title: Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum).
abstract: BACKGROUND
  MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are two major classes of small RNAs. They play important regulatory roles in plants and animals by regulating transcription, stability and/or translation of target genes in a sequence-complementary dependent manner. Over 4,000 miRNAs and several classes of siRNAs have been identified in plants, but in tobacco only computational prediction has been performed and no tobacco-specific miRNA has been experimentally identified. Wounding is believed to induce defensive response in tobacco, but the mechanism responsible for this response is yet to be uncovered.
  
  
  RESULTS
  To get insight into the role of small RNAs in damage-induced responses, we sequenced and analysed small RNA populations in roots and leaves from wounding or topping treated tobacco plants. In addition to confirmation of expression of 27 known miRNA families, we identified 59 novel tobacco-specific miRNA members of 38 families and a large number of loci generating phased 21- or 24-nt small RNAs (including ta-siRNAs). A number of miRNAs and phased small RNAs were found to be responsive to wounding or topping treatment. Targets of small RNAs were further surveyed by degradome sequencing.
  
  
  CONCLUSIONS
  The expression changes of miRNAs and phased small RNAs responsive to wounding or topping and identification of defense related targets for these small RNAs suggest that the inducible defense response in tobacco might be controlled by pathways involving small RNAs.
authors.affiliation: Department of Agronomy and James D, Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
authors.forename: She
authors.initials: S
authors.lastname: Tang
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.forename: Zefeng
authors.initials: Z
authors.lastname: Li
authors.forename: Yijie
authors.initials: Y
authors.lastname: Gui
authors.forename: Bingguang
authors.initials: B
authors.lastname: Xiao
authors.forename: Jiahua
authors.initials: J
authors.lastname: Xie
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D035683:MicroRNAs / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics; D018517:Plant Roots / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D014026:Nicotiana / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering