Transcriptome and gene expression analysis of the rice leaf folder, Cnaphalocrosis medinalis

Rice responds to Spodoptera frugiperda infestation via epigenetic regulation of H3K9ac in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways

KEY MESSAGE

This study provided important insights into the complex epigenetic regulatory of H3K9ac-modified genes involved in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways of rice in response to Spodoptera frugiperda infestation. Physiological and molecular mechanisms underlying plant responses to insect herbivores have been well studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of hidden genes remain largely unknown. Histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plants that can activate gene transcription. In this study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using CUT&Tag-seq and RNA-seq. There were 3269 and 4609 up-regulated genes identified in plants infested by FAW larvae for 3 h and 12 h, respectively, which were mainly enriched in alpha-linolenic acid and phenylpropanoid pathways according to transcriptomic analysis. In addition, CUT&Tag-seq analysis revealed increased H3K9ac in FAW-infested plants, and there were 422 and 543 up-regulated genes enriched with H3K9ac observed at 3 h and 12 h after FAW feeding, respectively. Genes with increased H3K9ac were mainly enriched in the transcription start site (TSS), suggesting that H3K9ac is related to gene transcription. Integrative analysis of both RNA-seq and CUT&Tag-seq data showed that up-expressed genes with H3K9ac enrichment were mainly involved in the jasmonic acid (JA) and phenylpropanoid pathways. Particularly, two spermidine hydroxycinnamoyl transferase genes SHT1 and SHT2 involved in phenolamide biosynthesis were highly modified by H3K9ac in FAW-infested plants. Furthermore, the Ossht1 and Ossht2 transgenic lines exhibited decreased resistance against FAW larvae. Our findings suggest that rice responds to insect herbivory via H3K9ac epigenetic regulation in the JA signaling and phenolamide biosynthesis pathways.

Functional Identification of Olfactory Receptors of Cnaphalocrocis medinalis (Lepidoptera: Crambidae) for Plant Odor

Cnaphalocrocis medinalis (Lepidoptera: Crambidae) is a migratory insect pest on rice crops. The migratory C. medinalis population in a particular location may be immigrants, local populations, emigrants, or a mix of these. Immigrants are strongly attracted to plant odor. We conducted research to identify the olfactory receptors in a floral scent mixture that is strongly attractive to C. medinalis. Through gene cloning, 12 olfactory receptor (OR) genes were amplified and expressed in Xenopus oocytes in vitro, and three of them were found to be responsive to plant foliar and floral volatiles. These were CmedOR31, a specific receptor for geraniol; CmedOR32, a broad-spectrum OR gene that responded to both foliar and floral odors; and CmedOR1, which strongly responded to 10-4 M phenylacetaldehyde. The electrophysiological response to phenylacetaldehyde was extremely high, with a current of 3200 ± 86 nA and an extremely high sensitivity. We compared the phylogenetic tree and sequence similarity of CmedOR genes and found that CmedOR1 belonged to a uniquely conserved OR pedigree in the evolution of Glossata species, and the ORs of this pedigree strongly responded to phenylacetaldehyde. The expression of OR1 was significantly higher in the females than in the males. Localization of CmedOR1 in the antennae of C. medinalis by fluorescence in situ hybridization showed that CmedOR1 was expressed in both males and females. CmedOR1 may be an odor receptor used by females to locate food sources. The function of these ORs and their role in pest monitoring were discussed.

Moth sex pheromones affect interspecific competition among sympatric species and possibly population distribution by modulating pre-mating behavior

Premating behaviors mediated by pheromones play pivotal roles in animal mating choices. In natural populations of the striped stem borer Chilo suppressalis and the rice leaf roller Cnaphalocrocis medinalis in the rice field habitat, we discovered that Z11-16:Ald, a major component of the C. suppressalis pheromone, modulated the premating behavior of C. medinalis. Z11-16:Ald evoked a strong olfactory response in male antennae and strongly inhibited the sex pheromone trapping of male C. medinalis in the field. The functions of three C. medinalis sex pheromone receptor genes (CmedPR1-3) were verified through heterologous expression in Xenopus oocytes. CmedPR1 responded to Z11-18:OH and Z11-18:Ald, as well as the interspecific pheromone compound Z11-16:Ac of sympatric species; CmedPR2 responded to Z13-18:OH and Z13-18:Ald, as well as the sex pheromone compounds Z11-16:Ald and Z9-16:Ald of sympatric species; and CmedPR3 responded to Z11-18:OH and Z13-18:OH, as well as the interspecific pheromones Z11-16:OH, Z9-16:Ald, Z11-16:Ac, and Z11-16:Ald of sympatric species. Thus, CmedPR2 and CmedPR3 share the ligand Z11-16:Ald, which is not a component of the C. medinalis sex pheromone. Therefore, the sex pheromones of interspecific species affected the input of neural signals by stimulating the sex pheromone receptors on the antennae of male C. medinalis moths, thereby inhibiting the olfactory responses of the male moths to the sex pheromones. Our results demonstrate chemical communication among sympatric species in the rice field habitat, the recognition of intra- and interspecific sex pheromones by olfactory receptors, and how insect premating behaviors are modulated to possibly affect resource partitioning.

Glucosamine-6-phosphate N-acetyltransferase gene silencing by parental RNA interference in rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

Parental RNAi (pRNAi) is a response of RNA interference in which treated insect pests progenies showed a gene silencing phenotypes. pRNAi of CmGNA gene has been studied in Cnaphalocrocis medinalis via injection. Our results showed significant reduction in ovulation per female that was 26% and 35.26% in G1 and G2 generations, respectively. Significant reduction of hatched eggs per female were observed 23.53% and 45.26% as compared to control in G1–G2 generations, respectively. We also observed the significant variation in the sex ratio between female (40% and 53%) in G1–G2 generations, and in male (65%) in G1 generation as compared to control. Our results also demonstrated the significant larval mortality (63% and 55%) and pupal mortality (55% and 41%), and significant reduction of mRNA expression level in G1 and G2 generations. Our findings have confirmed that effectiveness of pRNAi induced silencing on the CmGNA target gene in G1–G2 generations of C. medinalis. These results suggested the potential role of pRNAi in insect pest resistance management strategies.

Cloning, Characterization, and RNA Interference Effect of the UDP-N-Acetylglucosamine Pyrophosphorylase Gene in Cnaphalocrocis medinalis

The rice leaf folder, Cnaphalocrocis medinalis is a major pest of rice and is difficult to control. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is a key enzyme in the chitin synthesis pathway in insects. In this study, the UAP gene from C. medinalis (CmUAP) was cloned and characterized. The cDNA of CmUAP is 1788 bp in length, containing an open reading frame of 1464 nucleotides that encodes 487 amino acids. Homology and phylogenetic analyses of the predicted protein indicated that CmUAP shared 91.79%, 87.89%, and 82.75% identities with UAPs of Glyphodes pyloalis, Ostrinia furnacalis, and Heortia vitessoides, respectively. Expression pattern analyses by droplet digital PCR demonstrated that CmUAP was expressed at all developmental stages and in 12 tissues of C. medinalis adults. Silencing of CmUAP by injection of double-stranded RNA specific to CmUAP caused death, slow growth, reduced feeding and excretion, and weight loss in C. medinalis larvae; meanwhile, severe developmental disorders were observed. The findings suggest that CmUAP is essential for the growth and development of C. medinalis, and that targeting the CmUAP gene through RNAi technology can be used for biological control of this insect.

Characterization, Knockdown and Parental Effect of Hexokinase Gene of Cnaphalocrocis medinalis (Lepidoptera: Pyralidae) Revealed by RNA Interference

Hexokinase (HK) is a key enzyme in chitin biosynthesis in insects and plays an important role in development and energy regulation. It also performs a crucial role in the synthesis of Glucose-6-phosphate and its putative functions are studied via injection of dsRNA corresponding to the hexokinase gene from Cnaphalocrocis medinalis (CmHK). This study was designed to analyze the characteristics and expression patterns of HK-related genes in various tissues of C. medinalis at different developmental stages. The CmHK ORF is a 1359 bp in length, encoding a protein of 452 amino acids, with homology and cluster analysis showing that CmHK shares an 85.11% sequence similarity with hexokinase from Ostrinia furnacalis.CmHK was highly expressed in the ovary and in the fifth instar larvae. Injection of dsCmHK significantly suppressed mRNA expression (73.6%) 120 h post-dsRNA injection as compared to a control group. The results demonstrated an increased incidence of larval and pupal mortality of 80% and 78%, respectively, with significant variation in the sex ratio between males (68.33%) and females (35%), overt larval deformities, and a reduction in average weight gain observed 120 h post-dsRNA injection. In addition, dsCmHK-injected C. medinalis showed a significant reduction in ovulation per female and larval hatching rate, along with increased larval and pupal mortality and variation in male and female emergence over three generations (G1, G2, and G3). Taken together, the outcomes of the study provide a foundation to study gene function and a new dimension to control C. medinalis by transgenic RNAi technology.

An overview of the transcriptional responses of two tolerant and susceptible sugarcane cultivars to borer (Diatraea saccharalis) infestation

Diatraea saccharalis constitutes a threat to the sugarcane productivity, and obtaining borer tolerant cultivars is an alternative method of control. Although there are studies about the relationship between the interaction of D. saccharalis with sugarcane, little is known about the molecular and genomic basis of defense mechanisms that confer tolerance to sugarcane cultivars. Here, we analyzed the transcriptional profile of two sugarcane cultivars in response to borer attack, RB867515 and SP80-3280, which are considered tolerant and sensitive to the borer attack, respectively. A sugarcane genome and transcriptome were used for read mapping. Differentially expressed transcripts and genes were identified and termed to as DETs and DEGs, according to the sugarcane database adopted. A total of 745 DETs and 416 DEGs were identified (log₂|ratio| > 0.81; FDR corrected P value ≤ 0.01) after borer infestation. Following annotation of up- and down-regulated DETs and DEGs by similarity searches, the sugarcane cultivars demonstrated an up-regulation of jasmonic acid (JA), ethylene (ET), and defense protein genes, as well as a down-regulation of pathways involved in photosynthesis and energy metabolism. The expression analysis also highlighted that RB867515 cultivar is possibly more transcriptionally activated after 12 h from infestation than SP80-3280, which could imply in quicker responses by probably triggering more defense-related genes and mediating metabolic pathways to cope with borer attack.

Identification and temporal expression profiles of cuticular proteins in the endoparasitoid wasp, Microplitis mediator

Recently, parasitoid wasp species Microplitis mediator has evoked increasing research attention due to its possible use in the control of Lepidoptera insects. Because insect development involves changes in cuticle composition, identification and expression analysis of M. mediator cuticular proteins may clarify the mechanisms involved in parasite development processes. We found 70 cuticular proteins from the M. mediator transcriptome and divided them into seven distinct families. Expression profiling indicated that most of these cuticular protein genes have expression peaks specific for one particular developmental stage of M. mediator. Eggs and pupae have the highest number of transcriptionally active cuticular protein genes (47 and 52 respectively). Only 12 of these genes maintained high expression activity during late larval development. Functional analysis of two larval proteins, MmCPR3 and MmCPR14, suggested their important role in the proper organization of the cuticle layers of larvae. During M. mediator larval development, normal cuticle formation can be supported by a limited number of cuticular proteins.

Potential targets for controlling Bactrocera dorsalis using cuticle- and hormone-related genes revealed by a developmental transcriptome analysis

BACKGROUND

The oriental fruit fly, Bactrocera dorsalis (Hendel), is an important agricultural pest and has developed resistance to many insecticides. To investigate vital genes participating in metamorphosis for development of additional control strategies, a comprehensive transcriptome analysis covering ten developmental stages of B. dorsalis was performed.

RESULTS

There were 2132, 952, 1062, 2301 and 1333 differentially expressed genes identified during hatching, 1st-instar larval molting, 2nd-instar larval molting, pupariation and emergence, respectively. Further expression analyses indicated that genes in hormone- (20-hydroxyecdysone and juvenile hormone) and cuticle- (chitin and cuticle protein) related pathways were essential for metamorphosis in B. dorsalis. Among chitinase (Cht) genes, BdCht-5, -8 and -10 were differentially expressed during larval-larval, larval-pupal and pupal-adult moltings. However, BdCht7 was differentially expressed during egg-larval and larval-larval moltings. Knockdown of BdCht7 at the 1st-instar larval stage disrupted normal development of larvae and was lethal to B. dorsalis. Among cuticle protein (CP) genes, 15 genes (BdCPLCG-1, BdCPLCP-2, BdCPAP1-B2, BdRR1-21, BdRR1-31, BdRR2-15, BdRR2-26, BdRR2-30, BdRR2-32, BdTweedle-9, BdTweedle-24, BdRR2-10, BdCPAP3-C1, BdRR1-34 and BdRR1-41) were differentially expressed during four of five types of moltings. Among hormone-relative genes, BdJHBP-4, -9 and -13 were differentially expressed during all five types of moltings, whereas BdJHBP-5, -12 and BdHR4 were differentially expressed during four of five types of moltings.

CONCLUSION

This study reveals critical genes involved in development and metamorphosis of B. dorsaslis, and BdCht7 is dispensable for larval survival. It also provides comprehensive transcriptome information for finding more molecular targets to control this pest. © 2020 Society of Chemical Industry.

Phenotyping and Genotype × Environment Interaction of Resistance to Leaffolder, Cnaphalocrocis medinalis Guenee (Lepidoptera: Pyralidae) in Rice

Rice leaffolder, Cnaphalocrocis medinalis is one of the key foliage feeding insects of great concern throughout Asia as it results in significant yield losses. High visibility of damage is triggering farmers to apply toxic pesticides for its management. Therefore, it is vital to identify new stable sources of resistance for leaffolder. Phenotyping of 160 recombinant inbred lines (RILs) of a cross between a resistant parent, W1263 and a susceptible parent, TN1 using a rapid field screening method for three seasons resulted in identification of nine RILs as stable sources of resistance to rice leaffolder. Phenotypic frequency distributions were found continuous indicating that the resistance is a quantitative trait governed by polygenes. Phenotypic data for three seasons were analyzed using Genotype and Genotype × Environment Interaction (GGE) analysis for identification of stable resistant lines. Additive main effect and multiplicative interaction (AMMI) analysis showed that 86.41% of the total sum of square of damaged leaf area was attributed to genotype (GEN) effect; 0.48% to environment (ENV) effects and 5.68% to genotype by environment (G × E) interaction effects. Damage area, damage score and leaf length showed very high broad-sense heritability across three environments. However, leaf width had low heritability indicating higher environment influence. Phylogenetic analysis grouped these 160 RILs and parents into five clusters based on resistant reaction. AMMI and GGE biplot analysis revealed that stable genotypes G8 (MP114) and G3 (MP108) with lower damage area and damage score can be utilized in developing cultivars with leaffolder resistance.

Comparative transcriptome analysis provides insights of anti-insect molecular mechanism of Cassia obtusifolia trypsin inhibitor against Pieris rapae

Pieris rapae, a serious Lepidoptera pest of cultivated crucifers, utilizes midgut enzymes to digest food and detoxify secondary metabolites from host plants. A recombinant trypsin inhibitor (COTI) from nonhost plant, Cassia obtusifolia, significantly decreased activities of trypsin-like proteases in the larval midgut on Pieris rapae and could suppress the growth of larvae. In order to know how COTI took effect, transcriptional profiles of P. rapae midgut in response to COTI was studied. A total of 51,544 unigenes were generated and 45.86% of which had homologs in public databases. Most of the regulated genes associated with digestion, detoxification, homeostasis, and resistance were downregulated after ingestion of COTI. Meanwhile, several unigenes in the integrin signaling pathway might be involved in response to COTI. Furthermore, using comparative transcriptome analysis, we detected differently expressing genes and identified a new reference gene, UPF3, by qRT-polymerase chain reaction (PCR). Therefore, it was suggested that not only proteolysis inhibition, but also suppression of expression of genes involved in metabolism, development, signaling, and defense might account for the anti-insect resistance of COTI.

De novo characterization of venom apparatus transcriptome of Pardosa pseudoannulata and analysis of its gene expression in response to Bt protein

Background

Pardosa pseudoannulata is a prevailing spider species, and has been regarded as an important bio-control agent of insect pests in farmland of China. However, the available genomic and transcriptomic databases of P. pseudoannulata and their venom are limited, which severely hampers functional genomic analysis of P. pseudoannulata. Recently high-throughput sequencing technology has been proved to be an efficient tool for profiling the transcriptome of relevant non-target organisms exposed to Bacillus thuringiensis (Bt) protein through food webs.

Results

In this study, the transcriptome of the venom apparatus was analyzed. A total of 113,358 non-redundant unigenes were yielded, among which 34,041 unigenes with complete or various length encoding regions were assigned biological function annotations and annotated with gene ontology and karyotic orthologous group terms. In addition, 3726 unigenes involved in response to stimulus and 720 unigenes associated with immune-response pathways were identified. Furthermore, we investigated transcriptomic changes in the venom apparatus using tag-based DGE technique. A total of 1724 differentially expressed genes (DEGs) were detected, while 75 and 372 DEGs were functionally annotated with KEGG pathways and GO terms, respectively. qPCR analyses were performed to verify the DEGs directly or indirectly related to immune and stress responses, including genes encoding heat shock protein, toll-like receptor, GST and NADH dehydrogenase.

Conclusion

This is the first study conducted to specifically investigate the venom apparatus of P. pseudoannulata in response to Bt protein exposure through tritrophic chain. A substantial fraction of transcript sequences was generated by high-throughput sequencing of the venom apparatus of P. pseudoannulata. Then a comparative transcriptome analysis showing a large number of candidate genes involved in immune response were identified by the tag-based DGE technology. This transcriptome dataset will provide a comprehensive sequence resource for furture molecular genetic research of the venom apparatus of P. pseudoannulata.

Electronic supplementary material

The online version of this article (10.1186/s12896-017-0392-z) contains supplementary material, which is available to authorized users.

Temporal transcriptomic profiling of the ant-feeding assassin bug Acanthaspis cincticrus reveals a biased expression of genes associated with predation in nymphs

Acanthaspis cincticrus (Stål) is an assassin bug with a specialized camouflaging behavior to ambush ants in the nymphal stages. In this study, we comprehensively sequenced all the life stages of A. cincticrus, including the eggs, five nymph instars, female and male adults using Illumina HiSeq technology. We obtained 176 million clean sequence reads. The assembled 84,055 unigenes were annotated and classified functionally based on protein databases. Among the unigenes, 29.03% were annotated by one or more databases, suggesting their well-conserved functions. Comparison of the gene expression profiles in the egg, nymph and adult stages revealed certain bias. Functional enrichment analysis of significantly differentially expressed genes (SDEGs) showed positive correlation with specific physiological processes within each stage, including venom, aggression, olfactory recognition as well as growth and development. Relative expression of ten SDEGs involved in predation process was validated using quantitative real-time PCR (qRT-PCR).

RNA-seq of Rice Yellow Stem Borer Scirpophaga incertulas Reveals Molecular Insights During Four Larval Developmental Stages

The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ∼229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches.

Molecular identification of differential expression genes associated with sex pheromone biosynthesis in Spodoptera exigua

Species-specific sex pheromone is biosynthesized and released in most female moths as a chemical cue in mating communication. However, information on genes involved in this pathway is limited. The beet armyworm, Spodoptera exigua, is a cosmopolitan agricultural pest that causes severe economic losses to many crops. In China, the female sex pheromones in sex pheromone glands (PGs) of S. exigua have been measured which comprises (Z,E)-9,12-tetradecadienyl acetate, (Z)-9-tetradecen-l-ol, (Z)-9-tetradecenyl acetate, and (Z,E)-9,12-tetradecadien-1-ol in a ratio of 47:18:18:17. Fifty-nine putative genes related to sex pheromone biosynthesis were identified in the present study by sequencing and analyzing the sex pheromone gland (PG) transcriptome of S. exigua. Expression profiles revealed that two desaturase (SexiDes5 and SexiDes11) and three fatty acyl reductase (SexiFAR2, 3, and 9) genes had PG-specific expression, and phylogenetic analysis demonstrated that they clustered with genes known to be involved in pheromone synthesis in other moth species. Our results provide crucial background information that could facilitate the elucidation of sex pheromone biosynthesis pathway of S. exigua as well as other Spodoptera species and help identify potential targets for disrupting sexual communication in S. exigua for developing novel environment-friendly pesticides.

Transcriptome Characterization of Dendrolimus punctatus and Expression Profiles at Different Developmental Stages

The pine moth Dendrolimus punctatus (Walker) is a common insect pest that confers serious damage to conifer forests in south of China. Extensive physiology and ecology studies on D. punctatus have been carried out, but the lack of genetic information has limited our understanding of the molecular mechanisms behind its development and resistance. Using RNA-seq approach, we characterized the transcriptome of this pine moth and investigated its developmental expression profiles during egg, larval, pupal, and adult stages. A total of 107.6 million raw reads were generated that were assembled into 70,664 unigenes. More than 30% unigenes were annotated by searching for homology in protein databases. To better understand the process of metamorphosis, we pairwise compared four developmental phases and obtained 17,624 differential expression genes. Functional enrichment analysis of differentially expressed genes showed positive correlation with specific physiological activities of each stage, and these results were confirmed by qRT-PCR experiments. This study provides a valuable genomic resource of D. punctatus covering all its developmental stages, and will promote future studies on biological processes at the molecular level.

De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae

The small white butterfly Pieris rapae is one of the most destructive pests of Brassicaceae. Yet little is understood about its genes involved in development. To facilitate research on P. rapae, we sequenced the transcriptome of P. rapae during six developmental stages, including the egg, three larval stages, the pupa, and the adult. In total, 240 million high-quality reads were obtained. De novo assembly generated 96,069 unigenes with an average length of 1353 nt. Of these, 31,629 unigenes had homologs as determined by a blastx search against the NR database with a cut-off e-value of 10⁻⁵. Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to functionally annotate those genes. Then, 849 genes involved in seven canonical development signaling pathway were identified, including dozens of key genes such as Hippo, Notch, and JAK2. A total of 21,883 differentially expressed (cut-off of 2-fold) unigenes were detected across the developmental stages, most of which were found between the egg and first larval stages. Interestingly, only 34 differentially expressed unigenes, most of which are cuticle protein related genes, were detected with a cut-off of 2¹⁰-fold. Furthermore, we identified 32 heat shock protein (Hsp) genes that were expressed with complete open reading frames. Based on phylogenetic trees of the Hsp genes, we found that Hsp genes with close evolutionary relationships had similar expression pattern. Additionally, partial pattern recognition receptors genes were found to be developmental regulated. This study provides comprehensive sequence resources for P. rapae and numerous differential expressed genes, and these findings will lay the foundation for future functional genomics studies on this species.

Molecular Characterization and Sex Distribution of Chemosensory Receptor Gene Family Based on Transcriptome Analysis of Scaeva pyrastri

Chemosensory receptors play key roles in insect behavior. Thus, genes encoding these receptors have great potential for use in integrated pest management. The hover fly Scaeva pyrastri (L.) is an important pollinating insect and a natural enemy of aphids, mainly distributed in the Palearctic and Nearctic regions. However, a systematic identification of their chemosensory receptor genes in the antennae has not been reported. In the present study, we assembled the antennal transcriptome of S. pyrastri by using Illumina sequencing technology. Analysis of the transcriptome data identified 60 candidate chemosensory genes, including 38 for odorant receptors (ORs), 16 for ionotropic receptors (IRs), and 6 for gustatory receptors (GRs). The numbers are similar to those of other Diptera species, suggesting that we were able to successfully identify S. pyrastri chemosensory genes. We analyzed the expression patterns of all genes by using reverse transcriptase PCR (RT-PCR), and found that some genes exhibited sex-biased or sex-specific expression. These candidate chemosensory genes and their tissue expression profiles provide information for further studies aimed at fully understanding the molecular basis behind chemoreception-related behaviors in S. pyrastri.

Defense Responses in Rice Induced by Silicon Amendment against Infestation by the Leaf Folder Cnaphalocrocis medinalis

Silicon (Si) amendment to plants can confer enhanced resistance to herbivores. In the present study, the physiological and cytological mechanisms underlying the enhanced resistance of plants with Si addition were investigated for one of the most destructive rice pests in Asian countries, the rice leaf folder, Cnaphalocrocis medinalis (Guenée). Activities of defense-related enzymes, superoxide dismutase, peroxidase, catalase, phenylalanine ammonia-lyase, and polyphenol oxidase, and concentrations of malondialdehyde and soluble protein in leaves were measured in rice plants with or without leaf folder infestation and with or without Si amendment at 0.32 g Si/kg soil. Silicon amendment significantly reduced leaf folder larval survival. Silicon addition alone did not change activities of defense-related enzymes and malondialdehyde concentration in rice leaves. With leaf folder infestation, activities of the defense-related enzymes increased and malondialdehyde concentration decreased in plants amended with Si. Soluble protein content increased with Si addition when the plants were not infested, but was reduced more in the infested plants with Si amendment than in those without Si addition. Regardless of leaf folder infestation, Si amendment significantly increased leaf Si content through increases in the number and width of silica cells. Our results show that Si addition enhances rice resistance to the leaf folder through priming the feeding stress defense system, reduction in soluble protein content and cell silicification of rice leaves.

Identification and Expression Profiles of Sex Pheromone Biosynthesis and Transport Related Genes in Spodoptera litura

Although the general pathway of sex pheromone synthesis in moth species has been established, the molecular mechanisms remain poorly understood. The common cutworm Spodoptera litura is an important agricultural pest worldwide and causes huge economic losses annually. The female sex pheromone of S. litura comprises Z9,E11-14:OAc, Z9,E12-14:OAc, Z9-14:OAc, and E11-14:OAc. By sequencing and analyzing the transcriptomic data of the sex pheromone glands, we identified 94 candidate genes related to pheromone biosynthesis (55 genes) or chemoreception (39 genes). Gene expression patterns and phylogenetic analysis revealed that two desaturase genes (SlitDes5 and SlitDes11) and one fatty acyl reductase gene (SlitFAR3) showed pheromone gland (PG) biased or specific expression, and clustered with genes known to be involved in pheromone synthesis in other moth species. Furthermore, 4 chemoreception related genes (SlitOBP6, SlitOBP11, SlitCSP3, and SlitCSP14) also showed higher expression in the PG, and could be additional candidate genes involved in sex pheromone transport. This study provides the first solid background information that should facilitate further elucidation of sex pheromone biosynthesis and transport, and indicates potential targets to disrupt sexual communication in S. litura for a novel pest management strategy.

Identification of Genes Putatively Involved in Chitin Metabolism and Insecticide Detoxification in the Rice Leaf Folder (Cnaphalocrocis medinalis) Larvae through Transcriptomic Analysis

The rice leaf roller (Cnaphalocrocis medinalis) is one of the most destructive agricultural pests. Due to its migratory behavior, it is difficult to control worldwide. To date, little is known about major genes of C. medinalis involved in chitin metabolism and insecticide detoxification. In order to obtain a comprehensive genome dataset of C. medinalis, we conducted de novo transcriptome sequencing which focused on the major feeding stage of fourth-instar larvae, and our work revealed useful information on chitin metabolism and insecticide detoxification and target genes of C. medinalis. We acquired 29,367,797 Illumina reads and assembled these reads into 63,174 unigenes with an average length of 753 bp. Among these unigenes, 31,810 were annotated against the National Center for Biotechnology Information non-redundant (NCBI nr) protein database, resulting in 24,246, 8669 and 18,176 assigned to Swiss-Prot, clusters of orthologous group (COG), and gene ontology (GO), respectively. We were able to map 10,043 unigenes into 285 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Specifically, 16 genes, including five chitin deacetylases, two chitin synthases, five chitinases and four other related enzymes, were identified to be putatively involved in chitin biosynthesis and degradation, whereas 360 genes, including cytochrome P450s, glutathione S-transferases, esterases, and acetylcholinesterases, were found to be potentially involved in insecticide detoxification or as insecticide targets. The reliability of the transcriptome data was determined by reverse transcription quantitative PCR (RT-qPCR) for the selected genes. Our data serves as a new and valuable sequence resource for genomic studies on C. medinalis. The findings should improve our understanding of C. medinalis genetics and contribute to management of this important agricultural pest.

GLUTATHIONE S-TRANSFERASE Genes IN THE RICE LEAFFOLDER, Cnaphalocrocis medinalis (LEPIDOPTERA: PYRALIDAE): IDENTIFICATION AND EXPRESSION PROFILES

In insects, glutathione S-transferases (GSTs) play critical roles in the detoxification of various insecticides, resulting in insecticide resistance. The rice leaffolder, Cnaphalocrocis medinalis, is an economically important pest of rice in Asia. GST genes have not been largely identified in this insect species. In the present study, by searching the transcriptome dataset, 25 candidate GST genes were identified in C. medinalis for the first time. Of these, 23 predicted GST proteins fell into five cytosolic classes (delta, epsilon, omega, sigma, and zeta), and two were assigned to the "unclassified" subgroup. Real-time quantitative PCR analysis showed that these GST genes were differentially expressed in various tissues, including the midgut, Malpighian tubules, and fat body of larvae, and the antenna, abdomen, and leg of adults, indicating diversified functions for these genes. Transcription levels of CmGSTd2, CmGSTe6, and CmGSTe7 increased significantly in larvae following exposure to chlorpyrifos, suggesting that these GST genes could be involved in the detoxification of this insecticide. The results of our study pave the way to a better understanding of the detoxification system of C. medinalis.

Silicon-mediated resistance in a susceptible rice variety to the rice leaf folder, Cnaphalocrocis medinalis Guenée (Lepidoptera: Pyralidae)

The rice leaf folder, Cnaphalocrocis medinalis (Guenée), is one of the most destructive rice pests in Asian countries. Rice varieties resistant to the rice leaf folder are generally characterized by high silicon content. In this study, silicon amendment, at 0.16 and 0.32 g Si/kg soil, enhanced resistance of a susceptible rice variety to the rice leaf folder. Silicon addition to rice plants at both the low and high rates significantly extended larval development and reduced larval survival rate and pupation rate in the rice leaf folder. When applied at the high rate, silicon amendment reduced third-instars' weight gain and pupal weight. Altogether, intrinsic rate of increase, finite rate of increase and net reproduction rate of the rice leaf folder population were all reduced at both the low and high silicon addition rates. Although the third instars consumed more in silicon-amended treatments, C:N ratio in rice leaves was significantly increased and food conversion efficiencies were reduced due to increased silicon concentration in rice leaves. Our results indicate that reduced food quality and food conversion efficiencies resulted from silicon addition account for the enhanced resistance in the susceptible rice variety to the rice leaf folder.

Accelerated and synchronized oviposition induced by flight of young females may intensify larval outbreaks of the rice leaf roller

Physiological management of migration-reproduction trade-offs in energy allocation often includes a package of adaptions referred to as the oogenesis-flight syndrome. In some species, this trade-off may be overestimated, because factors like flight behavior and environmental conditions may mitigate it. In this study, we examined the reproductive consequences induced by different flight scenarios in an economically-important Asian migrant insect, Cnaphalocrocis medinalis. We found that the influences of flight on reproduction are not absolutely positive or negative, but instead depend on the age at which the moth begins flight, flight duration, and how many consecutive nights they are flown. Adult flight on the 1st or 2nd night after emergence, flight for 6 h or 12 h nightly, and flight on the first two consecutive nights after emergence significantly accelerated onset of oviposition or enhanced synchrony of egg-laying. The latter can contribute to subsequent larval outbreaks. However, flight after the 3rd night, flight for 18 h at any age, or flight on more than 3 consecutive nights after adult emergence did not promote reproductive development, and in some scenarios even constrained adult reproduction. These results indicate that there is a migration/reproduction trade-off in C.medinalis, but that it is mitigated or eliminated by flight under appropriate conditions. The strategy of advanced and synchronized oviposition triggered by migratory flight of young females may be common in other migratory insect pests.

Scorpion peptide LqhIT2 activates phenylpropanoid pathways via jasmonate to increase rice resistance to rice leafrollers

LqhIT2 is an insect-specific toxin peptide identified in Leiurus quinquestriatus hebraeus that can be toxic to lepidoptera pests. However, whether LqhIT2 induces insect resistance in rice, and how the LqhIT2 influences the biochemical metabolism of rice plants remains unknown. Here, purified LqhIT2-GST fusion protein had toxicity to rice leafrollers. Meanwhile, in vitro and field trials showed that LqhIT2 transgenic rice plants were less damaged by rice leafrollers compared to the wild type plants. Introducing LqhIT2 primed the elevated expression of lipoxygenase, a key component of the jasmonic acid biosynthetic pathway, together with enhanced linolenic acid, cis-(+)-12-oxophytodienoic acid, jasmonic acid, and jasmonic acid-isoleucine levels. In addition, phenylalanine ammonia-lyase, a key gene of the phenylpropanoid pathway, was up-regulated. Correspondingly, the contents of downstream products of the phenylpropanoid pathway such as flavonoids and lignins, were also increased in LqhIT2 transgenic plants. These changes were paralleled by decreased starch, glucose, and glucose-6-phosphate accumulation, the key metabolites of glycolysis pathway that supplies the raw material and intermediate carbon products for phenylpropanoids biosyntheses. These findings suggest that, in addition to its own toxicity against pests, LqhIT2 activate the phenylpropanoid pathway via jasmonate-mediated priming, which subsequently increases flavonoid and lignin content and improves insect resistance in rice.

In planta anthocyanin degradation by a vacuolar class III peroxidase in Brunfelsia calycina flowers

In contrast to detailed knowledge regarding the biosynthesis of anthocyanins, the largest group of plant pigments, little is known about their in planta degradation. It has been suggested that anthocyanin degradation is enzymatically controlled and induced when beneficial to the plant. Here we investigated the enzymatic process in Brunfelsia calycina flowers, as they changed color from purple to white. We characterized the enzymatic process by which B. calycina protein extracts degrade anthocyanins. A candidate peroxidase was partially purified and characterized and its intracellular localization was determined. The transcript sequence of this peroxidase was fully identified. A basic peroxidase, BcPrx01, is responsible for the in planta degradation of anthocyanins in B. calycina flowers. BcPrx01 has the ability to degrade complex anthocyanins, it co-localizes with these pigments in the vacuoles of petals, and both the mRNA and protein levels of BcPrx01 are greatly induced parallel to the degradation of anthocyanins. Both isoelectric focusing (IEF) gel analysis and 3D structure prediction indicated that BcPrx01 is cationic. Identification of BcPrx01 is a significant breakthrough both in the understanding of anthocyanin catabolism in plants and in the field of peroxidases, where such a consistent relationship between expression levels, in planta subcellular localization and activity has seldom been demonstrated.

Optimized scorpion polypeptide LMX: a pest control protein effective against rice leaf folder

Lepidopteran insect pests are the main class of pests causing significant damage to crop plant yields. Insecticidal scorpion peptides exhibit toxicity specific for insects. Here, we report that a peptide LMX, optimized from the insect-specific scorpion neurotoxin LqhIT2, showed high levels of activity against rice leaf folder in vitro and in planta. Oral ingestion of LMX protein led to a significant decrease in feeding on rice leaves, repression of larval growth and development, delay in molting, and increase in larval lethality. Compared with LqhIT2 protein, the stability and insecticidal efficacy of LMX was better. Meanwhile, biochemical analysis showed that LMX protein ingestion dramatically decreased ecdysone content in rice leaf folder larvae, and down-regulated enzymatic activities of the detoxification system (α-naphthyl acetate esterase and glutathione S-transferase), the digestive system (tryptase and chymotrypsin), and the antioxidant system (catalase). These changes were tightly correlated with the dosage of LMX protein. Transgene analysis showed that the rate of leaf damage, and the number of damaged tillers and leaves in the transgenic line were greatly reduced relative to wild type plants and empty vector plants. Based on these observations, we propose that the insect-specific scorpion neurotoxin peptide LMX is an attractive and effective alternative molecule for the protection of rice from rice leaf folder.

De novo assembly and transcriptome analysis of contrasting sugarcane varieties

Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.

Development and characterization of microsatellite markers for rice leaffolder, Cnaphalocrocis medinalis (Guenée) and cross-species amplification in other Pyralididae

Rice leaffolder, Cnaphalocrocis medinalis (Guenée), is a destructive and widespread pest on rice. In this study, 20 microsatellite markers were isolated and characterized from C. medinalis partial genomic libraries using the method of fast isolation by AFLP of sequence containing repeats. Of these markers, 18 markers displayed polymorphisms. Polymorphisms were evaluated in 48 individuals from two natural populations. The number of alleles per locus ranged from 2 to 15, and the expected and observed heterozygosities ranged from 0.324 to 0.934 and from 0.304 to 0.917, respectively. Cross-species amplification was also performed to test the transferability of the 20 microsatellite markers and a moderate level of cross amplication was observed across the three species of Pyralididae (26.67 %). These microsatellite loci would facilitate the future study on population genetics and molecular genetics of rice leaffolder and would also be useful for study in Chilo suppressalis, Scirpophaga incertulas and Pyrausta nubilalis.

Ecological adaption analysis of the cotton aphid (Aphis gossypii) in different phenotypes by transcriptome comparison

Background

The cotton aphid, Aphis gossypii Glover, is a destructive insect pest worldwide; it directly or indirectly damages (virus transmission) 300 species of host plants. Knowledge of their ecologically adaptive mechanisms at the molecular level may provide an essential and urgent method to effectively control this pest. However, no transcriptome information is available for the cotton aphid and sequence data are scarce. Therefore, we obtained transcriptome data.

Results

To facilitate such a study, two cotton aphid transcriptomes at different growth stages of cotton, seedling and summer, were sequenced. A total of 161,396 and 66,668 contigs were obtained and assembled into 83,671 and 42,438 transcripts, respectively. After combining the raw date for both transcriptomes, the sequences were reassembled into 66,695 transcripts, and 52,160 were annotated based on BLASTX analyses. Comparison of the transcriptomes revealed that summer presented less challenges for the cotton aphids than the seedling stage of cotton. In total, 58 putative heat shock protein genes and 66 candidate cytochrome p450 genes were identified with BLASTX.

Conclusions

Our results form a basis for exploring the molecular mechanisms of ecological adaption in the cotton aphid. Our study also provides a baseline for the exploration of abiotic stress responses. In addition, it provides large-scale sequence information for further studies on this species.

Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis)

BACKGROUND

The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference.

RESULTS

Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(-5)) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements.

CONCLUSIONS

Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies.

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.

Sequencing and de novo assembly of the Asian clam (Corbicula fluminea) transcriptome using the Illumina GAIIx method

Background

The Asian clam (Corbicula fluminea) is currently one of the most economically important aquatic species in China and has been used as a test organism in many environmental studies. However, the lack of genomic resources, such as sequenced genome, expressed sequence tags (ESTs) and transcriptome sequences has hindered the research on C. fluminea. Recent advances in large-scale RNA-Seq enable generation of genomic resources in a short time, and provide large expression datasets for functional genomic analysis.

Methodology/Principal Findings

We used a next-generation high-throughput DNA sequencing technique with an Illumina GAIIx method to analyze the transcriptome from the whole bodies of C. fluminea. More than 62,250,336 high-quality reads were generated based on the raw data, and 134,684 unigenes with a mean length of 791 bp were assembled using the Velvet and Oases software. All of the assembly unigenes were annotated by running BLASTx and BLASTn similarity searches on the Nt, Nr, Swiss-Prot, COG and KEGG databases. In addition, the Clusters of Orthologous Groups (COGs), Gene Ontology (GO) terms and Kyoto Encyclopedia of Gene and Genome (KEGG) annotations were also assigned to each unigene transcript. To provide a preliminary verification of the assembly and annotation results, and search for potential environmental pollution biomarkers, 15 functional genes (five antioxidase genes, two cytochrome P450 genes, three GABA receptor-related genes and five heat shock protein genes) were cloned and identified. Expressions of the 15 selected genes following fluoxetine exposure confirmed that the genes are indeed linked to environmental stress.

Conclusions/Significance

The C. fluminea transcriptome advances the underlying molecular understanding of this freshwater clam, provides a basis for further exploration of C. fluminea as an environmental test organism and promotes further studies on other bivalve organisms.

Differential expression patterns in chemosensory and non-chemosensory tissues of putative chemosensory genes identified by transcriptome analysis of insect pest the purple stem borer Sesamia inferens (Walker)

Background

A large number of insect chemosensory genes from different gene subfamilies have been identified and annotated, but their functional diversity and complexity are largely unknown. A systemic examination of expression patterns in chemosensory organs could provide important information.

Methodology/Principal Findings

We identified 92 putative chemosensory genes by analysing the transcriptome of the antennae and female sex pheromone gland of the purple stem borer Sesamia inferens, among them 87 are novel in this species, including 24 transcripts encoding for odorant binding proteins (OBPs), 24 for chemosensory proteins (CSPs), 2 for sensory neuron membrane proteins (SNMPs), 39 for odorant receptors (ORs) and 3 for ionotropic receptors (IRs). The transcriptome analyses were validated and quantified with a detailed global expression profiling by Reverse Transcription-PCR for all 92 transcripts and by Quantitative Real Time RT-PCR for selected 16 ones. Among the chemosensory gene subfamilies, CSP transcripts are most widely and evenly expressed in different tissues and stages, OBP transcripts showed a clear antenna bias and most of OR transcripts are only detected in adult antennae. Our results also revealed that some OR transcripts, such as the transcripts of SNMP2 and 2 IRs were expressed in non-chemosensory tissues, and some CSP transcripts were antenna-biased expression. Furthermore, no chemosensory transcript is specific to female sex pheromone gland and very few are found in the heads.

Conclusion

Our study revealed that there are a large number of chemosensory genes expressed in S. inferens, and some of them displayed unusual expression profile in non-chemosensory tissues. The identification of a large set of putative chemosensory genes of each subfamily from a single insect species, together with their different expression profiles provide further information in understanding the functions of these chemosensory genes in S. inferens as well as other insects.

First Transcriptome and Digital Gene Expression Analysis in Neuroptera with an Emphasis on Chemoreception Genes in Chrysopa pallens (Rambur)

Background

Chrysopa pallens (Rambur) are the most important natural enemies and predators of various agricultural pests. Understanding the sophisticated olfactory system in insect antennae is crucial for studying the physiological bases of olfaction and also could lead to effective applications of C. pallens in integrated pest management. However no transcriptome information is available for Neuroptera, and sequence data for C. pallens are scarce, so obtaining more sequence data is a priority for researchers on this species.

Results

To facilitate identifying sets of genes involved in olfaction, a normalized transcriptome of C. pallens was sequenced. A total of 104,603 contigs were obtained and assembled into 10,662 clusters and 39,734 singletons; 20,524 were annotated based on BLASTX analyses. A large number of candidate chemosensory genes were identified, including 14 odorant-binding proteins (OBPs), 22 chemosensory proteins (CSPs), 16 ionotropic receptors, 14 odorant receptors, and genes potentially involved in olfactory modulation. To better understand the OBPs, CSPs and cytochrome P450s, phylogenetic trees were constructed. In addition, 10 digital gene expression libraries of different tissues were constructed and gene expression profiles were compared among different tissues in males and females.

Conclusions

Our results provide a basis for exploring the mechanisms of chemoreception in C. pallens, as well as other insects. The evolutionary analyses in our study provide new insights into the differentiation and evolution of insect OBPs and CSPs. Our study provided large-scale sequence information for further studies in C. pallens.

Analysis of the transcriptome of blowfly Chrysomya megacephala (Fabricius) larvae in responses to different edible oils

Background

Chrysomya megacephala (Fabricius), a prevalent necrophagous blowfly that is easily mass reared, is noted for being a mechanical vector of pathogenic microorganisms, a pollinator of numerous crops, and a resource insect in forensic investigation in the postmortem interval. In the present study, in order to comprehensively understand the physiological and biochemical functions of C. megacephala, we performed RNA-sequencing and digital gene expression (DGE) profiling using Solexa/Illumina sequencing technology.

Methodology/Principal Findings

A total of 39,098,662 clean reads were assembled into 27,588 unigenes with a mean length of 768 nt. All unigenes were searched against the Nt database, Nr database, Swiss-Prot, Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genome (KEGG) with the BLASTn or BLASTx algorithm (E-value<0.00001) for annotations. In total, 7,081 unigenes and 14,099 unigenes were functionally classified into 25 COG categories and 240 KEGG pathways, respectively. Furthermore, 20,216 unigenes were grouped into 48 sub-categories belonging to 3 main Gene Ontology (GO) categories (ontologies). Using the transcriptome data as references, we analyzed the differential gene expressions between a soybean oil-fed group (SOF) and a lard oil-fed group (LOF), compared to the negative control group (NC), using the DGE approach. We finally obtained 1,566 differentially expressed genes in SOF/NC, and 1,099 genes in LOF/NC. For further analysis, GO and KEGG functional enrichment were performed on all differentially expressed genes, and a group of differentially expressed candidate genes related to lipometabolism were identified.

Conclusions/Significance

This study provides a global survey of C. megacephala and provides the basis for further research on the functional genomics of this insect.