MicroRNAs (miRNAs) are known to modulate various immune responses and metabolic processes by targeting and silencing specific genes in invertebrates. However, the specific roles of miRNAs in the context of microsporidial infection in the shrimp Penaeus vannamei have not been well-defined. This study aimed to elucidate the functions of miRNAs in shrimp during the invasion by the microsporidian pathogen Ecytonucleospora hepatopenaei (EHP). To achieve this, we collected shrimp that had confirmed EHP infections and conducted a comprehensive transcriptional analysis. High-throughput sequencing data yielded 15,964,804 clean reads from the hepatopancreas of healthy shrimp and 14,301,330 clean reads from EHP-infected counterparts. From these samples, a total of 59 distinct miRNAs were identified. Notably, the expression levels of 31 miRNAs, with 16 being down-regulated and 15 up-regulated, were significantly altered in the hepatopancreas of EHP-infected shrimp when compared to the controls. The differentially expressed miRNAs were subjected to Gene Ontology (GO) analysis and target gene prediction to determine their biological relevance. The findings indicated that the miRNAs with altered expression are predominantly associated with immune response pathways and metabolic alterations, including those involved in the Toll-like receptor signaling pathway (Ko04620); the Toll and Imd signaling pathways (Ko04624); protein digestion and absorption (Ko04974); and the regulation of aldosterone synthesis and secretion (Ko04925). Collectively, our study advances our understanding of miRNAs’ roles within the innate immune system of shrimp and identifies potential novel targets for the management and prevention of EHP infections.
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