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Int J Mol Sci
2015 Jul 17;167:16347-77. doi: 10.3390/ijms160716347.
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Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge.
Gao Q
,
Liao M
,
Wang Y
,
Li B
,
Zhang Z
,
Rong X
,
Chen G
,
Wang L
.
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Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway.
Figure 1. The length distribution of assembled contigs in the sequenced cDNA library.
Figure 2. The length distribution of representative contigs in the sequenced cDNA library.
Figure 3. Species distribution of the BLAST matches of the transcriptome representative contigs.
Figure 4. Classification of the gene ontology (GO) for the sea cucumber coelomocytes transcriptome representative contigs.
Figure 5. Clusters of Orthologous Groups (COG) classification of the sea cucumber coelomocytes transcriptome representative contigs.
Figure 6. KEGG classification of the sea cucumber coelomocytes transcriptome representative contigs.
Figure 7. Summary of simple sequence repeat (SSR) identified from the sea cucumber coelomocytes transcriptome.
Figure 8. Differentially expressed genes from disease-resistant group (A), comparing with control group (K). Red points represent 13 up-regulated genes, and green points represent 345 down-regulated genes.
Figure 9. Differentially expressed genes from susceptibility group (S) comparing with control group (K). Red points represent 86 up-regulated genes, green point represents 16 down-regulated genes.
Figure 10. MAPK signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 11. ERBB signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 12. Lysosome signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 13. Endocytosis signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 14. Chemokine signaling pathway. Red boxes represent up-regulated genes, green boxes represent down-regulated genes, and blue box includes two genes of which one is an up-regulated gene and the other is a down-regulated gene.
Figure 15. Comparison of 22 putative disease-resistant gene expression levels between RNA-Seq (blue bar) and RT-PCR (red bar). “−â€indicates down-regulation.
Figure 16. Comparison of 14 putative susceptibility gene expression levels between RNA-Seq (blue bar) and RT-PCR (red bar). “−â€indicates down-regulation.
Ashburner,
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
2000, Pubmed
Ashburner,
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
2000,
Pubmed
Bache,
The growth-regulatory protein HCRP1/hVps37A is a subunit of mammalian ESCRT-I and mediates receptor down-regulation.
2004,
Pubmed
Balakrishnan,
A guide to best practices for Gene Ontology (GO) manual annotation.
2013,
Pubmed
Beg,
Activation of multiple NF-kappa B/Rel DNA-binding complexes by tumor necrosis factor.
1994,
Pubmed
Beinke,
Functions of NF-kappaB1 and NF-kappaB2 in immune cell biology.
2004,
Pubmed
Bogoyevitch,
Uses for JNK: the many and varied substrates of the c-Jun N-terminal kinases.
2006,
Pubmed
Bonifacino,
Coat proteins: shaping membrane transport.
2003,
Pubmed
Conesa,
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
2005,
Pubmed
Cong,
Characterization of an i-type lysozyme gene from the sea cucumber Stichopus japonicus, and enzymatic and nonenzymatic antimicrobial activities of its recombinant protein.
2009,
Pubmed
,
Echinobase
Craig,
MAP3Ks as central regulators of cell fate during development.
2008,
Pubmed
Dolmatova,
[Activity of antioxidant enzymes in coelomocytes of Eupentacta fraudatrix].
2004,
Pubmed
,
Echinobase
Dong,
Expression analysis of immune related genes identified from the coelomocytes of sea cucumber (Apostichopus japonicus) in response to LPS challenge.
2014,
Pubmed
,
Echinobase
Du,
Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
2012,
Pubmed
,
Echinobase
Farrar,
Turning transcription on or off with STAT5: when more is less.
2011,
Pubmed
Feng,
RIOK3 is an adaptor protein required for IRF3-mediated antiviral type I interferon production.
2014,
Pubmed
Förster,
Expression of the G-protein--coupled receptor BLR1 defines mature, recirculating B cells and a subset of T-helper memory cells.
1994,
Pubmed
Gliński,
Immune phenomena in echinoderms.
2000,
Pubmed
,
Echinobase
Götz,
High-throughput functional annotation and data mining with the Blast2GO suite.
2008,
Pubmed
Gowda,
T-antigen binding lectin with antibacterial activity from marine invertebrate, sea cucumber (Holothuria scabra): possible involvement in differential recognition of bacteria.
2008,
Pubmed
,
Echinobase
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Haas,
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
2013,
Pubmed
Hicks,
Hypothermia differentially increases extracellular signal-regulated kinase and stress-activated protein kinase/c-Jun terminal kinase activation in the hippocampus during reperfusion after asphyxial cardiac arrest.
2000,
Pubmed
Hirst,
Clathrin and adaptors.
1998,
Pubmed
Joberty,
The cell-polarity protein Par6 links Par3 and atypical protein kinase C to Cdc42.
2000,
Pubmed
Kirchhausen,
Linking cargo to vesicle formation: receptor tail interactions with coat proteins.
1997,
Pubmed
Klamp,
A giant GTPase, very large inducible GTPase-1, is inducible by IFNs.
2003,
Pubmed
Kremer,
Septins regulate actin organization and cell-cycle arrest through nuclear accumulation of NCK mediated by SOCS7.
2007,
Pubmed
Le Borgne,
The mammalian AP-3 adaptor-like complex mediates the intracellular transport of lysosomal membrane glycoproteins.
1998,
Pubmed
Lewin,
Sorting out adaptors.
1998,
Pubmed
Li,
Activation of mitogen-activated protein kinase kinase (MKK) 3 and MKK6 by type I interferons.
2005,
Pubmed
Li,
Transcriptome analysis and discovery of genes involved in immune pathways from hepatopancreas of microbial challenged mitten crab Eriocheir sinensis.
2013,
Pubmed
Li,
Characterization of skin ulceration syndrome associated microRNAs in sea cucumber Apostichopus japonicus by deep sequencing.
2012,
Pubmed
,
Echinobase
Lian,
Filamin a regulates neural progenitor proliferation and cortical size through Wee1-dependent Cdk1 phosphorylation.
2012,
Pubmed
Lin,
The role of Stat5a and Stat5b in signaling by IL-2 family cytokines.
2000,
Pubmed
Liu,
Identification of the pathogens associated with skin ulceration and peristome tumescence in cultured sea cucumbers Apostichopus japonicus (Selenka).
2010,
Pubmed
,
Echinobase
Livak,
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.
2001,
Pubmed
Ma,
Effects of dietary live yeast Hanseniaspora opuntiae C21 on the immune and disease resistance against Vibrio splendidus infection in juvenile sea cucumber Apostichopus japonicus.
2013,
Pubmed
,
Echinobase
Mack,
The ATP-binding cassette transporter ABCA2 as a mediator of intracellular trafficking.
2006,
Pubmed
Moon,
Rho GTPase-activating proteins in cell regulation.
2003,
Pubmed
Moriya,
KAAS: an automatic genome annotation and pathway reconstruction server.
2007,
Pubmed
Mu,
Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection.
2010,
Pubmed
Mullins,
Defective expression of the mu3 subunit of the AP-3 adaptor complex in the Drosophila pigmentation mutant carmine.
1999,
Pubmed
Oda,
A comprehensive pathway map of epidermal growth factor receptor signaling.
2005,
Pubmed
Peden,
Localization of the AP-3 adaptor complex defines a novel endosomal exit site for lysosomal membrane proteins.
2004,
Pubmed
Qiu,
Identification and characterization of a cell surface scavenger receptor cysteine-rich protein of Sciaenops ocellatus: bacterial interaction and its dependence on the conserved structural features of the SRCR domain.
2013,
Pubmed
Rossi,
The biology of chemokines and their receptors.
2000,
Pubmed
Samuel,
Hrp12, a novel heat-responsive, tissue-specific, phosphorylated protein isolated from mouse liver.
1997,
Pubmed
Schroeder,
The RIN: an RNA integrity number for assigning integrity values to RNA measurements.
2006,
Pubmed
Tsang,
A systematic analysis of human CHMP protein interactions: additional MIT domain-containing proteins bind to multiple components of the human ESCRT III complex.
2006,
Pubmed
Van Aelst,
Rho GTPases and signaling networks.
1997,
Pubmed
Velculescu,
Gene expression analysis goes digital.
2007,
Pubmed
Vicari,
TECK: a novel CC chemokine specifically expressed by thymic dendritic cells and potentially involved in T cell development.
1997,
Pubmed
Vitale,
Distinct Rab-binding domains mediate the interaction of Rabaptin-5 with GTP-bound Rab4 and Rab5.
1998,
Pubmed
Wallin,
Heat-shock proteins as activators of the innate immune system.
2002,
Pubmed
Wang,
Molecular characterization and expression analysis of heat shock cognate 70 after heat stress and lipopolysaccharide challenge in sea cucumber (Apostichopus japonicus).
2013,
Pubmed
,
Echinobase
Wang,
RNA-Seq: a revolutionary tool for transcriptomics.
2009,
Pubmed
Yang,
Expression of immune-related genes in embryos and larvae of sea cucumber Apostichopus japonicus.
2010,
Pubmed
,
Echinobase
You,
BatchPrimer3: a high throughput web application for PCR and sequencing primer design.
2008,
Pubmed
Zhang,
iTRAQ-based proteomics reveals novel members involved in pathogen challenge in sea cucumber Apostichopus japonicus.
2014,
Pubmed
,
Echinobase
Zhang,
Proteomic identification of differentially expressed proteins in sea cucumber Apostichopus japonicus coelomocytes after Vibrio splendidus infection.
2014,
Pubmed
,
Echinobase
Zhou,
Molecular characterization and expression analysis of a complement component 3 in the sea cucumber (Apostichopus japonicus).
2011,
Pubmed
,
Echinobase
Zügel,
Role of heat shock proteins in protection from and pathogenesis of infectious diseases.
1999,
Pubmed
