Ecytonucleospora hepatopenaei (EHP), an emerging microsporidian, has caused significant economic losses to the Asian aquaculture industry. This study investigates the infection dynamics of EHP through deep transcriptomic sequencing of infected shrimp samples at different time points. The analysis revealed distinct periodic changes in metabolism, immune response, and DNA repair during EHP infection. Shrimp rapidly mobilize energy metabolism and activate immune pathways in the early stage (day 2), followed by immune suppression and metabolic regulation in the mid-stage (days 4–6), and enhanced immune responses by day 8. Trend analysis supports an 8-day infection cycle, with periodic changes in gene expression profiles, especially in energy metabolism, protein synthesis and degradation, and immune responses. Host gene expression displays a phased response aligning with EHP proliferation and its life cycle. EHP's gene expression also shows periodicity, with upregulation of proliferation-associated genes on days 4 and 10. Weighted Gene Co-expression Network Analysis (WGCNA) identified key gene modules related to metabolic adaptation and immune suppression, indicating EHP's adaptation to the host environment. The study reveals a cyclical pattern of interaction between EHP and its host, providing insights into EHP's pathogenic mechanisms.
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