Detecting Let-7 isoforms of Salmonids by bioinformatics data

Document Type : Research Paper

Authors

1 Professor, Department of Fishery, Faculty of Natural Resources, University of Tehran, Karaj, Iran

2 Ph.D student, Professor, Department of Fishery, Faculty of Natural Resources, University of Tehran, Karaj, Iran

3 Assistant Professor, Department of Fishery, Faculty of Natural Resources, University of Tehran, Karaj, Iran.

Abstract

MicroRNAs are short noncoding RNAs that control gene expression in post-transcriptionally manner, estimated about 60% of all genes controlled by these RNAs. Among vertebrates in Salmonids this type of RNA poorly investigated. In this study for profiling isoforms of Let-7 MicroRNA of Salmonids, the data from NCBI database was extracted and analyzed. About 43 million reads with 22 nucleotides span were analyzed. Among them, 17.8 million reads were matched to to Let-7a isomer of this MicroRNA family. 9 Isoforms of this family detected in which 8 of them were detected before in other animals. One of detected isoforms was novel and not reported in other species. The novel isolated isoform in this study contains one nucleotide difference with Let-7f in Atlantic salmon (salmo salar). let-7a isomer abundantly expressed comparing with others. 20 loci for all isomers were on reference genome (Otsh.V1) in NCBI, and 7 of these loci organized as MicroRNA gene clusters in genome. The other 2 loci for Let-7c were detected on unplaced fragments of reference genome as well.

Keywords

Journal of Fisheries
Volume 73, Issue 4
January 2020
Pages 619-633

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