The ascomycete fungus Beauveria bassiana is a wide host range entomo- pathogenic fungus, which is commonly used as an environmental friendly biopesticide. However, the molecular mechanisms of host-pathogen interaction of B. bassiana are not well understood. Here, the high throughput next generation sequencing was performed to analyze the transcriptome of B. bassiana JEF-007 infected bean bug (Riptorus pedestris). Differentially expressed gene (DEG) analysis results showed that total 4,684 genes including 2,381 up and 2,303 down regulated genes were identified. Most of the DEGs were classified into single- organism, cellular and metabolism processes by gene ontology (GO) analysis. Metabolism pathway was the most abound category of DEGs via KEGG pathway mapping. Several possible candidates of virulence factors were dramatically expressed after infection, such as cytotoxic lectin, bacterial-like toxin, and proteins related to cell wall, hyphal growth, nutrient uptake and halogenated compounds synthesis. Furthermore, we also found the highest expression of a novel small RNA virus in the infected bean bug, but the relationship between fungal virulence and the RNA virus was under determination. The functional roles of these possible virulence factors are remained unclear, but this work provides a new insight for further fungal studies. Our results reflect systemic impacts of fungal pathogenesis and these findings represent a significant advance in the fungal functional genomics.

The pheromone biosynthesis in Plutella xylostella is more active in the scotophase than in the photophase, which suggests that there may be changes of gene expression in the pheromone glands. To identify genes contributing to change in pheromone production, we analyzed transcriptomes from pheromone glands of both decapitated females in the photophase and normal ones in the scotophase. Comparative analysis were performed with transcriptomes of pheromone glands from non-decapitated (PG) females and decapitated ones for identification and expression of putative genes associated with pheromone biosynthesis pathway. Deep sequencing for mRNAs in the pheromone gland yielded approximately 7.5Gb and totally 17265 transcript were constructed under a homology cutoff of 10-6 Evalue. Genes putatively involved in pheromone biosynthesis were identified such as acetyl-CoA carboxylase, acetyl-CoAdehydrogenase, fatty acid synthase (FAS), desaturases (Δ9 and Δ 11) and fatty acid reductases (FAR) including pgFAR, alcohol oxidase, aldehyde oxidase and aldehyde reductase, etc. Expression of 6 signal genes involving in pheromone biosynthesis such as acyl-CoA desaturase, FAR, PBAN receptor, fatty acid transporter, acyl-CoA binding protein did not exhibited ant significant different in both transcriptomes. Quantitative RT-PCR revealed that expressions of FAS, Δ11 desaturase and pgFAR were higher in PG than that in ΔPG. Based on results, Δ11 desaturase and pgFAR may have a crucial role in sex pheromone biosynthesis of P. xylostella.

Upon freezing temperatures, most insects should avoid cellular freezing by migration to warm hibernating sites, by becoming cold-hardy or by undergoing diapause development. However, a highly threatened butterfly, Parnassius bremeri, terminates egg diapause at early winter season and grows during entire winter and spring. Thus, the cold hardiness of P. bremeri needs to be explored to understand its cold tolerance limit and physiological factors. Supercooling points (SCPs) of P. bremeri vary from -10℃ to -48℃ among season. Especially, the young larvae during Jan – Mar kept SCPs at below -20℃. Larval plasma contained high level of glycerol (39.7 mM) at March, but it decreased the level (2.4 mM) at May. Transcriptome analysis indicated high levels of gene expressions associated with glycerol synthesis. Temporal expression patterns of polyol synthesis genes supported the change of glycerol. This study suggests that glycerol is a major cryoprotectant of P. bremeri to be cold-handy against freezing temperatures during winter.

The Asian honeybee, Apis cerana, is a native honeybee species in Korea which is important in agriculture for pollination and honey production. For better understanding of the physiology of A. cerana, high-throughput Illumina transcriptome sequencing was performed to analyze the gene expression profiles of queen, worker and larva. A total of 219,799,682 clean reads corresponding to 22.2Gb of nucleotide sequences was obtained from the whole body total RNA samples. The Apis mellifera reference mRNA sequence database was used to measure the gene expression level with Bowtie2 and eXpress software and the Illumina short reads were mapped to 11,459 out of 11,736 A. mellifera reference genes. Total of 9,221 genes with FPKM value greater than 5 of each sample group were subjected to evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) with BLASTX for gene ontology analysis. The differential gene expression between queen and worker, and worker and larva were analyzed to screen the overexpressed genes in each sample group. in the queen and worker sample group, total of 1,766 genes were differentially expressed with 887 and 879 genes overexpressed over two folds in queen and worker, respectively. In the worker and larva sample group, total of 1,410 genes were differentially expressed with 1,009 and 401 genes overexpressed over two folds in worker and larva, respectively.

Rice stripe virus (RSV) is one of the serious plant pathogenic viruses for rice and mediated by small brown planthopper, Laodalphax striatellus. So far, the studies have been mainly focused on the interaction between the host plant and the virus. In this study, for better comprehension of the interactions among Rice stripe virus, rice and small brown planthopper, transcriptomes of the RSV-viruliferous (RVLS) and non-viruliferous L. striatellus (NVLS) were comparatively analysed. For this, non-viruliferous L. striatellus were collected from non-infected rice field and fed RSV-infected rice for 5 days. With the RNAs prepared from the RSV-viruliferous and the non-viruliferous small brown planthoppers, we conducted Illumina RNA sequencing (Hiseq 2000) and then two transcriptome databases were generated from RVLS and NVLS, respectively. The transcriptome of RVLS and NVLS were campared to figure out how the gene expression of the insects affected by Rice Stripe Virus. RSV-dependently regulated genes analysed from this study may have important functions in the transmission and replication of RSV.

Teratocytes (TCs) are the cells derived from the embryonic serosal membrane of some parasitic hymenopteran insects. As a parasitic factor, TCs are multifunctional in host regulation by inducing nutritional, immune, and developmental alterations. However, little is understood about their genetic constituents. This study reveals a comprehensive view of the genes expressed by TCs through a transcriptome analysis based on RNAseq technology. More than 6.29 Gb sequences were used to assemble 34,686 contigs (>200 bp) and annotated into different functional categories. The TC transcriptome profile was clearly distinct from those of hemocytes and the fat body. The TC transcriptome contained components of insulin signaling and biosynthesis of juvenile hormone and 20-hydroxyecdysone. TCs also expressed various groups of digestive enzymes, supporting its nutritional role for the growing parasitoid larvae in parasitism. Furthermore, this transcriptome analysis annotated two kinds of immunosuppressive serine protease inhibitors (serpins) and Rho GTPase-activating proteins (RhoGAPs). To determine the biological functions of these factors, we devised ex vivo RNA interference (RNAi) by conducting knockdown of gene expression in in vitro cultured TCs followed by injection of the treated TCs to test insects. Ex vivo RNAi revealed that some serpins and RhoGAPs expressed in TCs inhibited host cellular immunity. This study reports a transcriptome of the unique TC animal cell, and its immunosuppressive genetic factors using ex vivo RNAi technology.

Previously, we demonstrated the presence of a second copy of LPS myristoyl transferase in enterohemorrhagic Escherichia coli O157:H7, an important zoonotic diarrheagenic food-borne pathogen; the pO157-encoded ecf (an eae-conserved fragment) and the chromosomally-encoded lpxM (also referred to as msbM) genes. Although both genes share the same function as an LPS myristoyl transferase, the pO157-encoded ecf is thermoregulated via an intrinsically curved DNA while the chromosomal lpxM is regulated by the PhoP/Q two component regulatory system. However, it is unclear why E. coli O157: H7 carries two copies of LPS myristoyl transferase that are differentially regulated. In this study, a whole genome-scale transcriptome specific to E. coli O157:H7 was carried out for identification of the genes differentially expressed in the amyristoylated E. coli O157:H7. The results identified a total of 110 EHEC genes that were up- or down-regulated in the amyristoylated E. coli O157:H7 strain, including genes associated with virulence (26.36%), metabolism (20.91%), transport (10.91%), signal transduction (4.55%), genetic information processing (3.64%), stress response (2.73%), regulatory function (2.73%), motility/adherence (3.64%), cell envelope (2.73%), cell division (1.82%) and ORFs of unknown function (17.27%). Of particular interest, the expression of LEE pathogenicity island genes was significantly influenced by LPS structural defects.

Sacbrood virus (SBV) is one of the most fatal pathogens against Asian honeybee, Apis cerana. This virus cause failure of the insect larvae to pupate and death of the adult insects. This study has analyzed the host genes affected by viral infection, by comparing the expression level of host transcripts infected with or without SBV. As a first step, we sequenced the cDNA libraries of Asian honeybee by using illumina RNA sequencing. The sequences were de novo assembled to acquire honeybee transcriptome sequences. The transcriptome was annotated by the sequence comparison to known protein sequences by BLASTX and evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database with functional categories and description. By mapping the RNA-seq data to de novo assembled transcripts, we characterized the differentially expressed transcripts between SBV-infected and non-infected Asian honeybee.

Rice stripe virus disease (RSVD), one of the most serious disease of rice is mediated through the sucking by small brown planthopper, Laodalphax striatellus. So far, the studies have been mainly focused on the interaction between the host plant and the virus. In this study, for better comprehension of the interactions among the host plant, vector insect and plant-pathogenic virus, we investigated transcriptome of the vector insect and the differences between viruliferous and naïve L.striatellus. For this, naïve L. striatellus were collected from non-infected rice field and 50 L.striatellus of them were fed RSV-infected rice for 5 days. With the RSV-viruliferous and the naïve insects, we conducted Illumina RNA sequencing (Hiseq 2000) and obtained 175,243,488 and 146,031,348 reads from viruliferous and naïve L.striatellus, respectively. These reads were assembled into contigs and two transcriptome databases were generated. The transcriptome of naïve and RSV-viruliferous L. striatellus were campared to figure out up-regulated or down-regulated genes. These RSV-dependently regulated genes may have important function in the behavior of planthoppers or the transmission of RSV.

To investigate genes differentially expressed in the venom of social and solitary wasps, a comparative transcriptome analysis was conducted. Subtractive expressed sequence tag (EST) libraries specific to the venom gland and sac (gland/sac) of a social wasp species, Vespa tropica and a solitary hunting wasp species, Rhynchium brunneum, was constructed by suppression subtractive hybridization. In BLASTx analysis, 41% and 56% of the total ESTs showed statistically best-matched hits (E ≤ 10-4) in the libraries of V. tropica and R. brunneum, respectively. Although the functional category analysis did not show remarkable differences in the distribution of functional categories between the two venom gland/sac cDNA libraries, perhaps due to the lack of functional information on many of the venom components, there were groups of genes that are specific to either V. tropica or R. brunneum. Venom allergen 5 and serine protease were found to be social wasp-specific venom transcripts. In contrast, venom peptides, metalloendopeptidases, arginine kinase and dendrotoxin were observed in solitary wasp at much higher frequencies.

Cotesia plutellae has been known as a natural enemy against the Diamondback moth, Plutella xylostella via laying eggs into a larva. When the larva hatches from the egg, teratocytes also are released and expected to work as immune suppressor via secreting immune suppressive factors. In order to analyze the gene expression in teratocytes, total RNAs were isolated and genes expressed in the teratocyte were sequenced by Illumina HiSeq2000 RNASeq analysis. The information on RNA sequences was assembled by Trinity and contigs were annotated by Blast analysis. The levels of gene expression were calculated by FPKM. Approximately, 6.3 Gbs were obtained and 34,686 contigs were found and annotated. Forty two percent of contigs were homologous to previously reported genes and classified by gene ontologies: the highly abundant components are metabolic process, biological regulation and cellular process in biological function; binding, catalytic activity and transporter activity in molecular function; cell part, membrane part and organelle in cellular function, respectively. In addition, some teratocyte transcripts of C. plutellae are related to host regulation such as immunosuppression and nutrition: Ankyrin repeat proteins, Serpin, protease, lipase, chitinase and scavenger receptor.

The physiology of parasitic wasp control of their lepidopteran hosts' not only includes injecting their egg but also various factors such as symbiotic virus. This study was focused on the investigation of sophisticated interaction between parasitoid (Diadegma fenestrale) and their host (Plutella xylostella) in P. xylostella larva at transcriptome level, to check whether it is parasitized or not. Short-read deep sequencing method (Hiseq2000) was used for the transcriptome analysis. De novo assembly of cDNA sequence data generated 196,081 contigs between 201bp and 15,853bp in length. Some detoxification enzymes such as cytochrome P450 and Immune-related genes such as antimicrobial peptides were up-regulated after parasitism. Expression of symbiotic ichnovirus genes was detected in parasitized larvae with 55 contigs identified from five ichnovirus gene families including vankyrin, viral innexin, repeat elements, a cysteine-rich motif, and polar residue rich protein. This investigation provides a detailed information on differential expression of P. xylostella larval genes and symbiotic ichnovirus genes following parasitization.

Among hemipteran insects which is the most important insect vector of plant viruses, small brown planthopper, Laodelphax striatellus, transmits the rice stripe virus (RSV) causing rice stripe disease. For effective control of RSV, it is important to understand interaction between RSV and L. striatellus. Therefore, in this study, expressed sequence tag (EST) databases were generated based on 454 GS-FLX pyrosequencing for comparative transcriptome analysis between nonviruliferous and RSV-viruliferous L. striatellus. By comparing the two EST libraries, we showed that 108 host genes were significantly up-regulated and 28 host genes were significantly down-regulated in viruliferous insects. Interestingly, genes encoding ribosomal proteins were mainly up-regulated in viruliferous L. striatellus, whereas genes related to translation were concentrated in the downregulated cohort. These RSV-dependently regulated genes may have important function in the behavior of planthopper or the transmission of RSV.

The oriental fruit moth (Grapholita molesta) and the plum fruit moth (G. dimorpha) are internal feeders of apples. Their sympatric and similar sex pheromone compositions suggest their recent divergence in speciation. This study aims to determine genetic factors in this speciation by comparing transcriptomes associated in sex pheromone biosynthesis in these sibling species. Total RNAs were collected two female abodominal tips and read by a short read deep sequencing technology using an lllumina HiSeq. Almost 3-4 Gb reads were de novo assembled and resulted in 76,361 contigs of G. dimorpha and 104,463 contigs of G. molesta. More than 70% of these contigs were annotated and classified by a typical GO analysis. Transcriptomes related with sex pheromone biosynthesis were selected and grouped into fatty acid synthase, fatty acid oxidation. These analyses identified sex pheromone biosynthesis machineries

The cotton aphid, Aphis gossypii (Glover), is one of the most serious pest in seed potato and various vegetable cultivation. The imidacloprid-resistant strain (IR) was over 200-fold more resistant to imidacloprid compared to a susceptible strain (S) as judged by LC50 values. The IR showed cross resistances to other neonicotinoid insecticides. IEF and 2DE analyses revealed that general esterase isozyme patterns in IR were almost identical to those of S. Nevertheless, a significantly overexpressed protein spot was detected in IR. To identify differentially expressed genes in IR, comparative transcriptome analyses based on GS-FLX were conducted using total RNAs extracted from both IR and S strains, which generated ca. 290 Mb reads for each strain. Generally, most nicotinic acetylcholine receptor subunit genes, such as alpha 2 and beta 1, were more transcribed in S than in IR. In contrast, only alpha 5 subunit gene was 1.8 fold more expressed in IR. Seven ATP-binding cassette (ABC) transporter genes were newly identified in A. gossypii, among which only ABCC9 gene was highly expressed in IR. Therefore, this ABCC subfamily, a member of the MRP subfamily which is involved in multi-drug resistance, could be one of the main factors associated with imidacloprid resistance in A. gossypii.

Background : Several members of the genus Clausena have a great potential as a candidate for the identification of new drug lead molecules, but lack of their genomic information can be a hindrance for the verification of the genetic background for future use. To broaden and delve into the genomic features of this genus, Clausena excavata, an important medicinal plant in many Asian countries, was used for RNA-seq analysis. Methods and Results : A ten ㎍ of the total RNA was used for mRNA isolation using oligo-dT beads and random sheared mRNAs were used to prepare a cDNA library for a illumina hiseq 2500 analysis. In total, 17,580,456 trimmed clear reads from the illumina hiseq 2500 were used for de novo assembly using three assemblers, CLC genomics workbench, velvet-oases, and Trinity. A total of 16,638 non-redundant unigenes with an average length of 755 bp were generated by the assembly. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2,305 genes in the cellular component, 5,577 in the biological processes, and 8,056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4,374 genes. Among annotated genes, 3,006 were mapped to 123 metabolic pathways by KEGG metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five Clausena species; eight of them exhibited polymorphism. Conclusion : In the present study, genomic resources of the genus Clausena were enriched through RNA-seq and SSR markers, which will serve as valuable resources for genomic/genetic studies of the genus Clausena and close relatives.

Arsenic (As) is accumulated in rice grain due to environmental reasons such as polluted ground water and soil, and As toxicity constitutes a serious threat to human health. However, the accurate information required for understanding As-responsive mechanisms remain mostly unknown in rice. Here, we performed the comparative genome-wide transcriptome analysis between As tolerance type (ATT) rice mutant induced by γ-irradiation and its wild type (WT). As compared to WT after As treatment of 150 ppm, ATT exhibited the phenotypic differences such as vigorous growth in shoots and root hairs, and low accumulation of H2O2 in rice roots. In transcriptome analysis, we found between WT and ATT that As toxicity commonly affected to inhibit gene regulations involved in photosynthesis, mitochondrial electron transport and lipid biosynthesis metabolism. While, many genes associated with cysteine synthesis metabolism considerably up regulated in both As-treated plants. Additionally, we found the potential As tolerance-related genes involved in abiotic stress-responsive mechanism and RNA-protein synthesis for protein degradation and modification. To further analyzes the genetic variations of As-responsive genes, the DNA polymorphic DEGs associated with oxidoreductase significantly distributed in ATT more than in WT.