Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing

PLoS One. 2013;8(2):e57233. doi: 10.1371/journal.pone.0057233. Epub 2013 Feb 21.

Abstract

Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Conserved Sequence
  • Evolution, Molecular
  • Gene Expression Regulation, Plant*
  • High-Throughput Nucleotide Sequencing
  • Inverted Repeat Sequences
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Plant Leaves / genetics*
  • Plant Stems / genetics*
  • RNA, Plant / chemistry
  • RNA, Plant / genetics*
  • Sequence Analysis, RNA
  • Solanum tuberosum / genetics*
  • Transcriptome*

Substances

  • MicroRNAs
  • RNA, Plant

Associated data

  • GEO/GSE39230

Grant support

This work was supported by the Scottish Government Rural and Environment Science and Analytical Services Division (RESAS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.