title: Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing.
abstract: BACKGROUND
  Long non-coding RNAs (lncRNAs) have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms. However, information regarding the number, sequences, characteristics and potential functions of lncRNAs in plants is so far overly limited.
  
  
  RESULTS
  Using high-throughput sequencing and bioinformatics analysis, we identified a total of 23,324 putative lncRNAs from control, osmotic stress- and salt stress-treated leaf and root samples of Medicago truncatula, a model legume species. Out of these lncRNAs, 7,863 and 5,561 lncRNAs were identified from osmotic stress-treated leaf and root samples, respectively. While, 7,361 and 7,874 lncRNAs were identified from salt stress-treated leaf and root samples, respectively. To reveal their potential functions, we analyzed Gene Ontology (GO) terms of genes that overlap with or are neighbors of the stress-responsive lncRNAs. Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.
  
  
  CONCLUSIONS
  LncRNAs are likely involved in regulating plant's responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes. These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. tzwang@ibcas.ac.cn.|Research Network of Global Change Biology, Beijing Institutes of Life Science, the Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. tzwang@ibcas.ac.cn.
authors.forename: Tian-Zuo
authors.initials: TZ
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. liumin10@ibcas.ac.cn.
authors.forename: Min
authors.initials: M
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. zhaomingui@ibcas.ac.cn.
authors.forename: Min-Gui
authors.initials: MG
authors.lastname: Zhao
authors.affiliation: Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA. rchen@noble.org.
authors.forename: Rujin
authors.initials: R
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. whzhang@ibcas.ac.cn.|Research Network of Global Change Biology, Beijing Institutes of Life Science, the Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. whzhang@ibcas.ac.cn.
authors.forename: Wen-Hao
authors.initials: WH
authors.lastname: Zhang
mesh_terms: D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000187:drug effects; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D046913:Medicago truncatula / Q000235:genetics*; D009997:Osmotic Pressure / Q000187:drug effects; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012965:Sodium Chloride / Q000494:pharmacology*; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding; D012965:Sodium Chloride