Transcriptome Analysis of Milkfish after Exposure to Aeromonas hydrophila using Next-Generation Sequencing
Jaime Lorenzo N. Dinglasan1, Lorenz Rhuel P. Ragasa1,
Anacleto M. Argayosa1,2, Zubaida U. Basiao1, and Michael C. Velarde1*
1Institute of Biology, College of Science
University of the Philippines Diliman, Quezon City 1101 Philippines
2Department of Biological Sciences, College of Arts Sciences and Education
Trinity University of Asia, Quezon City 1102 Philippines
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.
Southeast Asia’s total aquaculture production is about 9% of the world’s total aquaculture production. Chanos chanos (milkfish) is the top finfish product produced in this region, and the Philippines is one of the major milkfish-producing countries (Martinez et al. 2006). This particular finfish is the most commercially important aquaculture species in the Philippines, being produced at about 0.35 million metric tonnes per year – more than the next most produced finfish, Oreochromis niloticus (tilapia) (BAS 2013). Milkfish are suitable for production in the country due to their environmental adaptability and their suitability to tropical conditions, as their reproductive patterns are reliant on warm temperature and plentiful sunlight (Martinez et al. 2006). However, milkfish are still susceptible to diseases (Chang 2006, Dequito et al. 2015, Virgula et al. 2017, Echem et al. 2018). One such disease that causes high mortality rate is due to the gram-negative bacterium Aeromonas hydrophila (Lio-po and Duremdez-Fernandez 1986, Emata 1994). In contrast to gram-positive bacteria, the cell wall of gram-negative bacteria contains lipopolysaccharides (LPS) as its major component (Anwar and Choi 2014) that contributes to structural integrity, as well as increased pathogenicity of gram-negative bacteria (Turska-Szewczuk et al. 2013). Exposure to inactivated bacteria will allow the stimulation of the host . . . . read more
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