Transcriptomic and Metabolomic Analyses Provide Insights into Cryptocaryon irritans Resistance in Golden Pompano (Trachinotus ovatus)

Golden pompano (Trachinotus ovatus) is an economically important fish species along China’s southern coast. However, infections by Cryptocaryon irritans severely constrain the healthy and sustainable development of the aquaculture industry. To investigate the genetic basis of resistance to this parasite in golden pompano, this study employed transcriptomic and metabolomic analyses to compare differences between susceptible (ES) and resistant (RS) groups following C. irritans challenge. Transcriptome analysis identified 2031 differentially expressed genes (DEGs) between EST and RST groups, comprising 1004 up-regulated and 1027 down-regulated genes. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that these DEGs were primarily enriched in lipid metabolism and amino acid metabolism pathways. Untargeted metabolomics detected 461 significantly differentially abundant metabolites (295 up-regulated, 166 down-regulated), confirming pronounced metabolic differences between ES and RS groups, particularly in lipid and amino acid metabolism. Further, KEGG enrichment highlighted steroid hormone biosynthesis, α-linolenic acid metabolism, and arachidonic acid metabolism as the most significantly altered pathways upon infection. This integrated transcriptomic and metabolomic study reveals substantial differences in gene expression and metabolite profiles between susceptible and resistant golden pompano in response to C. irritans. These changes predominantly involve lipid metabolism and amino acid metabolism, suggesting that these processes are critical in determining host resistance/susceptibility.