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Background  False kelpfish ( Sebastiscus marmoratus ) is one of the target species in artificial breeding in China, and is susceptible to infection by  Cryptocaryon irritans , which is an obligate parasitic ciliate that lives in the epithelium of the fish gills, skin and fins. Here, we sought to understand the mechanisms of molecular immunity of  S. marmoratus  against  C. irritans  infection.    Methods  We carried out an extensive analysis of the transcriptome of  S. marmoratus  immune-related tissues. A paired-end library was constructed from the cDNA synthesized using a Genomic Sample Prep Kit. Five normalized cDNA libraries were constructed using RNA from the control group and the four groups of  C. irritans -infected fish. The libraries were sequenced on an Illumina Mi-Seq platform, and functional annotation of the transcriptome was performed using bioinformatics software.    Results  The data produced a total of 149,983,397 clean reads from five cDNA libraries constructed from  S. marmoratus  immune-related tissues. A total of 33,291 unigenes were assembled with an average length of 1768 bp. In eggNOG (Evolutionary Genealogy of Genes: non-supervised orthologous groups) categories, 333 unigenes (0.94%) were assigned to defense mechanisms. In the immune system process sub-categories of gene ontology (GO) enrichment analysis, with the passage of time post-infection, the number of differentially expressed genes (DEGs) was reduced from 24 h to 48 h but then increased from 72 h to 96 h. Specifically, the immune-related differentially expressed genes (IRDEGs), which belong to the KEGG (Kyoto encyclopedia of genes and genomes) pathways, such as the complement and coagulation cascades, chemokine signalling pathways and toll-like receptor signalling pathways were mainly observed at 24 h post-infection.    Conclusions  Infection with  C. irritans  resulted in a large number of DEGs in the immune-related tissues of  S. marmoratus . The rapid and significant response of the  S. marmoratus  immune signalling pathways following  C. irritans  infection may be associated with their involvement in the immune process.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2508-7) contains supplementary material, which is available to authorized users.

parasites and vectors

Transcriptomic analysis reveals the key immune-related signalling pathways of Sebastiscus marmoratus in response to infection with the parasitic ciliate Cryptocaryon irritans