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.
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.
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.
authors.forename: Yinnan
authors.initials: Y
authors.lastname: Mu
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Li
authors.affiliation: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Deep Sea Biology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.
authors.forename: Jingqun
authors.initials: J
authors.lastname: Ao
authors.affiliation: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.affiliation: Key Laboratory of Marine Biogenetics and Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China; Collaborative Innovation Center of Deep Sea Biology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Chen
mesh_terms: D000818:Animals; D029941:Fish Proteins / Q000378:metabolism; D020869:Gene Expression Profiling; D063990:Gene Ontology; D007109:Immunity / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010473:Perciformes / Q000235:genetics / Q000276:immunology* / Q000821:virology*; D011070:Poly I-C / Q000494:pharmacology; D017421:Sequence Analysis; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D013154:Spleen / Q000166:cytology / Q000276:immunology* / Q000378:metabolism*
chemical_list: D029941:Fish Proteins; D011070:Poly I-C