title: Genome-wide characterization of microRNA in foxtail millet (Setaria italica).
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood.
  
  
  RESULTS
  In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing.
  
  
  CONCLUSIONS
  We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.
authors: Fei
authors: F
authors: Yi
authors: Shaojun
authors: S
authors: Xie
authors: Yuwei
authors: Y
authors: Liu
authors: Xin
authors: X
authors: Qi
authors: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China. yujj@cau.edu.cn.
authors: Jingjuan
authors: J
authors: Yu
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D032983:Setaria Plant / Q000235:genetics*; D045868:Sorghum / Q000235:genetics; D026801:Synteny / Q000235:genetics
chemical_list: D035683:MicroRNAs