NGS-based transcriptome analysis of starry flounder (Platichthys stellatus) reveals key immune-related genes and host defense mechanisms against Streptococcus parauberis infection.

The starry flounder (Platichthys stellatus) is a high-value aquaculture species in Korea, but its farming is hindered by Streptococcus parauberis infection. We used NGS-based de novo assembly to identify immunity-related genes and molecular markers in starry flounder. Using de novo assembly, we analyzed transcriptomic changes in liver and leukocytes following infection. The liver exhibited greater transcriptional variability, indicating its role in systemic immune regulation, while the leukocytes focused on pathogen recognition. Transcriptomic profiling revealed a temporal shift in immune response: early activation of DNA damage repair pathways at 3 h post-infection indicated rapid host recognition and stress response, which later transitioned into immune modulation and energy conservation at 48 h, as evidenced by the downregulation of MAPK, TNF, and NF-κB signaling pathways. This pattern reflects a dynamic and regulated host defense strategy. These findings provide foundational data for disease-resistant strain development, demonstrating the utility of NGS-based transcriptomics in identifying key immune genes in non-model fish species.