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

Quan Zhang,Aiqin Li,Chuanzhi Zhao,Ming Li,Xingjun Wang,Jean-François Picimbon,Mingnan Sun,Lei Hou,Wei Sun,Changsheng Li,Yan Liu,Han Xia,Shuzhen Zhao,Yanxiu Zhao

doi:10.1186/1471-2229-13-180

Abstract

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.

Highlights

MicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation
Given that the target genes of microRNAs are predominantly transcription factors [8], we thought that it would be interesting to investigate the role of miRNAs in the regulation of salt tolerance in T. salsuginea
The control library (CL) was constructed using plants grown in Hoagland solution without NaCl, and the treatment library (TL) used plants treated with 200 mM NaCl for 24 h

Summary

Introduction

MicroRNAs are key regulators of plant growth and development with important roles in environmental adaptation. Thellungiella salsuginea, previously named Thellungiella halophila, separated from Arabidopsis around 15–30 million years ago and occupies an intermediate position between the Brassica and Arabidopsis clades [1,2,3]. Whereas this crucifer exhibits tolerance to high salt, drought, and cold stress, its close relative Arabidopsis thaliana is cytosol, including sugars, polyols, and amino acids, is considered to be an effective strategy for acquiring tolerance to salt stress [5]. Given that the target genes of microRNAs (miRNAs) are predominantly transcription factors [8], we thought that it would be interesting to investigate the role of miRNAs in the regulation of salt tolerance in T. salsuginea

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Discussion

Conclusion