Transcriptomic analysis of milkfish (Chanos chanos) gut reveals differential expression patterns in wild-caught and hatchery-produced fry

Milkfish ( Chanos chanos ) is among the top fisheries commodities in the Philippines, with production largely driven by the aquaculture sector. The industry sector primarily relies on hatchery-produced fry for grow-out culture. Omics technologies are increasingly used to provide insights into performance traits such as growth and immune function. In this study, RNA sequencing was used to assemble the gut transcriptome of C. chanos and to identify differentially expressed transcripts between hatchery-produced and wild-caught fry. A total of 32,920 gut transcripts with candidate coding regions were generated. Pairwise analysis revealed that 626 transcripts were differentially expressed, with 325 upregulated and 301 downregulated in the hatchery-produced fry compared with the wild-caught fry. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses demonstrated that the upregulated transcripts in hatchery-produced fry were associated with extracellular matrix integrity and organization and anatomical structure development, whereas the downregulated transcripts were enriched in GO terms and KEGG pathways relating to immune and defense responses. These findings elucidate transcriptomic differences between wild-caught and hatchery-produced milkfish fry and provide a foundation for future functional studies. These findings have important implications for improving aquaculture productivity through the development of fry selection and rearing strategies.