RESUMEN
BACKGROUND: The small non-coding microRNAs play a vital role in post-transcriptional gene regulation associated with different physiological events such as metabolism, stress, etc. The freshwater catfish, Clarias magur, can grow within hyper ammonia containing stagnant water bodies and/or muddy substratum. We intended to identify organ-specific miRNAs associated with ammonia stress management. METHODS AND RESULTS: The miRNA-libraries were generated from QC passed total RNA extracted from liver, muscle, and kidney of ammonia-treated (exposed to 25 mM NH4Cl for 14 days) and untreated catfish. The libraries were validated using High sensitivity D1000 Screen tape. The trimmed quality-filtered reads for control and treated samples of kidney were 19,406,210; 14,904,423; for liver 15,467,727; 18,582,072; and for muscle 25,081,345; 19,782,182 respectively. Total 120 known and 150 novel differentially expressed miRNAs were identified, out of which miR-200, miR-217, miR-122, miR-133, miR-145, miR-221, miR-19, miR-138, miR-34, and miR-184 were predicted to be involved in the metabolism of nitrogen. The key miRNAs targeted several genes associated with urea synthesis like Glutaminase 2, Argininosuccinate lyase, Glutamate dehydrogenase 1, Alanine aminotransferase 2-like, Aspartate aminotransferase, cytoplasmic-like, Glutamate ionotropic receptor NMDA type subunit 2A, etc. CONCLUSIONS: This is the first report of miRNAs, which serve as a vital resource for regulating nitrogen metabolism in freshwater catfish, C. magur. The data will be resourceful for further evaluating the regulatory role of miRNAs in fishes, which grow and reproduce very well in hazardous ammonia-contaminated water bodies.