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. 2014 May 12;9(5):e97471. doi: 10.1371/journal.pone.0097471. eCollection 2014.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Fish Proteins / metabolism
  • Gene Expression Profiling*
  • Gene Ontology
  • Immunity / genetics*
  • Molecular Sequence Annotation
  • Perciformes / genetics
  • Perciformes / immunology*
  • Perciformes / virology*
  • Poly I-C / pharmacology
  • Sequence Analysis
  • Signal Transduction / drug effects
  • Signal Transduction / genetics
  • Spleen / cytology
  • Spleen / immunology*
  • Spleen / metabolism*

Substances

  • Fish Proteins
  • Poly I-C

Grants and funding

The work was supported by grants from the National Basic Research Program of China (2012CB114402), National Natural Science Foundation of China (31125027 and 31372556), Nation '863' Project (2012AA092202), and fund of Xiamen south ocean research center (13GZP002NF08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.