Global identification of miRNAs and targets in Populus euphratica under salt stress
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Global identification of miRNAs and targets in Populus euphratica under salt stress Bosheng Li • Hui Duan • Jigang Li • Xing Wang Deng • Weilun Yin • Xinli Xia
Received: 30 September 2012 / Accepted: 10 January 2013 / Published online: 22 February 2013 Ó Springer Science+Business Media Dordrecht 2013
Abstract Populus euphratica, a typical hydro-halophyte, is ideal for studying salt stress responses in woody plants. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that fulfilled an important post-transcriptional regulatory function. MiRNA may regulate tolerance to salt stress but this has not been widely studied in P. euphratica. In this investigation, the small RNAome, degradome and transcriptome were studied in salt stress treated P. euphratica by deep sequencing. Two hundred and eleven conserved miRNAs between Populus trichocarpa and P. euphratica Electronic supplementary material The online version of this article (doi:10.1007/s11103-013-0010-y) contains supplementary material, which is available to authorized users. B. Li H. Duan W. Yin X. Xia College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing 100083, People’s Republic of China B. Li W. Yin X. Xia College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing 100083, People’s Republic of China B. Li H. Duan W. Yin X. Xia National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing 100083, People’s Republic of China B. Li J. Li X. W. Deng Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8104, USA W. Yin (&) X. Xia (&) Beijing Forestry University, Mailbox 69, No. 35 Qinghua East Road, Haidian District, Beijing, People’s Republic of China e-mail: [email protected] X. Xia e-mail: [email protected]
have been found. In addition, 162 new miRNAs, belonging to 93 families, were identified in P. euphratica. Degradome sequencing experimentally verified 112 targets that belonged to 51 identified miRNAs, few of which were known previously in P. euphratica. Transcriptome profiling showed that expression of 15 miRNA-target pairs displayed reverse changing pattern under salt stress. Together, these results indicate that, in P. euphratica under salt stress, a large number of new miRNAs could be discovered, and both known and new miRNA were functionally cleaving to their target mRNA. Expression of miRNA and target were correspondingly induced by salt stress but that it was a complex process in P. euphratica. Keywords Populus euphratica Salt stress Small RNAome Degradome Transcriptome
Introduction Populus euphratica is a saline, desert living poplar species. It is an ideal model for salt tolerance research into woody plants (Chen and Polle 2010; Ottow et al. 2005a). A number of micrological discoveries were observed in this hydro-halophyte, such as leaf morphological plasticity, decreased vessel diameters and adjustment to osmotic changes (Chen and Poll
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