Computational Identification, Target Prediction, and Validation of Conserved miRNAs in Insulin Plant (Costus pictus D. Don)

Insulin plant (Costus pictus D. Don) is an economically important medicinal plant for the content of its high value secondary metabolites, bioactive compounds, and remarkable flowering features. MicroRNAs are a class of short (∼21 nucleotides), endogenous, noncoding RNA molecules that play a vital r...

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Bibliographic Details
Published in:Applied biochemistry and biotechnology 2016-02, Vol.178 (3), p.513-526
Main Authors: Das, Akan, Das, Purabi, Kalita, Mohan C, Mondal, Tapan K
Format: Article
Language:English
Subjects:
Bioactive compounds
biochemical pathways
Biochemistry
Biotechnology
Chemistry
Chemistry and Materials Science
Costus
Costus - genetics
Economic importance
enzymes
flowering
Gene Expression
genes
Herbal medicine
Insulin
leaves
Medicinal plants
Metabolites
microRNA
MicroRNAs
MicroRNAs - genetics
non-coding RNA
nucleotides
Oryza sativa
Plant Leaves - genetics
Plant tissues
prediction
proteins
quantitative polymerase chain reaction
Regulation
rice
Secondary metabolites
tissues
transcription factors
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Summary:Insulin plant (Costus pictus D. Don) is an economically important medicinal plant for the content of its high value secondary metabolites, bioactive compounds, and remarkable flowering features. MicroRNAs are a class of short (∼21 nucleotides), endogenous, noncoding RNA molecules that play a vital role in regulating gene expression. Here, we used a computer-based homology approach to identify conserved miRNAs in Transcribed Sequence Assemblies (TSA) of C. pictus. It led us to identify 42 miRNAs of 13 different families in C. pictus for the first time. Using quantitative polymerase chain reaction (qPCR) assays, we further confirmed the expression of 8 miRNAs (miR394, miR159b, miR166k, miR172, miR159f, miR166, miR144, and miR858) in young and mature leaf tissues. A total of 109 potential target genes of the identified miRNAs were subsequently predicted in rice (Oryza sativa L.) genome. The target genes encode transcription factors, enzymes, and various functional proteins involved in the regulation of several metabolic pathways. The findings in the present study lay the foundation for further research on miRNAs and miRNA-mediated gene regulation in this important medicinal plant.
ISSN:0273-2289
1559-0291
DOI:10.1007/s12010-015-1891-9