Parallel comparison reveals conservation and re-wiring of abiotic stress response networks across three plant species

Abstract Abiotic stresses trigger significant alterations in plant morphology, yield, and nutrient composition. To counter these stresses, plants have developed strategies involving gene expression adjustments, impacting their growth and development to ensure survival and reproduction. Although transcriptomic studies have extensively examined stress responses, our understanding of their conservation remains limited. We conducted a comprehensive study on the effects of 24 different environmental and nutrient conditions on the growth yield of three hydroponically grown leafy crops (cai xin, lettuce, and spinach). This research identified optimal conditions for maximizing yield and vitamin content and pinpointed conditions that induce abiotic stress. Our findings highlight the substantial impact of stress on various plant functions, with photosynthesis playing a pivotal role in vitamin content regulation. A detailed comparative analysis of gene expression across these crops revealed conserved gene sets potentially crucial for abiotic stress response. Furthermore, we introduced a novel method that merges regression and genomics to construct reliable gene regulatory networks for stress response. Despite significant conservation of these networks among the studied crops, their key transcription factors showed limited similarity to those in Arabidopsis thaliana, suggesting notable functional divergence. To give easy access to the data and comparative transcriptomic tools, we established StressPlantTools, an public online database (https://stress.sbs.ntu.edu.sg/), facilitating further research into stress-responsive genes.