title: Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava.
abstract: BACKGROUND
  Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs.
  
  
  RESULTS
  In order to understand sncRNAs' roles in plant chilling response and stress acclimation, we performed a comprehensive study of miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate chilling stresses, that underwent further severe chilling stress after chilling acclimation at moderate stress, and that grew under the normal condition. We also included castor bean (Ricinus communis) in our study to understand conservation of sncRNAs. In addition to known miRNAs, we identified 32 (22 and 10) novel miRNAs as well as 47 (26 and 21) putative secondary siRNA-yielding and 8 (7 and 1) nat-siRNA-yielding candidate loci in Cassava and castor bean, respectively. Among the expressed sncRNAs, 114 miRNAs, 12 ta-siRNAs and 2 nat-siRNAs showed significant expression changes under chilling stresses.
  
  
  CONCLUSIONS
  Systematic and computational analysis of microRNAome and experimental validation collectively showed that miRNAs, ta-siRNAs, and possibly nat-siRNAs play important roles in chilling response and chilling acclimation in Cassava by regulating stress-related pathways, e.g. Auxin signal transduction. The conservation of these sncRNA might shed lights on the role of sncRNA-mediated pathways affected by chilling stress and stress acclimation in Euphorbiaceous plants.
authors: Jing
authors: J
authors: Xia
authors: Changying
authors: C
authors: Zeng
authors: Zheng
authors: Z
authors: Chen
authors: Kevin
authors: K
authors: Zhang
authors: Xin
authors: X
authors: Chen
authors: Yufei
authors: Y
authors: Zhou
authors: Shun
authors: S
authors: Song
authors: Cheng
authors: C
authors: Lu
authors: Ruiju
authors: R
authors: Yang
authors: Zi
authors: Z
authors: Yang
authors: Junfei
authors: J
authors: Zhou
authors: Hai
authors: H
authors: Peng
authors: Wenquan
authors: W
authors: Wang
authors: Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China. mmpeng_2000@yahoo.com.
authors: Ming
authors: M
authors: Peng
authors: Weixiong
authors: W
authors: Zhang
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D001483:Base Sequence; D003080:Cold Temperature; D019295:Computational Biology; D017124:Conserved Sequence; D017343:Genes, Plant / Q000235:genetics; D002365:Manihot / Q000235:genetics / Q000502:physiology*; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D034741:RNA, Small Interfering / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering