Cell-type specific early perception of nine phytohormones revealed by single-nucleus transcriptomics in Arabidopsis

Plant development and stress responses are coordinated through phytohormone-mediated gene networks, yet resolving their spatiotemporal crosstalk remains challenging. Here, we generate a single-nucleus transcriptomic atlas of Arabidopsis seedlings, capturing early (0.5 h, 3 h) responses to 9 hormones across ~500,000 nuclei, including auxin, cytokinin, ABA, gibberellin, strigolactone, brassinosteroid, ethylene, JA, and SA. Within this window, most hormones showed rapid and cell-type-specific responses, whereas JA, SA, ABA showed more sustained and convergent responses by 3 h. Co-directional transcriptomic overlap was strongest at 0.5 h, while the JA-, SA-, and ABA-related responses showed the highest overlap at 3 h. Pathway-level analysis indicated asymmetric relationships among JA, SA, and ABA across biosynthetic and catabolic layers. Spatially, transcriptomic response overlap separated shoots from other tissues, with guard cells as shoot-side outliers showing weak JA–SA–ABA overlap. We further identified an SA-induced guard-cell-specific MYB60-centered module linked to ABA-associated stomatal regulators, suggesting a circuit that may fine-tune stomatal dynamics. Together, this atlas provides a high-resolution view of phytohormone response dynamics and interactions. Here the authors describe cell-type-specific responses of Arabidopsis seedlings to nine phytohormones. They characterize transcriptional crosstalk among them, and identify a guard-cell MYB60 module linked to stomatal regulation.