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Open Access Research article

Endogenous small-noncoding RNAs and their roles in chilling response and stress acclimation in Cassava

Jing Xia13, Changying Zeng2, Zheng Chen13, Kevin Zhang13, Xin Chen2, Yufei Zhou2, Shun Song2, Cheng Lu2, Ruiju Yang2, Zi Yang2, Junfei Zhou1, Hai Peng1, Wenquan Wang2, Ming Peng2* and Weixiong Zhang134*

Author Affiliations

1 Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China

2 The Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China

3 Department of Computer Science and Engineering, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA

4 Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA

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BMC Genomics 2014, 15:634  doi:10.1186/1471-2164-15-634

Published: 29 July 2014

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.

Conclusion

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.

Keywords:
microRNA; tasiRNA; chilling acclimation; Cassava