title: Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco.
abstract: Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL).
  
  
  
  In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed miRNAs (DEMs) and DEGs revealed 92 mRNA-miRNA interactions between CL and DL plants, and 32 mRNA-miRNA interactions between DL and WL plants.
  
  
  
  This study provides a global view of the transcriptional and the post-transcriptional responses of tobacco under drought stress and re-watering conditions. Our results establish an empirical foundation that should prove valuable for further investigations into the molecular mechanisms through which tobacco, and plants more generally, respond to drought stress at multiple molecular genetic levels.
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Qiansi
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Key Laboratory of Cultivation and Protection for Non-wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410000, China.|College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, 410000, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.affiliation: School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
authors.forename: Zhongchun
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Tie
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Chen
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Lifeng
authors.initials: L
authors.lastname: Jin
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Niu
authors.initials: N
authors.lastname: Zhai
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Qingxia
authors.initials: Q
authors.lastname: Zheng
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Ran
authors.initials: R
authors.lastname: Wang
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Guoyun
authors.initials: G
authors.lastname: Xu
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China. Liu_pingping2012@163.com.
authors.forename: Pingping
authors.initials: P
authors.lastname: Liu
authors.affiliation: Zhengzhou Tobacco Research Institute, Zhengzhou, 450001, China. Joanzhn@163.com.
authors.forename: Huina
authors.initials: H
authors.lastname: Zhou
mesh_terms: D055864:Droughts; D020869:Gene Expression Profiling; D035683:MicroRNAs / Q000235:genetics*; D010641:Phenotype; D018515:Plant Leaves / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D014026:Nicotiana / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000502:physiology*; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D014867:Water / Q000494:pharmacology*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors; D014867:Water