PMID- 31346855 OWN - NLM STAT- MEDLINE DCOM- 20200205 LR - 20210110 IS - 1436-2236 (Electronic) IS - 1436-2228 (Linking) VI - 21 IP - 5 DP - 2019 Oct TI - Liver-Specific microRNA Identification in Farmed Carp, Labeo bata (Hamilton, 1822), Fed with Starch Diet Using High-Throughput Sequencing. PG - 589-595 LID - 10.1007/s10126-019-09912-y [doi] AB - The liver is an important central organ, which controls carbohydrate metabolism through maintaining glucose homeostasis by a tightly regulated system of genes or enzymes. The microRNAs are small non-coding RNAs playing an important role in the regulation of genes associated with developmental biology, physiology, metabolism, etc. Thus, in this study, we have intended to detect liver-specific microRNAs in farmed carp, Labeo bata, upon being fed a diet with different levels of carbohydrates. Here, we have conducted the experiment for 45 days using fingerlings of farmed carp fed with 20% (control), 40%, and 60% gelatinized starch levels. The liver tissues were collected from each treatment and processed for RNA isolation, small RNA library preparation, and high-throughput sequencing using Illumina NexSeq500. Through sequencing, 15,779,417 reads in 20% CHO, 13,959,039 in 40% CHO, and 13,661,950 in 60% CHO reads were generated for control and treated fishes using three small RNA libraries. We have investigated 445 novel and 231 conserved microRNAs in 20%, 40%, and 60% carbohydrate (CHO), respectively, through computational analysis. The differential expression analysis of miRNAs was carried out between different treatments compared with control and this study depicted 117 known and 114 novel miRNA genes involved in carbohydrate metabolic pathways. Further, target prediction and gene ontology analysis revealed that miRNAs were involved in several pathways such as signaling pathway, G protein pathway, complement receptor-mediated pathway, dopamine receptor signaling pathway, epidermal growth factor pathway, and notch signaling pathway. The predicted miRNA sites in targeted genes were associated with cellular activities, developmental biology, DNA binding, Golgi apparatus, extracellular region, catalytic activity, MAPK cascade, etc. Overall, we have generated a vital resource of liver-specific miRNAs involved in metabolic gene regulation. These studies further will help develop miRNA inhibitors to study their role during carbohydrate metabolism in farmed carp. FAU - Rasal, Kiran D AU - Rasal KD AD - Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, 751002, India. FAU - Iquebal, Mir Asif AU - Iquebal MA AD - Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India. FAU - Jaiswal, Sarika AU - Jaiswal S AD - Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India. FAU - Dixit, Sangita AU - Dixit S AD - Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, 751002, India. FAU - Vasam, Manohar AU - Vasam M AD - Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, 751002, India. FAU - Nandi, Samiran AU - Nandi S AD - Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, 751002, India. FAU - Raza, Mustafa AU - Raza M AD - Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India. FAU - Sahoo, Lakshman AU - Sahoo L AD - Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, 751002, India. FAU - Angadi, U B AU - Angadi UB AD - Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India. FAU - Rai, Anil AU - Rai A AD - Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India. FAU - Kumar, Dinesh AU - Kumar D AD - Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, 110012, India. FAU - Sundaray, Jitendra Kumar AU - Sundaray JK AD - Fish Genetics and Biotechnology Division, ICAR - Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, 751002, India. jsundaray@gmail.com. LA - eng PT - Journal Article DEP - 20190725 PL - United States TA - Mar Biotechnol (NY) JT - Marine biotechnology (New York, N.Y.) JID - 100892712 RN - 0 (Fish Proteins) RN - 0 (MicroRNAs) RN - 0 (Receptors, Complement) RN - 0 (Receptors, Dopamine) RN - 0 (Receptors, Notch) RN - 62229-50-9 (Epidermal Growth Factor) RN - 9005-25-8 (Starch) RN - EC 2.7.11.24 (Mitogen-Activated Protein Kinases) RN - EC 3.6.1.- (GTP-Binding Proteins) SB - IM MH - Animal Feed MH - Animals MH - Aquaculture MH - Carps MH - Diet/methods MH - Epidermal Growth Factor/genetics/metabolism MH - Fish Proteins/classification/*genetics/metabolism MH - GTP-Binding Proteins/genetics/metabolism MH - *Gene Expression Regulation, Developmental MH - High-Throughput Nucleotide Sequencing MH - Liver/*drug effects/metabolism MH - MicroRNAs/classification/*genetics/metabolism MH - Mitogen-Activated Protein Kinases/genetics/metabolism MH - Molecular Sequence Annotation MH - Receptors, Complement/genetics/metabolism MH - Receptors, Dopamine/genetics/metabolism MH - Receptors, Notch/genetics/metabolism MH - Signal Transduction MH - Starch/*administration & dosage/metabolism OTO - NOTNLM OT - Labeo bata OT - Liver OT - MicroRNA OT - Next-generation sequencing EDAT- 2019/07/28 06:00 MHDA- 2020/02/06 06:00 CRDT- 2019/07/27 06:00 PHST- 2019/04/29 00:00 [received] PHST- 2019/07/05 00:00 [accepted] PHST- 2019/07/28 06:00 [pubmed] PHST- 2020/02/06 06:00 [medline] PHST- 2019/07/27 06:00 [entrez] AID - 10.1007/s10126-019-09912-y [pii] AID - 10.1007/s10126-019-09912-y [doi] PST - ppublish SO - Mar Biotechnol (NY). 2019 Oct;21(5):589-595. doi: 10.1007/s10126-019-09912-y. Epub 2019 Jul 25.