetic information resources on this species, providing a shortcut that will support studies on B. dorsalis. Methodology/Principal Findings We performed de novo assembly of a transcriptome using short read sequencing technology (Illumina). The results generated 484,628 contigs, 70,640 scaffolds, and 49,804 unigenes. Of those unigenes, 27,455 (55.13%) matched known proteins in the NCBI database, as determined by BLAST search. Clusters of orthologous groups (COG), gene orthology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to better understand the functions of these unigenes. Genes related to insecticide resistance were analyzed in additional detail. Digital gene expression (DGE) libraries showed differences in gene expression profiles at different developmental stages (eggs, third-instar larvae, pupae, and adults). To confirm the DGE results, the expression profiles of six randomly selected genes were analyzed. Conclusion/Significance This transcriptome greatly improves our genetic understanding of B. dorsalis and makes a huge number of gene sequences available for further study, including both genes of known importance and genes of unknown function. The DGE data provide comprehensive insight into gene expression profiles at different developmental stages. This facilitates the study of the role of each gene in the developmental process and in insecticide resistance.

In silico cloning and annotation of genes involved in the digestion, detoxification and RNA interference mechanism in the midgut of Bactrocera dorsalis [Hendel (Diptera: Tephritidae)]

As the second largest organ in insects, the insect midgut is the major tissue involved in the digestion of food and detoxification of xenobiotics, such as insecticides, and the first barrier and target for oral RNA interference (RNAi). In this study, we performed a midgut‐specific transcriptome analysis in the oriental fruit fly, Bactrocera dorsalis, an economically important worldwide pest, with many populations showing high levels of insecticide resistance. Using high‐throughput sequencing, 52 838 060 short reads were generated and assembled to 25 236 unigenes with a mean length of 758 bp. Interestingly, 34 unique sequences encoding digestion enzymes were newly described and these included aminopeptidase and trypsin, genes associated with Bacillus thuringiensis resistance and fitness cost. Second, 41 transcripts were annotated to particular detoxification genes such as glutathione S‐transferases, carboxylesterases and cytochrome P450s, and the subsequent phylogenetic analysis indicated homology with tissue‐specific and insecticide resistance‐related genes of Drosophila melanogaster. Third, we identified the genes involved in the mechanism of RNAi and the uptake of double‐stranded RNA. The sequences encoding Dicer‐2, R2D2, AGO2, and Eater were confirmed, but SID and SR‐CI were absent in the midgut transcriptome. In conclusion, the results provide basic molecular information to better understand the mechanisms of food digestion, insecticide resistance and oral RNAi in this important pest insect in agriculture. Specific genes in these systems can be used in the future as potential targets for pest control, for instance, with RNAi technology.

Evaluation of suitable reference genes for quantitative RT-PCR during development and abiotic stress in Panonychus citri (McGregor) (Acari: Tetranychidae)

Quantitative real time reverse transcriptase polymerase chain reaction (RT-qPCR) is preferred for gene expression analysis in living organisms. Currently, it is a valuable tool for biological and ecological studies as it provides a relatively straightforward way to assess the relevance of transcriptional regulation under developmental and stress tolerance conditions. However, studies have shown that some commonly used reference genes varied among different experimental treatments, thus, systematic evaluation of reference genes is critical for gene expression profiling, which is often neglected in gene expression studies of arthropods. The aim of this study is to identify the suitable reference genes for RT-qPCR experiments involving various developmental stages and/or under abiotic stresses in citrus red mite Panonychus citri, a key pest in citrus orchards worldwide. GeNorm, NormFinder, and Bestkeeper software analysis indicates that elongation factor-1 alpha (ELF1A), RNA polymerase II largest subunit, alpha tublin, and glyceraldhyde-3-phosphate dehydrogenase (GAPDH) are the most stable reference genes in various developmental stages, meanwhile, ELF1A and GAPDH were the most stable reference genes under various abiotic stresses. Furthermore, this study will serve as a resource to screen reference genes for gene expression studies in any other spider mite species.

Analysis of insecticide resistance-related genes of the Carmine spider mite Tetranychus cinnabarinus based on a de novo assembled transcriptome.

The carmine spider mite (CSM), Tetranychus cinnabarinus, is an important pest mite in agriculture, because it can develop insecticide resistance easily. To gain valuable gene information and molecular basis for the future insecticide resistance study of CSM, the first transcriptome analysis of CSM was conducted. A total of 45,016 contigs and 25,519 unigenes were generated from the de novo transcriptome assembly, and 15,167 unigenes were annotated via BLAST querying against current databases, including nr, SwissProt, the Clusters of Orthologous Groups (COGs), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). Aligning the transcript to Tetranychus urticae genome, the 19255 (75.45%) of the transcripts had significant (e-value <10−5) matches to T. urticae DNA genome, 19111 sequences matched to T. urticae proteome with an average protein length coverage of 42.55%. Core Eukaryotic Genes Mapping Approach (CEGMA) analysis identified 435 core eukaryotic genes (CEGs) in the CSM dataset corresponding to 95% coverage. Ten gene categories that relate to insecticide resistance in arthropod were generated from CSM transcriptome, including 53 P450-, 22 GSTs-, 23 CarEs-, 1 AChE-, 7 GluCls-, 9 nAChRs-, 8 GABA receptor-, 1 sodium channel-, 6 ATPase- and 12 Cyt b genes. We developed significant molecular resources for T. cinnabarinus putatively involved in insecticide resistance. The transcriptome assembly analysis will significantly facilitate our study on the mechanism of adapting environmental stress (including insecticide) in CSM at the molecular level, and will be very important for developing new control strategies against this pest mite.

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

The citrus red mite, Panonychus citri, is known for its ability rapidly to evolve resistance to insecticides/acaricides and to adapt to hosts that produce toxins. In this study, we constructed an unprecedented four gigabase pair transcriptome of P. citri, which was assembled into 64 149 unique transcripts, the functions of which were annotated by five public databases. A total of 116 unique transcripts were identified as representatives of potential involvement in the detoxification of xenobiotics. Genes recorded to encoding insecticide/acaricide target proteins were also obtained from the P. citri transcriptome. In order to explore novel candidate genes potentially involved in the pesticide detoxification of P. citri, we also constructed digital gene expression libraries of short‐term transcriptome responses of P. citri to pesticides, which resulted in the identification of 120 unique transcripts potentially associated with insecticide/acaricide detoxification. Our study will facilitate molecular research on pesticide resistance in citrus red mites, as well as in other phytophagous mites.

Biochemical and molecular characterisation of acetylcholinesterase in four field populations of Bactrocera dorsalis (Hendel) (Diptera: Tephritidae).

BACKGROUND The oriental fruit fly, Bactrocera dorsalis, is a major pest that infects fruits and agricultural products worldwide. The latest resistance monitoring of B. dorsalis from mainland China has identified high levels of resistance to insecticides. In this study, the biochemical and molecular characteristics of acetylcholinesterase (AChE) in four field populations of B. dorsalis are investigated. RESULTS Among the four populations, the DG population and its purified AChE were found to be the least susceptible to malathion and five inhibitors, whereas the KM population and its purified AChE were the most susceptible. The highest catalytic activity of purified AChE was found for the KM population, and the catalytic activity of the DG population was the lowest. Among developmental stages, the AChE purified from larvae was found to be the most insusceptible to inhibitors, but its catalytic activity was the highest. Sequence analysis of the cDNA encoding AChE showed that some residue differences existed. However, no significant differences in expression levels of the AChE gene among populations and developmental stages were detected. CONCLUSION The results suggest that the decrease in susceptibility of B. dorsalis was mainly caused by decrease in AChE activity, and they provide a broad view on the relation between AChE and resistance.

Molecular Characterization of the cDNA Encoding Ecdysone Receptor Isoform B1 and Its Expression in the Oriental Fruit Fly, Bactrocera dorsalis (Diptera: Tephritidae)

ABSTRACT The 20-hydroxyecdysone (20E) plays a critical role in a series of biological processes, via the ecdysone receptor/USP heterodimeric complex in arthropod. In order to clarify the regulatory mechanism of 20E, we characterized a full-length cDNA encoding a putative ecdysone receptor isoform B1 and named it as BdEcR-B1 in the oriental fruit fly, Bactrocera dorsalis. The BdEcR-B1 gene was 3,111 bp long, with an open reading frame of 2,304 bp, which encoded 767 amino acids with a predicated molecular weight of 83.3 kDa and an isoelectric point of 6.74. Alignment analysis revealed that the deduced protein sequence had 80% identity to EcR-B1 isoforms of various dipteran species, indicating that this gene was highly conserved during the evolution of the Diptera. Phylogenetic analysis suggested that BdEcR-B1 was orthologous to the EcR-B1 proteins identified in other insect species. Quantitative real-time PCR showed that BdEcR-B1 was expressed at all tested developmental stages, and the expression of BdEcR-B1 reached a significantly higher level just prior to the larval-pupa molt stage and in 4-d old pupa than those in other stages. Moreover, the BdEcR-B1 gene much more strongly expressed in gut and Malpighian tubule than those in the trachea and fat body, which suggests that this gene may be involved in tissue-specific function during larval development.

Silencing NADPH-cytochrome P450 reductase results in reduced acaricide resistance in Tetranychus cinnabarinus (Boisduval).

Cytochrome P450 monooxygenases (P450s) are involved in metabolic resistance to insecticides and require NADPH cytochrome P450 reductase (CPR) to transfer electrons when they catalyze oxidation reactions. The carmine spider mite, Tetranychus cinnabarinus is an important pest mite of crop and vegetable plants worldwide, and its resistance to acaricides has quickly developed. However, the role of CPR on the formation of acaricide-resistance in T. cinnabarinus is still unclear. In this study, a full-length cDNA encoding CPR was cloned and characterized from T. cinnabarinus (designated TcCPR). TcCPR expression was detectable in all developmental stages of T. cinnabarinus, but it’s much lower in eggs. TcCPR was up-regulated and more inducible with fenpropathrin treatment in the fenpropathrin-resistant (FeR) strain compared with the susceptible SS strain. Feeding of double-strand RNA was effective in silencing the transcription of TcCPR in T. cinnabarinus, which resulted in decreasing the activity of P450s and increasing the susceptibility to fenpropathrin in the FeR strain but not in the susceptible strain. The current results provide first evidence that the down-regulation of TcCPR contributed to an increase of the susceptibility to fenpropathrin in resistant mites. TcCPR could be considered as a novel target for the development of new pesticides.

Reference Gene Validation for Quantitative PCR Under Various Biotic and Abiotic Stress Conditions in Toxoptera citricida (Hemiptera, Aphidiae).

ABSTRACT The regulation of mRNA expression level is critical for gene expression studies. Currently, quantitative reverse transcription polymerase chain reaction (qRT-PCR) is commonly used to investigate mRNA expression level of genes under various experimental conditions. An important factor that determines the optimal quantification of qRT-PCR data is the choice of the reference gene for normalization. To advance gene expression studies in Toxoptera citricida (Kirkaldy), an important citrus pest and a main vector of the Citrus tristeza virus, we used five tools (GeNorm, NormFinder, BestKeeper, ΔCt methods, and Ref Finder) to evaluate seven candidate reference genes (elongation factor-1 alpha [EF1&agr;], beta tubulin [β-TUB], 18S ribosomal RNA [18S], RNA polymerase II large subunit (RNAP II), beta actin (β-ACT), alpha tubulin, and glyceraldhyde-3-phosphate dehydrogenase) under different biotic (developmental stages and wing dimorphism) and abiotic stress (thermal, starvation, and UV irradiation) conditions. The results showed that EF1&agr; and 18S were the most stable genes under various biotic states, β-ACT and β-TUB during thermal stress, EF1&agr; and RNAP II under starvation stress, and RNAP II, β-ACT, and EF1&agr; under UV irradiation stress conditions. This study provides useful resources for the transcriptional profiling of genes in T. citricida and closely related aphid species.

Inducible Expression of Mu-Class Glutathione S-Transferases Is Associated with Fenpropathrin Resistance in Tetranychus cinnabarinus.

The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is a serious pest on a variety of economically important crops widely distributed in China, and its resistance to acaricides has quickly developed. In this study, we fully sequenced 13 GST genes of T. cinnabarinus (TcGSTs). The phylogenetic tree showed that five of them belonged to the delta class and the other eight belonged to the mu class. The alignment of gene sequences and comparison of gene expressions between a fenpropathrin-resistant strain (FR) and a susceptible strain (SS) showed that neither point mutation nor overexpression was detected in TcGSTs. However, when challenged by a sublethal dose of fenpropathrin, the mRNA levels of three GSTs from the mu class (TCGSTM2, TCGSTM3, and TCGSTM8) highly increased in FR, while in SS, the expression of these genes was still at the same level under the treatment. In conclusion, specific TcGSTs were identified that were inducible to stimulation by fenpropathrin, and proved that TcGSTs in FR were not constantly expressed at a high level, but could react much more quickly under the stress of fenpropathrin than SS.