Transcriptome Analysis of Milkfish after Exposure to Aeromonas hydrophila using Next-generation Sequencing

Milkfish is a major finfish product of the Philippines. But because the whole genome sequence of milkfish is still unknown, it is difficult to study the different molecular pathways involved in milkfish after bacterial exposure. Here, transcriptomic analyses by next-generation sequencing (NGS) were used to identify gene expression in milkfish liver after exposure to bacterial antigens from inactivated A. hydrophila. Obtained reads per individual were assembled de novo and fragments per kilobyte of exon per million mapped reads (FPKM) were measured to identify overall gene expression. Differential expression (DE) was analyzed by Cufflinks-Cuffdiff software. Gene ontology (GO) overrepresentation analysis revealed that milkfish exposed to A. hydrophila altered expression of genes involved in immune response pathways such as T cell and B cell signaling. The most differentially regulated genes include histamine n-methyltransferase (hnmt), nicotinamide phosphoribosyltransferase b (namptb), poliovirus receptor-related 2 like precursor (pvrl2), and the hepcidin antimicrobial peptide 1 – which are all involved in immunity. Overall, the study showed that milkfish liver contains immune-related genes that respond to bacterial antigens.