RNA sequencing (RNA Seq) is revolutionizing the study of the transcriptomes. Highly sensitive and accurate tool for measuring expression across the transcriptome, RNA Seq provides researchers with visibility into previously undetected changes occurring in disease states, in response to therapeutics, under different environmental conditions, and across a broad range of other study designs. RNA Seq allows researchers to detect both known and novel features in a single assay, enabling detection of transcript isoforms, gene fusions, single nucleotide variants, and other features without the limitation of prior knowledge.
We here outline the work published by Zhang X et al that establishes genes responsible for resistant to drought stress.
De Novo transcriptome assembly followed by gene identification identified 55,268 unique genes. Gene annotation was performed for 36,265 genes to capture information like conserved domains, gene ontology terms and metabolic pathways. Differential gene expression analysis identifies genes that are upregulate under drought stress in pathways such as carbon metabolism, starch and sucrose metabolism, amino acid biosynthesis, phenyl propanoid biosynthesis and plant hormone signal transduction.
Transcriptome assembly and Differential gene expression Analysis Workflow
Here we observed how next generation sequencing for transcriptome analysis coupled with Bioinformatics tools for assembly and differential gene expression helped in screening out functional genes which showed high resistance stress under drought conditions. Hundreds of candidate genes were identified under severe drought stress, including transcriptional factors such as MYB, G2-like, ERF, C2H2, NAC, NF-X1, GRF, HD-ZIP, HB-other, HSF, C3H, GRAS, WRKY, bHLH and Trihelix. Weighted gene co-expression network analysis displayed key hub genes related to drought stress. These genes could be valuable resource for further investigation into the molecular mechanism for drought stress in C. thesioides.
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Reference: https://www.sciencedirect.com/science/article/abs/pii/S0378111919305426