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Zhang Y, Wang F, Feng Q, Wang H, Tang T, Huang D, Liu F. Involvement of trehalose-6-phosphate synthase in innate immunity of Musca domestica. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 91:85-92. [PMID: 30385314 DOI: 10.1016/j.dci.2018.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/24/2018] [Accepted: 10/28/2018] [Indexed: 06/08/2023]
Abstract
Trehalose-6-phosphate synthase (TPS) is responsible for synthesizing trehalose, which is prevalent in crustaceans and insects as blood-sugar. In this paper, a TPS gene from Musca domestica(MdTPS)has been cloned and characterized. MdTPS promoter was analyzed, and its transcriptional activity was verified in vitro by Sf9 cell. Quantitative RT-PCR analysis revealed that the MdTPS transcription was up-regulated following bacterial challenge by Escherichia coli or Staphylococcus aureus. Meanwhile, trehalose is accumulated in larvae upon bacterial challenge. Significantly increased mortality can be observed in MdTPS depleted (RNA interference, RNAi) larvae under bacterial infection. Interestingly, feeding trehalose led to increasing trehalose content in larvae, and the effects of RNAi targeting MdTPS on host survival against bacterial challenge was partly counteracted. Taken together, these results suggest that MdTPS acts as an inducible anti-stress gene that takes part in immune defense in M. domestica via synthesizing its product trehalose.
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Affiliation(s)
- Yuming Zhang
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Fan Wang
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Qin Feng
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Hongxin Wang
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Ting Tang
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Dawei Huang
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Fengsong Liu
- Key Laboratory of Invertebrate Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, 071002, China.
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Tang T, Li W, Wang X, Wu Y, Liu F. A house fly TNF ortholog Eiger regulates immune defense via cooperating with Toll and Imd pathways. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 90:21-28. [PMID: 30165084 DOI: 10.1016/j.dci.2018.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
In mammals, the TNF family is important inflammatory cytokines. Eiger, the invertebrate ortholog of TNF identified firstly in Drosophila, has been implicated in immune response with an unknown molecular mechanism. The present work reports a novel eiger like gene (Mdeiger) from Musca domestica. Mdeiger was significantly up-regulated upon challenge with either Escherichia coli or Staphylococcus aureus. Silencing Mdeiger led to higher mortalities of larvae post either E. coli or S. aureus infection, enhanced the expressions of attacin and diptericin, but blocked the induction of ceropin and muscin, and inhibited the activation of phenoloxidase following bacterial challenge. Meanwhile, the expression of dorsal and JNK was inhibited while that of relish was enhanced in Mdeiger-depleted larvae. We suppose that, by coordinating with the Imd, Toll and JNK pathways, Mdeiger be involved in regulating the innate immune response through controlling the capacity of phenoloxidase and the expression of antimicrobial peptide genes synergistically.
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Affiliation(s)
- Ting Tang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Wenqian Li
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Xiaofen Wang
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Yinjian Wu
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China
| | - Fengsong Liu
- The Key Laboratory of Zoological Systematics and Application, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
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Transcriptomic Analysis of Musca domestica to Reveal Key Genes of the Prophenoloxidase-Activating System. G3-GENES GENOMES GENETICS 2015; 5:1827-41. [PMID: 26156588 PMCID: PMC4555219 DOI: 10.1534/g3.115.016899] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The proPO system regulates melanization in arthropods. However, the genes that are involved in the proPO system in housefly Musca domestica remain unclear. Thus, this study analyzed the combined transcriptome obtained from M. domestica larvae, pupae, and adults that were either normal or bacteria-challenged by an Escherichia coli and Staphylococcus aureus mixture. A total of 54,821,138 clean reads (4.93 Gb) were yielded by Illumina sequencing, which were de novo assembled into 89,842 unigenes. Of the 89,842 unigenes, based on a similarity search with known genes in other insects, 24 putative genes related to the proPO system were identified. Eight of the identified genes encoded for peptidoglycan recognition receptors, two encoded for prophenoloxidases, three encoded for prophenoloxidase-activating enzymes, and 11 encoded for serine proteinase inhibitors. The expression levels of these identified genes were investigated by qRT-PCR assay, which were consistent with expected activation process of the proPO system, and their activation functions were confirmed by the measurement of phenoloxidase activity in bacteria-infected larvae after proPO antibody blockage, suggesting these candidate genes might have potentially different roles in the activation of proPO system. Collectively, this study has provided the comprehensive transcriptomic data of an insect and some fundamental basis toward achieving understanding of the activation mechanisms and immune functions of the proPO system in M. domestica.
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Zhou X, Qian K, Tong Y, Zhu JJ, Qiu X, Zeng X. De novo transcriptome of the Hemimetabolous German cockroach (Blattella germanica). PLoS One 2014; 9:e106932. [PMID: 25265537 PMCID: PMC4180286 DOI: 10.1371/journal.pone.0106932] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/10/2014] [Indexed: 11/23/2022] Open
Abstract
Background The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica. Methodology/Principal Findings A total of 1,365,609 raw reads with an average length of 529 bp were generated via pyrosequencing the mixed cDNA library from different life stages of German cockroach including maturing oothecae, nymphs, adult females and males. The raw reads were de novo assembled to 48,800 contigs and 3,961 singletons with high-quality unique sequences. These sequences were annotated and classified functionally in terms of BLAST, GO and KEGG, and the genes putatively coding detoxification enzyme systems, insecticide targets, key components in systematic RNA interference, immunity and chemoreception pathways were identified. A total of 3,601 SSRs (Simple Sequence Repeats) loci were also predicted. Conclusions/Significance The whole transcriptome pyrosequencing data from this study provides a usable genetic resource for future identification of potential functional genes involved in various biological processes.
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Affiliation(s)
- Xiaojie Zhou
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kun Qian
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Ying Tong
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Junwei Jerry Zhu
- United States Department of Agriculture, Agricultural Research Service, Lincoln, Nebraska, United States of America
| | - Xinghui Qiu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (XQ); (XPZ)
| | - Xiaopeng Zeng
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
- * E-mail: (XQ); (XPZ)
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Tang T, Li X, Yang X, Yu X, Wang J, Liu F, Huang D. Transcriptional response of Musca domestica larvae to bacterial infection. PLoS One 2014; 9:e104867. [PMID: 25137050 PMCID: PMC4138075 DOI: 10.1371/journal.pone.0104867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 07/18/2014] [Indexed: 11/18/2022] Open
Abstract
The house fly Musca domestica, a cosmopolitan dipteran insect, is a significant vector for human and animal bacterial pathogens, but little is known about its immune response to these pathogens. To address this issue, we inoculated the larvae with a mixture of Escherichia coli and Staphylococcus aureus and profiled the transcriptome 6, 24, and 48 h thereafter. Many genes known to controlling innate immunity in insects were induced following infection, including genes encoding pattern recognition proteins (PGRPs), various components of the Toll and IMD signaling pathways and of the proPO-activating and redox systems, and multiple antimicrobial peptides. Interestingly, we also uncovered a large set of novel immune response genes including two broad-spectrum antimicrobial peptides (muscin and domesticin), which might have evolved to adapt to house-fly's unique ecological environments. Finally, genes mediating oxidative phosphorylation were repressed at 48 h post-infection, suggesting disruption of energy homeostasis and mitochondrial function at the late stages of infection. Collectively, our data reveal dynamic changes in gene expression following bacterial infection in the house fly, paving the way for future in-depth analysis of M. domestica's immune system.
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Affiliation(s)
- Ting Tang
- College of Life Sciences, Hebei University, Baoding, China
| | - Xiang Li
- College of Life Sciences, Hebei University, Baoding, China
| | - Xue Yang
- College of Life Sciences, Hebei University, Baoding, China
| | - Xue Yu
- College of Life Sciences, Hebei University, Baoding, China
| | - Jianhui Wang
- Department of Pathology, Yale University, New Haven, Connecticut, United States of America
| | - Fengsong Liu
- College of Life Sciences, Hebei University, Baoding, China
- * E-mail: (FSL); (DWH)
| | - Dawei Huang
- College of Life Sciences, Hebei University, Baoding, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (FSL); (DWH)
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Gao J, Wang X, Zou Z, Jia X, Wang Y, Zhang Z. Transcriptome analysis of the differences in gene expression between testis and ovary in green mud crab (Scylla paramamosain). BMC Genomics 2014; 15:585. [PMID: 25015001 PMCID: PMC4124137 DOI: 10.1186/1471-2164-15-585] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/30/2014] [Indexed: 12/30/2022] Open
Abstract
Background The green mud crab (Scylla paramamosain) is the most prevalent crustacean on the southeast coast of China. The molecular regulatory mechanism of sex determination and gonadal differentiation in this species has received considerable attention in recent years because of the huge differences—both biological and economic—between male and female crabs. In this study, next-generation sequencing technology was used to develop deep-coverage transcriptomic sequencing data for the testis and ovary of S. paramamosain. Results A total of 365,116 reads (testis 171,962, ovary 193,154) with an average sequence length of 285 bp were produced from testis and ovary cDNA libraries. After filtering out contaminating reads, the clean reads were assembled, producing a total of 21,791 isotigs and leaving 22,814 reads as singlets. Using the BLASTX program, 3,471 unique sequences (2,275 isotigs and 1,196 singletons) were annotated with known protein sequences from the NCBI non-redundant (Nr) protein sequence database. The Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses allowed the 224 unique sequences that were annotated with enzyme code (EC) numbers to be mapped into 174 KEGG pathways. After comparing the ovary and testis libraries, 4,021 gonad-differentially, 10,522 ovary-specifically, and 19,013 testis-specifically expressed genes were identified. Moreover, 33 ovary-specific, 14 testis-specific, and 34 gonad-differential transcripts were confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, 8,610 putative simple sequence repeats (SSRs) and 23,879 potential single nucleotide polymorphisms (SNPs) were identified. Conclusion This is the first large-scale RNA sequencing of S. paramamosain to be reported. We have identified many important functional genes and made a preliminary attempt to construct the regulatory network involved in the gonadal development of crustaceans. The annotated transcriptome data will provide fundamental support for future research into the reproduction biology of S. paramamosain. A large number of candidate SSRs and SNPs were detected, which could be used as genetic markers for population genetics and functional genomics in this species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-585) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Yilei Wang
- Key Laboratory of Healthy Mariculture in the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, 361021 Xiamen, China.
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Nandety RS, Kamita SG, Hammock BD, Falk BW. Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis). PLoS One 2013; 8:e81681. [PMID: 24339955 PMCID: PMC3858241 DOI: 10.1371/journal.pone.0081681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Raja Sekhar Nandety
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Shizuo G. Kamita
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bruce D. Hammock
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bryce W. Falk
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Cui Z, Li X, Liu Y, Song C, Hui M, Shi G, Luo D, Li Y. Transcriptome profiling analysis on whole bodies of microbial challenged Eriocheir sinensis larvae for immune gene identification and SNP development. PLoS One 2013; 8:e82156. [PMID: 24324760 PMCID: PMC3852986 DOI: 10.1371/journal.pone.0082156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 10/21/2013] [Indexed: 01/04/2023] Open
Abstract
To study crab immunogenetics of individuals, newly hatched Eriocheir sinensis larvae were stimulated with a mixture of three pathogen strains (Gram-positive bacteria Micrococcus luteus, Gram-negative bacteria Vibrio alginolyticus and fungi Pichia pastoris; 108 cfu·mL-1). A total of 44,767,566 Illumina clean reads corresponding to 4.52 Gb nucleotides were generated and assembled into 100,252 unigenes (average length: 1,042 bp; range: 201-19,357 bp). 17,097 (26.09%) of 65,535 non-redundant unigenes were annotated in NCBI non-redundant protein (Nr) database. Moreover, 23,188 (35.38%) unigenes were assigned to three Gene Ontology (GO) categories, 15,071 (23.00%) to twenty-six Clusters of orthologous Groups (COG) and 8,574 (13.08%) to six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Numerous genes were further identified to be associated with multiple immune pathways, including Toll, immune deficiency (IMD), janus kinase (JAK)-signal transducers and activators of transcription (STAT) and mitogen-activated protein kinase (MAPK) pathways. Some of them, such as tumor necrosis factor receptor associated factor 6 (TRAF6), fibroblast growth factor (FGF), protein-tyrosine phosphatase (PTP), JNK-interacting protein 1 (JIP1), were first identified in E. sinensis. TRAF6 was even first discovered in crabs. Additionally, 49,555 single nucleotide polymorphisms (SNPs) were developed from over 13,309 unigenes. This is the first transcriptome report of whole bodies of E. sinensis larvae after immune challenge. Data generated here not only provide detail information to identify novel genes in genome reference-free E. sinensis, but also facilitate our understanding on host immunity and defense mechanism of the crab at whole transcriptome level.
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Affiliation(s)
- Zhaoxia Cui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory for Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
| | - Xihong Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Chengwen Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Hui
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guohui Shi
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Danli Luo
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingdong Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Pavlidi N, Dermauw W, Rombauts S, Chrisargiris A, Van Leeuwen T, Vontas J. Analysis of the Olive Fruit Fly Bactrocera oleae Transcriptome and Phylogenetic Classification of the Major Detoxification Gene Families. PLoS One 2013; 8:e66533. [PMID: 23824998 PMCID: PMC3688913 DOI: 10.1371/journal.pone.0066533] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/06/2013] [Indexed: 12/23/2022] Open
Abstract
The olive fruit fly Bactrocera oleae has a unique ability to cope with olive flesh, and is the most destructive pest of olives worldwide. Its control has been largely based on the use of chemical insecticides, however, the selection of insecticide resistance against several insecticides has evolved. The study of detoxification mechanisms, which allow the olive fruit fly to defend against insecticides, and/or phytotoxins possibly present in the mesocarp, has been hampered by the lack of genomic information in this species. In the NCBI database less than 1,000 nucleotide sequences have been deposited, with less than 10 detoxification gene homologues in total. We used 454 pyrosequencing to produce, for the first time, a large transcriptome dataset for B. oleae. A total of 482,790 reads were assembled into 14,204 contigs. More than 60% of those contigs (8,630) were larger than 500 base pairs, and almost half of them matched with genes of the order of the Diptera. Analysis of the Gene Ontology (GO) distribution of unique contigs, suggests that, compared to other insects, the assembly is broadly representative for the B. oleae transcriptome. Furthermore, the transcriptome was found to contain 55 P450, 43 GST-, 15 CCE- and 18 ABC transporter-genes. Several of those detoxification genes, may putatively be involved in the ability of the olive fruit fly to deal with xenobiotics, such as plant phytotoxins and insecticides. In summary, our study has generated new data and genomic resources, which will substantially facilitate molecular studies in B. oleae, including elucidation of detoxification mechanisms of xenobiotic, as well as other important aspects of olive fruit fly biology.
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Affiliation(s)
- Nena Pavlidi
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Wannes Dermauw
- Department of Crop Protection, Ghent University, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | | | | | - John Vontas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- * E-mail:
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Hull JJ, Geib SM, Fabrick JA, Brent CS. Sequencing and de novo assembly of the western tarnished plant bug (Lygus hesperus) transcriptome. PLoS One 2013; 8:e55105. [PMID: 23357950 PMCID: PMC3554660 DOI: 10.1371/journal.pone.0055105] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 12/14/2012] [Indexed: 11/18/2022] Open
Abstract
Background Mirid plant bugs (Hemiptera: Miridae) are economically important insect pests of many crops worldwide. The western tarnished plant bug Lygus hesperus Knight is a pest of cotton, alfalfa, fruit and vegetable crops, and potentially of several emerging biofuel and natural product feedstocks in the western US. However, little is known about the underlying molecular genetics, biochemistry, or physiology of L. hesperus, including their ability to survive extreme environmental conditions. Methodology/Principal Findings We used 454 pyrosequencing of a normalized adult cDNA library and de novo assembly to obtain an adult L. hesperus transcriptome consisting of 1,429,818 transcriptomic reads representing 36,131 transcript isoforms (isotigs) that correspond to 19,742 genes. A search of the transcriptome against deposited L. hesperus protein sequences revealed that 86 out of 87 were represented. Comparison with the non-redundant database indicated that 54% of the transcriptome exhibited similarity (e-value ≤1−5) with known proteins. In addition, Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains were assigned to each transcript isoform. To gain insight into the molecular basis of the L. hesperus thermal stress response we used transcriptomic sequences to identify 52 potential heat shock protein (Hsp) homologs. A subset of these transcripts was sequence verified and their expression response to thermal stress monitored by semi-quantitative PCR. Potential homologs of Hsp70, Hsp40, and 2 small Hsps were found to be upregulated in the heat-challenged adults, suggesting a role in thermotolerance. Conclusions/Significance The L. hesperus transcriptome advances the underlying molecular understanding of this arthropod pest by significantly increasing the number of known genes, and provides the basis for further exploration and understanding of the fundamental mechanisms of abiotic stress responses.
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Affiliation(s)
- J Joe Hull
- Pest Management and Biocontrol Research Unit, Agricultural Research Service, United States Department of Agriculture, Maricopa, Arizona, USA.
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Zeng V, Extavour CG. ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2012. [PMID: 23180770 PMCID: PMC3504982 DOI: 10.1093/database/bas048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL:asgard.rc.fas.harvard.edu
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Affiliation(s)
- Victor Zeng
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Li J, Li X, Chen Y, Yang Z, Guo S. Solexa sequencing based transcriptome analysis of Helicoverpa armigera larvae. Mol Biol Rep 2012; 39:11051-9. [DOI: 10.1007/s11033-012-2008-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 10/01/2012] [Indexed: 12/19/2022]
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Tang T, Huang DW, Zhou CQ, Li X, Xie QJ, Liu FS. Molecular cloning and expression patterns of copper/zinc superoxide dismutase and manganese superoxide dismutase in Musca domestica. Gene 2012; 505:211-20. [DOI: 10.1016/j.gene.2012.06.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 06/04/2012] [Accepted: 06/15/2012] [Indexed: 10/28/2022]
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Tang T, Wu C, Li J, Ren G, Huang D, Liu F. Stress-induced HSP70 from Musca domestica plays a functionally significant role in the immune system. JOURNAL OF INSECT PHYSIOLOGY 2012; 58:1226-1234. [PMID: 22750549 DOI: 10.1016/j.jinsphys.2012.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/13/2012] [Accepted: 06/14/2012] [Indexed: 06/01/2023]
Abstract
As important molecular chaperones, members of the 70kDa heat shock protein (HSP70) family play essential roles in stress tolerance and innate immunity in organisms. The full-length complementary DNA (cDNA) of a novel inducible HSP70, named as MdHSP70, was isolated from Musca domestica. The cDNA clone consisted of 2411 bp with a 1956 bp open reading frame which encodes 651 amino acids. Using real-time quantitative polymerase chain reaction (qPCR), we investigated the transcriptional profile of the gene under heat shock, cadmium stress and in response to bacteria. Increased expression of MdHSP70 was observed in response to both heat shock and Cd stress. The expression of MdHSP70 was significantly induced by Escherichia coli or Staphylococcus aureus stimulation. Larvae were fed bacteria expressing dsRNA targeting the MdHSP70 gene. Our results showed high mortality in larvae treated with dsRNA of MdHSP70 at heat shock, Cd stress and bacterial invasion, suggesting that MdHSP70 is potentially involved in the stress and immune responses of the house fly and perhaps contributes to protection against cellular injury.
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Affiliation(s)
- Ting Tang
- College of Life Sciences, Hebei University, Baoding 071002, China
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Identification of two metallothionein genes and their roles in stress responses of Musca domestica toward hyperthermy and cadmium tolerance. Comp Biochem Physiol B Biochem Mol Biol 2011; 160:81-8. [DOI: 10.1016/j.cbpb.2011.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/26/2011] [Accepted: 06/27/2011] [Indexed: 11/22/2022]
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