1. Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)
- Author
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M Gayathri, V. Radhika, Kundapura V. Ravishankar, M Pichaimuthu, and Rekha Gupta
- Subjects
next generation sequencing ,0301 basic medicine ,Regulation of gene expression ,microrna ,Contig ,Plant culture ,RNA ,Plant Science ,Computational biology ,lcsh:Plant culture ,Horticulture ,Biology ,mirna targets ,Stem-loop ,DNA sequencing ,SB1-1110 ,03 medical and health sciences ,030104 developmental biology ,microRNA ,Gene expression ,abelmoschus esculentus ,lcsh:SB1-1110 ,Original Research Papers ,Transcription factor ,Ecology, Evolution, Behavior and Systematics - Abstract
MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in theregulation of gene expression in eukaryotes. Gene expression involves post-transcriptionalgene regulation by miRNAs. miRNAs are formed from precursor RNA molecules that fold intoa stem loop secondary structure. The mature miRNA is one end of the precursor miRNA,defined by the cut from ‘Drosha’ on either the 5’ or 3’ arm. In this study, we have used abioinformatics approach to identify miRNAs in 3,361 contigs obtained from partial genomesequence data of Abelmoschus esculentus (okra) sequenced by NGS technology. Using C-miiand psRNA Target tools, we identified two miRNAs and their target RNAs for which a regulatorymiRNA binding has been verified. Their targets consisted of transcription factors involved ingrowth and development, gene regulation and metabolism. Phylogenetic analysis of the newlyidentified miRNA family has been done to compare their level of conservation with respect tothe other members of the plant kingdom.
- Published
- 2018
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