title: Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis.
abstract: BACKGROUND
  Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for protein expression and purification. To discover and characterize the miRNAs and their cleaved target mRNAs in N. benthamiana, we sequenced small RNA transcriptomes and degradomes of two N. benthamiana accessions and validated them by Northern blots.
  
  
  RESULTS
  We used a comprehensive molecular approach to detect and to experimentally validate N. benthamiana miRNAs and their target mRNAs from various tissues. We identified 40 conserved miRNA families and 18 novel microRNA candidates and validated their target mRNAs with a genomic scale approach. The accumulation of thirteen novel miRNAs was confirmed by Northern blot analysis. The conserved and novel miRNA targets were found to be involved in various biological processes including transcription, RNA binding, DNA modification, signal transduction, stress response and metabolic process. Among the novel miRNA targets we found the mRNA of REPRESSOR OF SILENCING (ROS1). Regulation of ROS1 by a miRNA provides a new regulatory layer to reinforce transcriptional gene silencing by a post-transcriptional repression of ROS1 activity.
  
  
  CONCLUSIONS
  The identified conserved and novel miRNAs along with their target mRNAs also provides a tissue specific atlas of known and new miRNA expression and their cleaved target mRNAs of N. benthamiana. Thus this study will serve as a valuable resource to the plant research community that will be beneficial well into the future.
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. ivett.baksa@abc.hu.
authors.forename: Ivett
authors.initials: I
authors.lastname: Baksa
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. black007@abc.hu.
authors.forename: Tibor
authors.initials: T
authors.lastname: Nagy
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. barta@abc.hu.
authors.forename: Endre
authors.initials: E
authors.lastname: Barta
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. havelda@abc.hu.
authors.forename: Zoltán
authors.initials: Z
authors.lastname: Havelda
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. varallya@abc.hu.
authors.forename: Éva
authors.initials: É
authors.lastname: Várallyay
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. silhavy@abc.hu.
authors.forename: Dániel
authors.initials: D
authors.lastname: Silhavy
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. burgyan@abc.hu.
authors.forename: József
authors.initials: J
authors.lastname: Burgyán
authors.affiliation: Institute of Plant Biotechnology, National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Szent-Györgyi Albert ut 4, H-2100, Gödöllő, Hungary. szittya@abc.hu.
authors.forename: György
authors.initials: G
authors.lastname: Szittya
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D034622:RNA Interference; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D014026:Nicotiana / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant