Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response

BMC Plant Biology

Research Article

Lei Hou¹  Chuanzhi Zhao¹  Ming Li¹  Shuzhen Zhao¹  Han Xia¹  Changsheng Li¹  Mingnan Sun¹  Jean-François Picimbon¹  Aiqin Li¹  Quan Zhang²  Wei Sun²  Yan Liu²  Yanxiu Zhao²  Xingjun Wang³ 

[1] Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, 250100, Jinan, PR China;College of Life Sciences, Shandong Normal University, 250014, Jinan, PR China;College of Life Sciences, Shandong Normal University, 250014, Jinan, PR China;Bio-Tech Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, 250100, Jinan, PR China;

关键词: Thellungiella salsuginea;    Salt stress;    miRNA identification;    Solexa sequencing;    Expression analysis;   

DOI  :  10.1186/1471-2229-13-180

 received in 2013-08-06, accepted in 2013-11-04,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundMicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation. The microRNAs from the halophyte species Thellungiella salsuginea (salt cress), which exhibits extreme salt stress tolerance, remain to be investigated. The sequenced genome of T. salsuginea and the availability of high-throughput sequencing technology enabled us to discover the conserved and novel miRNAs in this plant species. It is interesting to identify the microRNAs from T. salsuginea genome wide and study their roles in salt stress response.ResultsIn this study, two T. salsuginea small RNA libraries were constructed and sequenced using Solexa technology. We identified 109 miRNAs that had previously been reported in other plant species. A total of 137 novel miRNA candidates were identified, among which the miR* sequence of 26 miRNAs was detected. In addition, 143 and 425 target mRNAs were predicted for the previously identified and Thellungiella-specific miRNAs, respectively. A quarter of these putative targets encode transcription factors. Furthermore, numerous signaling factor encoding genes, defense-related genes, and transporter encoding genes were amongst the identified targets, some of which were shown to be important for salt tolerance. Cleavage sites of seven target genes were validated by 5’ RACE, and some of the miRNAs were confirmed by qRT-PCR analysis. The expression levels of 26 known miRNAs in the roots and leaves of plants subjected to NaCl treatment were determined by Affymetrix microarray analysis. The expression of most tested miRNA families was up- or down-regulated upon NaCl treatment. Differential response patterns between the leaves and roots were observed for these miRNAs.ConclusionsOur results indicated that diverse set of miRNAs of T. salsuginea were responsive to salt stress and could play an important role in the salt stress response.

【 授权许可】

Unknown   
© Zhang et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.