Organ-specific transcriptomic and proteomic changes in thermomorphogenesis in Arabidopsis thaliana seedlings

Plant acclimatisation to mild, yet prolonged temperature increases is critical for survival amid global warming. Temperature increases within the physiological range (24-30C, for the model Arabidopsis thaliana Col-0) promote coordinated response across the different plant organs, termed thermomorphogenesis. However, most transcriptomic studies analyse whole-seedling material, hindering insights into organ-specific responses. Here, we analysed public whole-seedling transcriptomes and produced transcriptomic and proteomic data for root, hypocotyl, and cotyledon in Arabidopsis under warm temperature (28C vs 21C). Although independent whole-seedling datasets showed broad rank-order concordance, standard thresholding for differentially expressed genes (DEGs) yielded limited cross-study overlap. We compared DEGs in whole seedling and dissected organs and observed that 67% of up-regulated and 78% of down-regulated genes in whole seedling are not DEGs in any individual organ, evidencing a need for organ-specific data. We then found that warm temperature mostly suppressed protein accumulation in hypocotyl, likely through translational inhibition. Furthermore, comparison of differentially expressed proteins (DEPs) and DEGs revealed widespread post-transcriptional regulation and transcriptional buffering. We identified several promising genes still uncharacterized for a function in thermomorphogenesis, such as DRG1-3 (up DEG in all organs and seedling), MSRB6 (up DEG in all organs and seedling, but down DEP in root and hypocotyl), AGL20/SOC1 (down DEG in all organs and most seedling datasets), and TPX2/PRXIIC (up DEP and DEG in root and most seedling datasets). Our organ-specific resource presents a detailed view on plant response to warm temperature and open new questions and research avenues in thermomorphogenesis.