Ichthyophthirius multifiliis (Ich) is a highly invasive protozoan parasite that causes massive disease outbreaks in freshwater fish, posing a significant threat to global aquaculture. Despite its impact, the molecular basis of differential host response to I. multifiliis exposure in goldfish (Carassius auratus) remain poorly understood. This study addressed this gap by comparing the transcriptome profiles of single-tail (S) and twin-tail (T) goldfish following parasite exposure to identify the genetic basis of host responses. RNA-seq analysis identified 9,408 differentially expressed genes (DEGs) between the two morphotypes, with 4,387 genes up-regulated and 5,021 down-regulated in the S group compared to the T group. Functional enrichment and KEGG analysis revealed that these DEGs were primarily involved in cellular and metabolic processes, as well as key immune signaling pathways, including NOD-like receptor, RIG-I-like receptor, C-type lectin receptor, chemokine, NF-κB, and JAK-STAT signaling. Among 92 genes associated with Ich responses across 10 immune pathways, 15 candidate genes were prioritized for further functional investigation. Quantitative RT-PCR validation of five key immune genes (GIMAP4, TRIM25, GFAP, C-type lectin, and CHRNA3) confirmed the reliability of the RNA-seq data. These results provide insight into morphotype-associated differences in transcriptomic immune responses to I. multifiliis exposure in goldfish and identify candidate pathways and genes for future functional studies.

Twin-tail Goldfish, Carassius Auratus, Ichthyophthirius Multifiliis, Transcriptome Analysis, Immune Response, Parasite Exposure