Transcriptomic insights into the effects of Hepatospora eriocheir (Microsporidia) infection in Eriocheir sinensis

The Chinese mitten crab ( Eriocheir sinensis ), a key species in China’s freshwater aquaculture, faces growing threats from Hepatopancreatic Necrosis Syndrome caused by the microsporidian parasite Hepatospora eriocheir . Deciphering the molecular mechanisms underlying host-pathogen interactions is essential for developing effective disease control strategies. While alternative splicing (AS) and alternative polyadenylation (APA) represent a critical regulatory mechanism in immune responses to pathogenic challenges, their functional significance in E. sinensis remains poorly characterized. This study employed RNA-seq to analyze hepatopancreas transcriptomes during H. eriocheir infection, systematically investigating differentially expressed genes (DEGs), AS and APA events dynamics. We identified 831 DEGs (|log2FoldChange| ≥ 1 and p -value < 0.05) enriched in immune-related pathways including G protein-coupled receptor signaling and epithelial morphogenesis. Additionally, 83 AS events and 914 APA events were detected, demonstrating their coordinated regulatory roles in infection responses. Our analysis revealed APA as a novel post-transcriptional modulator of host immunity, providing critical insights into molecular defense mechanisms against microsporidian invasion. These findings advance understanding of RNA processing regulation in invertebrate innate immunity and establish a framework for targeted disease management in crustacean aquaculture. • It was the first report of APA-mediated post-transcriptional regulation in E. sinensis during H. eriocheir infection. • 831 DEGs enriched in immune-related pathways (e.g., G protein-coupled receptor signaling) drive H. eriocheir resistance. • 83 AS and 914 APA events coordinately regulated host-pathogen interactions in crustacean immunity.