miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data

Author(s)

Bovolenta, Luiz Augusto ^[1] ; Pinhal, Danillo ^[2] ; Acencio, Marcio Luis ^[3] ; de Oliveira, Arthur Casulli ^[2] ; Moxon, Simon ^[4] ; Martins, Cesar ^[5] ; Lemke, Ney ^[1]

Affiliation

^[1] Sao Paulo State Univ UNESP, Inst Biosci Botucatu, Dept Biophys & Pharmacol, BR-18618689 Botucatu, SP - Brazil

^[2] Sao Paulo State Univ UNESP, Inst Biosci Botucatu, Dept Chem & Biol Sci, BR-18618689 Botucatu, SP - Brazil

^[3] Univ Luxembourg, Luxembourg Ctr Syst Biomed, Campus Belval, 7 Ave Hauts Fourneaux, L-4362 Esch Sur Alzette - Luxembourg

^[4] Univ East Anglia UEA, Sch Biol Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk - England

^[5] Sao Paulo State Univ UNESP, Inst Biosci Botucatu, Dept Struct & Funct Biol, BR-18618689 Botucatu, SP - Brazil

• Document type: Journal article
• Source: CELLS; v. 9, n. 8 AUG 2020.
• Web of Science Citations: 0

Abstract

Nile tilapia is the third most cultivated fish worldwide and a novel model species for evolutionary studies. Aiming to improve productivity and contribute to the selection of traits of economic impact, biotechnological approaches have been intensively applied to species enhancement. In this sense, recent studies have focused on the multiple roles played by microRNAs (miRNAs) in the post-transcriptional regulation of protein-coding genes involved in the emergence of phenotypes with relevance for aquaculture. However, there is still a growing demand for a reference resource dedicated to integrating Nile Tilapia miRNA information, obtained from both experimental and in silico approaches, and facilitating the analysis and interpretation of RNA sequencing data. Here, we present an open repository dedicated to Nile Tilapia miRNAs: the ``miRTil database{''}. The database stores data on 734 mature miRNAs identified in 11 distinct tissues and five key developmental stages. The database provides detailed information about miRNA structure, genomic context, predicted targets, expression profiles, and relative 5p/3p arm usage. Additionally, miRTil also includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions. (AU)

• FAPESP's process: 10/20684-3 - Development of machine learning approaches based on biological networks for prediction and determination of rules governing the emergence of phenotypes of interest
• Grantee: Marcio Luis Acencio
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 12/13450-1 - Large scale exploratory analysis of Nile tilapia's miRNA expression using bioinformatics tools.
• Grantee: Luiz Augusto Bovolenta
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 12/15589-7 - Investigation of the composition, function and evolutionary dynamics of microRNAs in fish genomes using RNA-Seq and reverse genetics
• Grantee: Danillo Pinhal
• Support Opportunities: Regular Research Grants
• FAPESP's process: 14/08420-1 - Analysis of highly expressed miRNAs in the heart of Nile Tilapia using bioinformatics
• Grantee: Arthur Casulli de Oliveira
• Support Opportunities: Scholarships abroad - Research Internship - Scientific Initiation
• FAPESP's process: 15/19176-7 - Discovering variations and functions from non-coding Small RNAs in Oreochromis niloticus
• Grantee: Luiz Augusto Bovolenta
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 11/06465-0 - Genome-wide identification and characterization of micro-RNAs in the fish Nile tilapia, Oreochromis niloticus
• Grantee: César Martins
• Support Opportunities: Regular Research Grants
• FAPESP's process: 13/03644-6 - Analysis of miRNA transcriptome in the cardiac muscle of Nile Tilapia fish using RNA-seq and comparative genomics
• Grantee: Arthur Casulli de Oliveira
• Support Opportunities: Scholarships in Brazil - Scientific Initiation