High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng

PLoS One. 2012;7(9):e44385. doi: 10.1371/journal.pone.0044385. Epub 2012 Sep 4.


microRNAs (miRNAs) play vital regulatory roles in many organisms through direct cleavage of transcripts, translational repression, or chromatin modification. Identification of miRNAs has been carried out in various plant species. However, no information is available for miRNAs from Panax ginseng, an economically significant medicinal plant species. Using the next generation high-throughput sequencing technology, we obtained 13,326,328 small RNA reads from the roots, stems, leaves and flowers of P. ginseng. Analysis of these small RNAs revealed the existence of a large, diverse and highly complicated small RNA population in P. ginseng. We identified 73 conserved miRNAs, which could be grouped into 33 families, and 28 non-conserved ones belonging to 9 families. Characterization of P. ginseng miRNA precursors revealed many features, such as production of two miRNAs from distinct regions of a precursor, clusters of two precursors in a transcript, and generation of miRNAs from both sense and antisense transcripts. It suggests the complexity of miRNA production in P. ginseng. Using a computational approach, we predicted for the conserved and non-conserved miRNA families 99 and 31 target genes, respectively, of which eight were experimentally validated. Among all predicted targets, only about 20% are conserved among various plant species, whereas the others appear to be non-conserved, indicating the diversity of miRNA functions. Consistently, many miRNAs exhibited tissue-specific expression patterns. Moreover, we identified five dehydration- and ten heat-responsive miRNAs and found the existence of a crosstalk among some of the stress-responsive miRNAs. Our results provide the first clue to the elucidation of miRNA functions in P. ginseng.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Conserved Sequence
  • Evolution, Molecular
  • Flowers / genetics
  • Flowers / metabolism
  • Gene Expression Regulation, Plant*
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / biosynthesis
  • MicroRNAs / chemistry*
  • MicroRNAs / genetics
  • Molecular Sequence Data
  • Panax / genetics
  • Panax / metabolism*
  • Plant Leaves / genetics
  • Plant Leaves / metabolism
  • Plant Roots / genetics
  • Plant Roots / metabolism
  • Plant Stems / genetics
  • Plant Stems / metabolism
  • Plants, Medicinal / genetics
  • Plants, Medicinal / metabolism*
  • RNA, Plant / biosynthesis
  • RNA, Plant / chemistry*
  • RNA, Plant / genetics
  • Sequence Analysis, RNA
  • Transcriptome


  • MicroRNAs
  • RNA, Plant

Grant support

This work was supported by the Natural Science Foundation of China (grant no. 81072993 to SL), the Major Scientific and Technological Special Project for Significant New Drugs Creation (grant no. 2012ZX09301002-001-031 to SL), the Program for Xiehe Scholars in Chinese Academy of Medical Sciences & Peking Union Medical College (to SL), the Scientific Research Foundation for Returned Oversea Chinese Scholars, Human Resources and Social Security Department of China (to SL), the Program for Xiehe Scholars and Innovative Research Team in Chinese Academy of Medical Sciences (grant no. YKRBH (2011)26 to SL), and the Central Public-Interest Scientific Institution Basal Research Fund of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences (to SL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.