Transcriptome Analysis Reveals the Mechanisms of Organismal Response in Exopalaemon carinicauda Infected by Metschnikowia bicuspidata

Exopalaemon carinicauda is a commercially significant aquaculture species in China. However, outbreaks of “zombie disease” caused by Metschnikowia bicuspidata infection have led to substantial economic losses in its farming industry. Despite its growing impact, the molecular basis of E. carinicauda’s response to M. bicuspidata infection remains unexplored. To elucidate the molecular mechanisms involved, this study conducted a transcriptomic analysis of the E. carinicauda hepatopancreas under M. bicuspidata infection and non-infection conditions. Following transcriptome assembly, 67,811 unigenes were generated, exhibiting high N50 value of 1977 base pairs and high complete BUSCO of 94.68%. Among these, 22,561 unigenes were successfully annotated. Comparative gene expression analysis of M. bicuspidata-infected and uninfected samples at 60 h post-infection revealed 1991 DEGs, comprising 1224 upregulated and 767 downregulated transcripts. Functional enrichment analysis revealed that numerous DEGs participate in immune-associated pathways, particularly those related to pattern recognition, lysosomal function, cellular stress responses, and programmed cell death. In addition, a significant proportion of DEGs were linked to metabolic processes such as glycerophospholipid metabolism and protein digestion and absorption. To verify the reliability of the transcriptomic results, eight DEGs were randomly chosen for qRT-PCR validation, and their expression profiles showed strong agreement with the RNA-Seq data. Overall, this study provides a transcriptomic overview of the hepatopancreatic response of E. carinicauda to M. bicuspidata infection, offering insights into the underlying molecular mechanisms and a theoretical foundation for the prevention and management of “Zombie disease.”