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Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum)

Characterization of flax miRNA genes

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Abstract

MicroRNAs (miRNAs) are small (20–24 nucleotide long) endogenous regulatory RNAs that play important roles in plant growth and development. They regulate gene expression at the post-transcriptional level by translational repression or target degradation and gene silencing. In this study, we identified 116 conserved miRNAs belonging to 23 families from the flax (Linum usitatissimum L.) genome using a computational approach. The precursor miRNAs varied in length; while most of the mature miRNAs were 21 nucleotide long, intergenic and showed conserved signatures of RNA polymerase II transcripts in their upstream regions. Promoter region analysis of the flax miRNA genes indicated prevalence of MYB transcription factor binding sites. Four miRNA gene clusters containing members of three phylogenetic groups were identified. Further, 142 target genes were predicted for these miRNAs and most of these represent transcriptional regulators. The miRNA encoding genes were expressed in diverse tissues as determined by digital expression analysis as well as real-time PCR. The expression of fourteen miRNAs and nine target genes was independently validated using the quantitative reverse transcription PCR (qRT-PCR). This study suggests that a large number of conserved plant miRNAs are also found in flax and these may play important roles in growth and development of flax.

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Acknowledgments

The authors thank Dr. Sam Griffiths-Jones (miRbase administrator, University of Manchester, UK) for providing universal nomenclature to the flax microRNA genes. Dr. Martin Lott, University of East Anglia, UK is acknowledged for his support and help during this study. VTB, VCP and SMK acknowledge the Council of Scientific and Industrial Research (CSIR), India for providing fellowships. This work was supported by the NRC-DBT collaborative project on flax. The collaborative project at CSIR-National Chemical Laboratory, Pune, India was supported by Department of Biotechnology, Govt. of India; while at Plant Biotechnology Institute, Saskatoon, Canada, the project was supported by NRC Genomics, Genome Canada and Genome Prairie.

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India

    Vitthal T. Barvkar, Varsha C. Pardeshi, Sandip M. Kale, Vidya S. Gupta & Narendra Y. Kadoo

  2. Plant Biotechnology Institute, NRC, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada

    Shuqing Qiu, Meaghen Rollins & Raju Datla

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  1. Vitthal T. Barvkar
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  2. Varsha C. Pardeshi
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425_2012_1833_MOESM4_ESM.tif

Hierarchical representation of GO terms overrepresented in biological process (a), cellular component (b) and molecular function (c) categories generated by agriGO analysis. The boxes represent GO terms, GO id, term definition and statistical information and are color coded as per the level of significance (0.05). Non-significant terms are shown as white boxes. The degree of color saturation of a box is positively correlated to the enrichment level of the term. Solid, dashed, and dotted lines represent two, one and zero enriched terms at both ends connected by the line, respectively. The rank direction of the graph is set to from left to right (TIFF 3284 kb)

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Barvkar, V.T., Pardeshi, V.C., Kale, S.M. et al. Genome-wide identification and characterization of microRNA genes and their targets in flax (Linum usitatissimum). Planta 237, 1149–1161 (2013). https://doi.org/10.1007/s00425-012-1833-5

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