Planta

, Volume 232, Issue 2, pp 417–434

Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum)

Original Article

DOI: 10.1007/s00425-010-1182-1

Cite this article as:
Xie, F., Frazier, T.P. & Zhang, B. Planta (2010) 232: 417. doi:10.1007/s00425-010-1182-1

Abstract

MicroRNAs (miRNAs) are a class of non-coding small endogenous RNAs with lengths of ~22 nucleotides (nt) that have been shown to regulate gene expression at the post-transcriptional levels by targeting mRNAs for degradation or by inhibiting protein translation. Although thousands of miRNAs have been identified in many species, miRNAs have not yet been identified in switchgrass (Panicum virgatum), one of the most important bioenergy crops in the United States and around the world. In this study, we identified 121 potential switchgrass miRNAs, belonging to 44 families, using a well-defined comparative genome-based computational approach. We also identified miRNA clusters and antisense miRNAs in switchgrass expressed sequences tags. These identified miRNAs potentially target 839 protein-coding genes, which can act as transcription factors, and take part in multiple biological and metabolic processes including sucrose and fat metabolism, signal transduction, stress response, and plant development. Gene ontology (GO) analysis, based on these targets, showed that 527 biological processes were involved. Twenty-five of these processes were demonstrated to participate in the metabolism of carbon, glucose, starch, fatty acid, and lignin and in xylem formation. According to pathway enrichment analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG), 118 metabolism networks were found. These networks are involved in sucrose metabolism, fat metabolism, carbon fixation, hormone regulation, oxidative stress response, and the processing of other secondary metabolites.

Keywords

Comparative genome Gene ontology MicroRNA Panicum Pathway Switchgrass 

Abbreviations

DCL1

Dicer-like 1

EST

Expressed sequence tag

GO

Gene ontology

KEGG

Kyoto Encyclopedia of Genes and Genomes

miRNA

MicroRNA

MFE

Minimal folding free energy

MFEI

Minimal folding free energy index

nt

Nucleotide

pre-miRNAs

miRNA precursor

NCBI

National Center for Biotechnology Information

RISC

RNA-induced silencing complex

SBP

Squamosa-promoter-binding protein-like protein

TAF

TBP-associated factors

TBP

TATA-binding protein

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Fuliang Xie
    • 1
  • Taylor P. Frazier
    • 1
  • Baohong Zhang
    • 1
  1. 1.Department of BiologyEast Carolina UniversityGreenvilleUSA

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