De novo characterization of the spleen transcriptome of the large yellow croaker (Pseudosciaena crocea) and analysis of the immune relevant genes and pathways involved in the antiviral response

Handle URI:
http://hdl.handle.net/10754/325339
Title:
De novo characterization of the spleen transcriptome of the large yellow croaker (Pseudosciaena crocea) and analysis of the immune relevant genes and pathways involved in the antiviral response
Authors:
Mu, Yinnan; Li, Mingyu; Ding, Feng ( 0000-0001-8237-4062 ) ; Ding, Yang; Ao, Jingqun; Hu, Songnian; Chen, Xinhua
Abstract:
The large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C)]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway, and T-cell receptor (TCR) signaling pathway were found to be changed after poly(I:C) induction by real-time polymerase chain reaction (PCR) analysis, suggesting that these signaling pathways may be regulated by poly(I:C), a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C) challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker. © 2014 Mu et al.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Mu Y, Li M, Ding F, Ding Y, Ao J, et al. (2014) De Novo Characterization of the Spleen Transcriptome of the Large Yellow Croaker (Pseudosciaena crocea) and Analysis of the Immune Relevant Genes and Pathways Involved in the Antiviral Response. PLoS ONE 9: e97471. doi:10.1371/journal.pone.0097471.
Publisher:
Public Library of Science
Journal:
PLoS ONE
Issue Date:
12-May-2014
DOI:
10.1371/journal.pone.0097471
PubMed ID:
24820969
PubMed Central ID:
PMC4018400
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMu, Yinnanen
dc.contributor.authorLi, Mingyuen
dc.contributor.authorDing, Fengen
dc.contributor.authorDing, Yangen
dc.contributor.authorAo, Jingqunen
dc.contributor.authorHu, Songnianen
dc.contributor.authorChen, Xinhuaen
dc.date.accessioned2014-08-27T09:47:53Zen
dc.date.available2014-08-27T09:47:53Zen
dc.date.issued2014-5-12en
dc.identifier.citationMu Y, Li M, Ding F, Ding Y, Ao J, et al. (2014) De Novo Characterization of the Spleen Transcriptome of the Large Yellow Croaker (Pseudosciaena crocea) and Analysis of the Immune Relevant Genes and Pathways Involved in the Antiviral Response. PLoS ONE 9: e97471. doi:10.1371/journal.pone.0097471.en
dc.identifier.issn19326203en
dc.identifier.pmid24820969en
dc.identifier.doi10.1371/journal.pone.0097471en
dc.identifier.urihttp://hdl.handle.net/10754/325339en
dc.description.abstractThe large yellow croaker (Pseudosciaena crocea) is an economically important marine fish in China. To understand the molecular basis for antiviral defense in this species, we used Illumia paired-end sequencing to characterize the spleen transcriptome of polyriboinosinic:polyribocytidylic acid [poly(I:C)]-induced large yellow croakers. The library produced 56,355,728 reads and assembled into 108,237 contigs. As a result, 15,192 unigenes were found from this transcriptome. Gene ontology analysis showed that 4,759 genes were involved in three major functional categories: biological process, cellular component, and molecular function. We further ascertained that numerous consensus sequences were homologous to known immune-relevant genes. Kyoto Encyclopedia of Genes and Genomes orthology mapping annotated 5,389 unigenes and identified numerous immune-relevant pathways. These immune-relevant genes and pathways revealed major antiviral immunity effectors, including but not limited to: pattern recognition receptors, adaptors and signal transducers, the interferons and interferon-stimulated genes, inflammatory cytokines and receptors, complement components, and B-cell and T-cell antigen activation molecules. Moreover, the partial genes of Toll-like receptor signaling pathway, RIG-I-like receptors signaling pathway, Janus kinase-Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway, and T-cell receptor (TCR) signaling pathway were found to be changed after poly(I:C) induction by real-time polymerase chain reaction (PCR) analysis, suggesting that these signaling pathways may be regulated by poly(I:C), a viral mimic. Overall, the antivirus-related genes and signaling pathways that were identified in response to poly(I:C) challenge provide valuable leads for further investigation of the antiviral defense mechanism in the large yellow croaker. © 2014 Mu et al.en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.subjectcaspase recruitment domain protein 15en
dc.subjectcaspase recruitment domain protein 4en
dc.subjectcomplement component C1qen
dc.subjectcomplement component C3ben
dc.subjectcomplement component C6en
dc.subjectinterleukin 1 receptor associated kinase 4en
dc.subjectinterleukin 10en
dc.subjectinterleukin 12p35en
dc.subjectinterleukin 12p40en
dc.subjectinterleukin 1betaen
dc.subjectinterleukin 2en
dc.subjectinterleukin 27en
dc.subjectinterleukin 6en
dc.subjectinterleukin 8en
dc.subjectJanus kinaseen
dc.subjectmyeloid differentiation factor 88en
dc.subjectpolyinosinic polycytidylic aciden
dc.subjectSTAT proteinen
dc.subjectT lymphocyte receptoren
dc.subjecttoll like receptor 1en
dc.subjecttoll like receptor 2en
dc.subjecttoll like receptor 3en
dc.subjecttoll like receptor 5en
dc.subjecttoll like receptor 9en
dc.subjecttransforming growth factor beta activated kinase 1en
dc.subjecttransforming growth factor beta1en
dc.subjecttransforming growth factor beta2en
dc.subjecttumor necrosis factor receptor associated factor 3en
dc.subjecttumor necrosis factor receptor associated factor 6en
dc.subjectadar geneen
dc.subjectAkt geneen
dc.subjectAP 1 geneen
dc.subjectbcl11a geneen
dc.subjectBCL6 geneen
dc.subjectbeta2m geneen
dc.subjectBlnk geneen
dc.subjectC1qBP geneen
dc.subjectC3b geneen
dc.subjectC6 geneen
dc.subjectCaN geneen
dc.subjectCC geneen
dc.subjectCC20 geneen
dc.subjectCC3 geneen
dc.subjectCCr12.3 geneen
dc.subjectCCr6a geneen
dc.subjectCCr7 geneen
dc.subjectCD22 geneen
dc.subjectCD3 gamma/delta geneen
dc.subjectCD3epsilon geneen
dc.subjectCD4 2 geneen
dc.subjectCD4 4 geneen
dc.subjectCD45 geneen
dc.subjectCD8 geneen
dc.subjectCD81 geneen
dc.subjectCFB geneen
dc.subjectCFB/C2B geneen
dc.subjectCmklr1 geneen
dc.subjectcontrolled studyen
dc.subjectCRAD9 geneen
dc.subjectCXCl12a geneen
dc.subjectCXCl12b geneen
dc.subjectCXCl14 geneen
dc.subjectCXCr3.1 geneen
dc.subjectCXCr3.2 geneen
dc.subjectCXCr4a geneen
dc.subjectCXCr4b geneen
dc.subjectCXCr7b geneen
dc.subjectEif2ak2 geneen
dc.subjectFADD geneen
dc.subjectfishen
dc.subjectFYN geneen
dc.subjectgeneen
dc.subjectgene expressionen
dc.subjectgene expression profilingen
dc.subjectgene libraryen
dc.subjectgene mappingen
dc.subjectgene sequenceen
dc.subjectgenetic analysisen
dc.subjectGig1 geneen
dc.subjectIFI30 geneen
dc.subjectIFI44L geneen
dc.subjectIFN1 geneen
dc.subjectIFN3 geneen
dc.subjectIFRD1 geneen
dc.subjectIFRD2 geneen
dc.subjectIgD geneen
dc.subjectIGH geneen
dc.subjectIgL geneen
dc.subjectIKKepsilon geneen
dc.subjectIL 10 geneen
dc.subjectIL 10Rbeta geneen
dc.subjectIL 12b geneen
dc.subjectIL 12p35 geneen
dc.subjectIL 12p40 geneen
dc.subjectIL 12Rbeta2 geneen
dc.subjectIL 17d geneen
dc.subjectIL 17R geneen
dc.subjectIL 17RA geneen
dc.subjectIL 1beta geneen
dc.subjectIL 1R1 geneen
dc.subjectIL 2 geneen
dc.subjectIL 21R geneen
dc.subjectIL 2Rbeta geneen
dc.subjectIL 2Rgamma a geneen
dc.subjectIL 6 geneen
dc.subjectIL 6R geneen
dc.subjectIL 7R geneen
dc.subjectIL 8 geneen
dc.subjectIRAK4 geneen
dc.subjectIRF1 geneen
dc.subjectIRF10 geneen
dc.subjectIRF2 geneen
dc.subjectIRF2a geneen
dc.subjectIRF2b geneen
dc.subjectIRF3 geneen
dc.subjectIRF4 geneen
dc.subjectIRF5 geneen
dc.subjectIRF6 geneen
dc.subjectIRF7 geneen
dc.subjectIrf8 geneen
dc.subjectIRF9 geneen
dc.subjectISG20 geneen
dc.subjectISG56 geneen
dc.subjectITK geneen
dc.subjectJAK1 geneen
dc.subjectJAK2 geneen
dc.subjectJak2a geneen
dc.subjectJak3 geneen
dc.subjectJNK geneen
dc.subjectlarge yellow croakeren
dc.subjectLCK geneen
dc.subjectMAPK1 geneen
dc.subjectMAPK10 geneen
dc.subjectMAPK11 geneen
dc.subjectMAPK12 geneen
dc.subjectMAPK3 geneen
dc.subjectMAPK7 geneen
dc.subjectMAPK8 geneen
dc.subjectmarine speciesen
dc.subjectMasp2 geneen
dc.subjectMBL2 geneen
dc.subjectMDA5 geneen
dc.subjectMHCIalpha geneen
dc.subjectMHCIbeta geneen
dc.subjectMxA geneen
dc.subjectMxb geneen
dc.subjectMxe geneen
dc.subjectmyd88 geneen
dc.subjectNAP1 geneen
dc.subjectNCK geneen
dc.subjectNFAT geneen
dc.subjectNFkappaB2 geneen
dc.subjectNLRC3 geneen
dc.subjectNLRC5 geneen
dc.subjectNLRX1 geneen
dc.subjectNOD1 geneen
dc.subjectNOD2 geneen
dc.subjectNOD3 geneen
dc.subjectoncogene rasen
dc.subjectP38 geneen
dc.subjectPAK geneen
dc.subjectPIK3C3 geneen
dc.subjectproto oncogeneen
dc.subjectRac1 geneen
dc.subjectRaf geneen
dc.subjectreal time polymerase chain reactionen
dc.subjectRIP2 geneen
dc.subjectsequence homologyen
dc.subjectsignal transductionen
dc.subjectSLP76 geneen
dc.subjectspleenen
dc.subjectStat1a geneen
dc.subjectStat1b geneen
dc.subjectSTAT3 geneen
dc.subjectSTAT4 geneen
dc.subjectStat5.1 geneen
dc.subjectStat5.2 geneen
dc.subjectStat6 geneen
dc.subjectTAB1 geneen
dc.subjectTAB2 geneen
dc.subjectTAK1 geneen
dc.subjectTANK geneen
dc.subjecttbk1 geneen
dc.subjectTCRa geneen
dc.subjectTCRb geneen
dc.subjectTCRV a geneen
dc.subjectTGF beta1 geneen
dc.subjectTGF beta2 geneen
dc.subjectTICAM1 geneen
dc.subjectTLR1 geneen
dc.subjecttlr2 geneen
dc.subjectTLR22 geneen
dc.subjectTLR3 geneen
dc.subjectTLR5b geneen
dc.subjectTLR9 geneen
dc.subjectTNF alpha geneen
dc.subjectTOLLIP geneen
dc.subjectTRADD geneen
dc.subjectTRAF3 geneen
dc.subjectTRAF6 geneen
dc.subjecttranscriptomicsen
dc.subjectTRBC geneen
dc.subjectTVA1 geneen
dc.subjectVAV geneen
dc.subjectviperin geneen
dc.titleDe novo characterization of the spleen transcriptome of the large yellow croaker (Pseudosciaena crocea) and analysis of the immune relevant genes and pathways involved in the antiviral responseen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC4018400en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionKey Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Chinaen
dc.contributor.institutionCollaborative Innovation Center of Deep Sea Biology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Chinaen
dc.contributor.institutionCAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, Chinaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorDing, Fengen
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.