RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants
Initiating the project on sequencing the Arabidopsis thaliana L. genome at the end of the twentieth century, researchers one day wished to expand the accumulated knowledge on Arabidopsis genetics to horticultural plants. The future arrived with the appearance of high-throughput sequencing technologies that allowed the investigation of transcriptomes of non-model plants at an unprecedented pace. RNA-seq experiments provide a unique opportunity of studying in depth the molecular-genetic basis for plant response to environmental cues.
Here we substantiate the potential of RNA-seq experiments in applications to horticultural plants. The basic steps in RNA-seq data analysis and available software packages are presented in the first section. Examples of RNA-seq data analyses, including studies of gene expression changes under various stresses in horticultural plants, and transcriptome analyses of the tolerance to abiotic stresses in horticultural plants are given in the second section.
KeywordsGenomics Horticultural plants RNA-seq Stress response Transcriptomics
We thank A.V. Kochetov, I. Lemnian, and N.A. Omelyanchuk for fruitful discussions and Dynasty Foundation (grant for young biologists), DFG (grant no. GR 3523/2), RAS program 6.6, and RFBR Foundation (grant no. 12-04-33112) for financial support.
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