Transcriptomic analysis of gene expression in immune pathways in the spleen of Takifugu rubripes after immunization with scuticociliate vaccine

Scuticociliatosis is one of the most important parasitic diseases of mariculture fishes. The control of this disease with various chemical drugs poses a serious threat to the environment and food safety. Vaccination is currently an effective way to prevent the disease and has strong application prospects, but there is still a gap in the research into the immunopreventive mechanism of a ciliate vaccine after the immunization of fish. In this study, we used Illumina HiSeq™ 2000 sequencing to compare the transcriptomic profiles in the spleens of Takifugu rubripes immunized with an anti-scuticociliate vaccine and control fish. A total of 15,839,040 clean reads were obtained in the immunized group, which contained 23.76 Gb of sequence information. A total of 155,877,318 clean reads were obtained in the control group, containing 23.39 Gb of sequence information. An evaluation of the base error rate, GC content, Q20 (%), and Q30 (%) showed that the quality and reliability of the sequences were good. The expression levels of individual genes were determined with the fragments per kilobase of exon model per million reads mapped (FPKM) method, and 278 differentially expressed genes (DEGs) were identified with the DESeq software, 179 of which were upregulated and 99 downregulated. These 278 DEGs were classified into three Gene Ontology (GO) categories: biological process, cellular component, and molecular function. A Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis assigned 128 DEGs to 65 pathways. The 20 most significantly enriched pathways included the cytokine-cytokine receptor interaction pathway, phagosome pathway, cell adhesion molecules, and intestinal immune network for IgA production pathway, which have been shown to be associated with diseases. The CSF1R, IL-10, NGFR, SF6B, IL8RB, EPOR, VEGFA, MHC-II, TUBA, collectin, MHC-I, iC3b, and cathepsin genes are involved in pathways known to be related to the immune system. This is the first transcriptomic analysis of the spleen of T. rubripes immunized with the scuticociliate Uronema marinum, and provides valuable reference data for research into the immunoprophylactic mechanisms of T. rubripes when challenged with a scuticociliate-directed vaccine.