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Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa

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An Erratum to this article was published on 24 February 2015

Abstract

Main conclusion

This study is the first endeavor on mining of miRNAs and analyzing their involvement in development and secondary metabolism of an endangered medicinal herb Picrorhiza kurroa (P. kurroa ).

miRNAs are ubiquitous non-coding RNA species that target complementary sequences of mRNA and result in either translational repression or target degradation in eukaryotes. The role of miRNAs has not been investigated in P. kurroa which is a medicinal herb of industrial value due to the presence of secondary metabolites, picroside-I and picroside-II. Computational identification of miRNAs was done in 6 transcriptomes of P. kurroa generated from root, shoot, and stolon organs varying for growth, development, and culture conditions. All available plant miRNA entries were retrieved from miRBase and used as backend datasets to computationally identify conserved miRNAs in transcriptome data sets. Total 18 conserved miRNAs were detected in P. kurroa followed by target prediction and functional annotation which suggested their possible role in controlling various biological processes. Validation of miRNA and expression analysis by qRT-PCR and 5′ RACE revealed that miRNA-4995 has a regulatory role in terpenoid biosynthesis ultimately affecting the production of picroside-I. miR-5532 and miR-5368 had negligible expression in field-grown samples as compared to in vitro-cultured samples suggesting their role in regulating P. kurroa growth in culture conditions. The study has thus identified novel functions for existing miRNAs which can be further validated for their potential regulatory role.

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Abbreviations

miRNA:

MicroRNA

P. kurroa :

Picrorhiza kurroa

PKS-25:

P. kurroa in vitro-cultured shoots grown at 25 °C

PKS-15:

P. kurroa in vitro-cultured shoots grown at 15 °C

PKR-25:

P. kurroa in vitro-cultured roots grown at 25 °C

PKSS:

P. kurroa field-grown shoots

PKSR:

P. kurroa field-grown roots

PKSTS:

P. kurroa field-grown stolons

P-I and II:

Picroside I and II

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Acknowledgments

The authors are thankful to the Department of Biotechnology, Ministry of Science & Technology, Government of India, for providing research grant in the form of a program support on high value medicinal plants to RSC.

Conflict of interest

Authors declare that they do not have any conflict of interest.

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Authors and Affiliations

  1. Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, Himachal Pradesh, India

    Ira Vashisht, Prashant Mishra, Tarun Pal, Sreekrishna Chanumolu, Tiratha Raj Singh & Rajinder Singh Chauhan

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  1. Ira Vashisht
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  2. Prashant Mishra
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  3. Tarun Pal
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  4. Sreekrishna Chanumolu
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Correspondence to Rajinder Singh Chauhan.

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Vashisht, I., Mishra, P., Pal, T. et al. Mining NGS transcriptomes for miRNAs and dissecting their role in regulating growth, development, and secondary metabolites production in different organs of a medicinal herb, Picrorhiza kurroa . Planta 241, 1255–1268 (2015). https://doi.org/10.1007/s00425-015-2255-y

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