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Int. J. Mol. Sci. 2015, 16(3), 5714-5740;

Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco

School of Agricultural Sciences, Xichang College, Xichang 615000, China
Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
Zunyi Academy of Agricultural Sciences, Zunyi 563102, China
Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
Department of Agronomy, Iowa State University, Ames, IA 50011, USA
These authors are equally contributed to this work.
Author to whom correspondence should be addressed.
Academic Editor: Ann Cuypers
Received: 7 December 2014 / Revised: 19 January 2015 / Accepted: 29 January 2015 / Published: 12 March 2015
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Drought stress response is a complex trait regulated at transcriptional and post-transcriptional levels in tobacco. Since the 1990s, many studies have shown that miRNAs act in many ways to regulate target expression in plant growth, development and stress response. The recent draft genome sequence of Nicotiana benthamiana has provided a framework for Digital Gene Expression (DGE) and small RNA sequencing to understand patterns of transcription in the context of plant response to environmental stress. We sequenced and analyzed three Digital Gene Expression (DGE) libraries from roots of normal and drought-stressed tobacco plants, and four small RNA populations from roots, stems and leaves of control or drought-treated tobacco plants, respectively. We identified 276 candidate drought responsive genes (DRGs) with sequence similarities to 64 known DRGs from other model plant crops, 82 were transcription factors (TFs) including WRKY, NAC, ERF and bZIP families. Of these tobacco DRGs, 54 differentially expressed DRGs included 21 TFs, which belonged to 4 TF families such as NAC (6), MYB (4), ERF (10), and bZIP (1). Additionally, we confirmed expression of 39 known miRNA families (122 members) and five conserved miRNA families, which showed differential regulation under drought stress. Targets of miRNAs were further surveyed based on a recently published study, of which ten targets were DRGs. An integrated gene regulatory network is proposed for the molecular mechanisms of tobacco root response to drought stress using differentially expressed DRGs, the changed expression profiles of miRNAs and their target transcripts. This network analysis serves as a reference for future studies on tobacco response stresses such as drought, cold and heavy metals. View Full-Text
Keywords: Nicotiana benthamiana; DGE; small RNA sequencing; drought responsive genes (DRGs); TFs; gene regulatory network Nicotiana benthamiana; DGE; small RNA sequencing; drought responsive genes (DRGs); TFs; gene regulatory network

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Yin, F.; Qin, C.; Gao, J.; Liu, M.; Luo, X.; Zhang, W.; Liu, H.; Liao, X.; Shen, Y.; Mao, L.; Zhang, Z.; Lin, H.; Lübberstedt, T.; Pan, G. Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco. Int. J. Mol. Sci. 2015, 16, 5714-5740.

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