Morphotype-Dependent Immune Responses to Ichthyophthirius multifiliis Infection in Goldfish (Carassius auratus): A Transcriptomic and Molecular Approach

Abstract Ichthyophthirius multifiliis (Ich) is a highly pathogenic protozoan parasite that causes white spot disease and poses a major threat to freshwater aquaculture worldwide. However, the molecular mechanisms underlying morphotype-dependent resistance to I. multifiliis infection in goldfish ( Carassius auratus ) remain poorly understood. It is crucial to determine if there is an incidental change in immune competence in ornamental fish on selection for the twin-tail trait, not only for understanding the biological costs of artificial selection, but also for disease management in goldfish farming. The present study was conducted to fill this gap by comparing the transcriptome of single tail (S) and twin tail (T) goldfish in their response to parasite exposure, in order to determine the genetic basis of the host response. A total of 9,408 differentially expressed genes (DEGs) were identified by RNA-seq analysis between the two morphotypes, of which 4,387 were upregulated in the S group and 5,021 were downregulated in the S group in comparison to the T group. The KEGG pathway analysis and functional enrichment showed that these DEGs were mainly related to the cellular and metabolic processes, and to important immune signaling pathways such as NOD-like receptor signaling pathway, RIG-I-like receptor signaling pathway, C-type lectin receptor signaling pathway, chemokine signaling pathway, NF-κB signaling pathway, and JAK-STAT signaling pathway. Of the 92 genes associated with Ich responses in 10 immune pathways, 15 genes were selected for additional functional studies. Five important genes involved in the immune system ( GIMAP4, TRIM25, GFAP, C-type lectin, CHRNA3 ) were validated by quantitative RT-PCR, and the RNA-seq data were found to be reliable. The results shed light on the morphotype-dependent differences in transcriptomic immune responses to I. multifiliis infection in goldfish and offer a potential list of pathways and genes to explore in goldfish in the future.