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Computational identification of conserved microRNAs and their putative targets in the Hypericum perforatum L. flower transcriptome

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Abstract

MicroRNAs (miRNAs) have recently emerged as important regulators of gene expression in plants. Many miRNA families and their targets have been extensively studied in model species and major crops. We have characterized mature miRNAs along with their precursors and potential targets in Hypericum to generate a comprehensive list of conserved miRNA families and to investigate the regulatory role of selected miRNAs in biological processes that occur in the flower. St. John’s wort (Hypericum perforatum L., 2n = 4x = 32), a medicinal plant that produces pharmaceutically important metabolites with therapeutic activities, was chosen because it is regarded as an attractive model system for the study of apomixis. A computational in silico prediction of structure, in combination with an in vitro validation, allowed us to identify 7 pre-miRNAs, including miR156, miR166, miR390, miR394, miR396, and miR414. We demonstrated that H. perforatum flowers share highly conserved miRNAs and that these miRNAs potentially target dozens of genes with a wide range of molecular functions, including metabolism, response to stress, flower development, and plant reproduction. Our analysis paves the way toward identifying flower-specific miRNAs that may differentiate the sexual and apomictic reproductive pathways.

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Acknowledgments

This research was supported by the following grants: Research Project for Young Researchers of the University of Padova (year 2010), “Comparative and functional genomics for cloning and characterizing genes for apomixis” (code: GRIC101130/10), Principal investigator: Giulio Galla. Academic Research Project of the University of Padova (year 2012), “Transcriptomics of reproductive organs in model species for comparative analysis of the genetic-molecular factors characterizing sexual and apomictic processes” (code: CPDA128282/12), Principal investigator: Gianni Barcaccia.

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  1. Laboratory of Genetics and Genomics, DAFNAE, University of Padova, Campus of Agripolis, Viale dell’Università 16, 35020, Legnaro, Italy

    Giulio Galla, Mirko Volpato & Gianni Barcaccia

  2. Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466, Gatersleben, Germany

    Timothy F. Sharbel

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  1. Giulio Galla
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Correspondence to Gianni Barcaccia.

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Communicated by E. Albertini.

Giulio Galla and Mirko Volpato have contributed equally to this work.

A contribution to the Special Issue “HAPRECI—Plant Reproduction Research in Europe”.

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Galla, G., Volpato, M., Sharbel, T.F. et al. Computational identification of conserved microRNAs and their putative targets in the Hypericum perforatum L. flower transcriptome. Plant Reprod 26, 209–229 (2013). https://doi.org/10.1007/s00497-013-0227-6

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