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Genome-wide identification and analysis of drought-responsive genes and microRNAs in tobacco
- Source :
- International Journal of Molecular Sciences, International Journal of Molecular Sciences, Vol 16, Iss 3, Pp 5714-5740 (2015), Volume 16, Issue 3, Pages 5714-5740
- Publication Year :
- 2014
-
Abstract
- 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.
- Subjects :
- 0106 biological sciences
Small RNA
Nicotiana benthamiana
gene regulatory network
01 natural sciences
Plant Roots
lcsh:Chemistry
Gene Expression Regulation, Plant
Gene expression
MYB
Gene Regulatory Networks
lcsh:QH301-705.5
DGE
Spectroscopy
2. Zero hunger
Genetics
Regulation of gene expression
small RNA sequencing
0303 health sciences
biology
food and beverages
General Medicine
Computer Science Applications
Droughts
TFs
Genome, Plant
Sequence analysis
Catalysis
Article
Inorganic Chemistry
03 medical and health sciences
Stress, Physiological
Tobacco
Physical and Theoretical Chemistry
Molecular Biology
Gene
030304 developmental biology
Sequence Analysis, RNA
Organic Chemistry
fungi
biology.organism_classification
WRKY protein domain
MicroRNAs
lcsh:Biology (General)
lcsh:QD1-999
drought responsive genes (DRGs)
010606 plant biology & botany
Subjects
Details
- ISSN :
- 14220067
- Volume :
- 16
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- International journal of molecular sciences
- Accession number :
- edsair.doi.dedup.....25f838235de73e12e12638e3f0214df0