Cross-species transcriptomics uncovers shared responses to water deficiency in plants

Deepening our knowledge of conserved molecular mechanisms governing stress responses in plants is fundamental for identifying new core genes and processes involved in tolerance to adverse environmental conditions. For this purpose, we developed a bioinformatic pipeline to retrieve and integrate stress-related RNA-seq transcriptomic data from species of interest and identify core species-specific and cross-species conserved genes and processes involved in stress responses. We utilized this approach to investigate the molecular mechanisms underpinning drought response in Arabidopsis thaliana, Triticum aestivum, and Solanum lycopersicum. We found that hormone signaling, reactive oxygen species catabolism, cell wall organization, photosynthesis, and defense mechanisms were dysregulated in response to drought in at least two species. Among the identified cross-species conserved differentially expressed genes, PUB19, EDL3, RAB18, and AAP6 confirmed to play a key role in drought response. Coexpression networks identified central genes underpinning drought-response, such as HB-7 in leaves and P5CS1 in roots. Leveraging PlantConnectome, several drought-responsive genes not classified as such in Gene Ontology were also detected, including EULS3, PUB19, BFT, DAA1, involved in carbohydrate recognition, ubiquitination, abscisic acid signaling, and membrane integrity maintenance, highlighting the need for further investigation. In conclusion, the developed approach proved effective in identifying core drought-responsive genes and processes and has the potential to be applied to other plant species and types of stress.