Exploring drought stress response through comparative transcriptomics

In the last decades, climate change has brought new challenges for plant growth, such as drought, heat and salinity, which can severely affect plant physiology by altering gene expression and as such metabolic pathways. Therefore, it is essential to study plant responses to these abiotic factors, in order to elucidate genes and metabolic pathways involved. In this work, we processed a large number of transcriptomic datasets both collected from public databases and newly generated here. We focused on data obtained from multiple organs of drought stressed plants representative of monocot (e.g. Triticum species) and dicot (e.g. Arabidopsis thaliana) species. Exploratory analyses on the whole sets of the considered bioprojects retrieved from SRA NCBI did not reveal a clear separation based on treatment, highlighting a remarkable variability across studies. On the other hand, we found evidence that filtering data on the basis of genotype, environment, and drought severity, coupled with removal of confounding factors, might overcome this problem. The differentially expressed genes here identified were compared across the analysed species and organs, in order to delineate patterns of conservation and divergence in gene expression dynamics. The comparative transcriptomics approaches, developed in the frame of the project PRIN 2022 URbEVOLUTION Prot. 2022RYTHE3 and applied here to drought stress, provide a solid basis for discovering novel genes and their related pathways involved in the response to this crucial stress.