A bioinformatics-based update on microRNAs and their targets in rainbow trout (Oncorhynchus mykiss).
MicroRNAs (miRNAs) participate in various vitally biological processes via controlling target genes activity and thousands of miRNAs have been identified in many species to date, including 18,698 known animal miRNA in miRBase. However, there are only limited studies reported in rainbow trout (Oncorhynchus mykiss) especially via the computational-based approaches. In present study, we systematically investigated the miRNAs in rainbow trout using a well-developed comparative genome-based homologue search. A total of 196 potential miRNAs, belonging to 124 miRNA families, were identified, most of which were firstly reported in rainbow trout. The length of miRNAs ranged from 17 to 24 nt with an average of 20 nt while the length of their precursors varied from 47 to 152 nt with an average of 85 nt. The identified miRNAs were not evenly distributed in each miRNA family, with only one member per family for a majority, and multiple members were also identified for several families. Nucleotide U was dominant in the pre-miRNAs with a percentage of 30.04%. The rainbow trout pre-miRNAs had relatively high negative minimal folding free energy (MFE) and adjusted MFE (AMFE). Not only the mature miRNAs but their precursor sequences are conserved among the living organisms. About 2466 O. mykiss genes were predicted as potential targets for 189 miRNAs. Gene Ontology (GO) analysis showed that nearly 2093, 2107, and 2081 target genes are involved in cellular component, molecular function, and biological processes respectively. KEGG pathway enrichment analysis illuminated that these miRNAs targets might regulate 105 metabolic pathways, including those of purine metabolism, nitrogen metabolism, and oxidative phosphorylation. This study has provided an update on rainbow trout miRNAs and their targets, which represents a foundation for future studies.
The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China. Electronic address: yangliandong1987@163.com.
Liandong
L
Yang
Shunping
S
He
D000818:Animals; D019295:Computational Biology; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D017686:Oncorhynchus mykiss / Q000235:genetics*
D035683:MicroRNAs
AGO; BLAST; Comparative genomics; EST; GO; Gene Ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; MFE; MFEI; MicroRNAs; NCBI; O. mykiss; Oncorhynchus mykiss; Rainbow trout; Targets; UTRs; argonaute; basic local alignment search tool; expressed sequence tag; miRISCs; miRNA; miRNA precursor; miRNA-induced silencing complexes; microRNA; minimal folding free energy; minimal folding free energy index; national center for biotechnology information; nt; nucleotide; pre-miRNA; pri-miRNA; primary miRNA; untranslated regions