title: Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance.
abstract: Eutrema salsugineum, a close relative of Arabidopsis thaliana, is a valuable halophytic model plant that has extreme tolerance to salinity. As posttranscriptional gene regulators, microRNAs (miRNAs) control gene expression and a variety of biological processes, including plant-stress responses. To identify salt-stress responsive miRNAs in E. salsugineum and reveal their possible roles in the adaptive response to salt stress, we chose the Solexa sequencing platform to screen the miRNAs in 4-week-old E. salsugineum seedlings under salt treatment. A total of 82 conserved miRNAs belonging to 27 miRNA families and 17 novel miRNAs were identified and 11 conserved miRNA families and 4 novel miRNAs showed a significant response to salt stress. To investigate the possible biological roles of miRNAs, 1060 potential targets were predicted. Moreover, 35 gene ontology (GO) categories and 1 pathway, including a few terms that were directly and indirectly related to salt stress, were significantly enriched in the salt-stress-responsive miRNAs targets. The relative expression analysis of six target genes was analyzed using quantitative real-time polymerase chain reaction (PCR) and showed a negative correlation with their corresponding miRNAs. Many stress regulatory and phytohormone regulatory cis-regulatory elements were widely present in the promoter region of the salt-responsive miRNA precursors. This study describes the large-scale characterization of E. salsugineum miRNAs and provides a useful resource for further understanding of miRNA functions in the regulation of the E. salsugineum salt-stress response.
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.|College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, BeGenomics, Chinese Academy of Sciences, Beijing, 100029, China.
authors.forename: Yimei
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Gong
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Xiong
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.
authors.forename: Wenwen
authors.initials: W
authors.lastname: Qi
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.
authors.forename: Qiuying
authors.initials: Q
authors.lastname: Pang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, BeGenomics, Chinese Academy of Sciences, Beijing, 100029, China.
authors.forename: Xumin
authors.initials: X
authors.lastname: Wang
authors.affiliation: Alkali Soil Natural Environmental Science Center, Northeast Forestry University/Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin, 150040, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
mesh_terms: D019607:Brassicaceae / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D054712:Salinity; D055049:Salt Tolerance; D055051:Salt-Tolerant Plants; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological
chemical_list: D035683:MicroRNAs; D012965:Sodium Chloride