title: Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches.
abstract: Wheat is the most highly cultivated plant species for its grain production throughout the world. Because small RNA-dependent gene regulation is critical for successful completion of plant life cycle including its productivity, identification of not only miRNAs but also confirming their targets in wheat is important. To identify small RNAs including novel miRNAs as well as miRNA targets in wheat, we constructed small RNA and degradome libraries from wheat seedlings. Small RNA analysis resulted in identification of most conserved miRNAs including novel miRNAs that can be grouped into 32 miRNA families. The sequence analysis also led to the characterization of two abundantly expressed rRNA-derived small RNAs. To identify miRNA targets, degradome library was sequenced and the bioinformatic analysis confirmed 53 genes as targets for miRNAs and Tas3-siRNAs. Degradome analysis also confirmed a conserved fine-tuning mechanism of Tas3-siRNA abundance by siRNA-mediated silencing of TAS3 transcripts in diverse plant species. These findings added additional information to the small RNA knowledge-base in wheat.
authors: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
authors: Yong-Fang
authors: YF
authors: Li
authors: Yun
authors: Y
authors: Zheng
authors: Guru
authors: G
authors: Jagadeeswaran
authors: Ramanjulu
authors: R
authors: Sunkar
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D004722:Endoribonucleases; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes; D018517:Plant Roots / Q000235:genetics; D018520:Plant Shoots / Q000235:genetics; D011117:Polyribonucleotide Nucleotidyltransferase; D059367:RNA Cleavage; D020365:RNA Helicases; D018749:RNA, Plant / Q000235:genetics* / Q000302:isolation & purification; D012335:RNA, Ribosomal / Q000235:genetics / Q000302:isolation & purification; D034741:RNA, Small Interfering / Q000235:genetics / Q000302:isolation & purification; D036226:Seedlings / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D009097:Multienzyme Complexes; D018749:RNA, Plant; D012335:RNA, Ribosomal; D034741:RNA, Small Interfering; C111244:degradosome; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D020365:RNA Helicases