Genome-wide identification and analysis of drought-responsive genes and microRNAs in tobacco

International Journal of Molecular Sciences
Fuqiang YinGuangtang Pan

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 sh...Continue Reading

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Citations

Jan 7, 2017·Mechanisms of Ageing and Development·Konstantinos Voskarides
Feb 9, 2018·The Plant Journal : for Cell and Molecular Biology·Julia LegenChristian Schmitz-Linneweber
May 24, 2020·Plant Biotechnology Journal·Qiang ZhaoYang-Yang Li
Aug 28, 2021·International Journal of Molecular Sciences·Yasmine S HezemaPraveen K Saxena

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Methods Mentioned

BETA
environmental stresses
MDA
PCR
transgenic
RNA-seq
reverse transcription-PCR

Software Mentioned

EnsemblCompara
Perl script
Cytoscape
R package
DGE
SOAP2
SPSS16
Blast2GO
AgriGO

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