Identification of common and unique stress responsive genes of Arabidopsis thaliana under different abiotic stress through RNA-Seq meta-analysis

Abiotic stress is a major constraint for crop productivity worldwide. To better understand the common biological mechanisms of abiotic stress responses in plants, we performed meta-analysis of 652 samples of RNA sequencing (RNA-Seq) data from 43 published abiotic stress experiments in Arabidopsis thaliana. These samples were categorized into eight different abiotic stresses including drought, heat, cold, salt, light and wounding. We developed a multi-step computational pipeline, which performs data downloading, preprocessing, read mapping, read counting and differential expression analyses for RNA-Seq data. We found that 5729 and 5062 genes are induced or repressed by only one type of abiotic stresses. There are only 18 and 12 genes that are induced or repressed by all stresses. The commonly induced genes are related to gene expression regulation by stress hormone abscisic acid. The commonly repressed genes are related to reduced growth and chloroplast activities. We compared stress responsive genes between any two types of stresses and found that heat and cold regulate similar set of genes. We also found that high light affects different set of genes than blue light and red light. Interestingly, ABA regulated genes are different from those regulated by other stresses. Finally, we found that membrane related genes are repressed by ABA, heat, cold and wounding but are up regulated by blue light and red light. The results from this work will be used to further characterize the gene regulatory networks underlying stress responsive genes in plants.