We performed single-nuclei RNA sequencing to profile transcriptomes of Arabidopsis leaves and seedlings at various developmental stages and under varying drought intensities. We built an atlas of 264,183 nuclei across 647 leaves, identifying transcriptional changes linked to leaf maturation across 15 stages. Nine distinct cell types were annotated using cell identity markers.

To examine the effect of drought stress, we withheld water from Arabidopsis rosettes for 9 days, reducing water content from 100% to 21%. This treatment decreased leaf size and biomass. By sequencing an additional 173,731 nuclei, we captured how drought altered cell-type specific transcriptional dynamics. Additionally, we treated rosette leaves with 8 different phytohormones and identified hundreds of hormone-responsive genes across mesophyll, epidermal, and vascular cell classes.

We further explored Arabidopsis cell-type transcriptional responses to stress by growing seedlings under increasing doses of hard agar (HA). We sequenced 595 shoots across 88 treatment conditions, totaling 456,008 nuclei. Our findings revealed dose-dependent gene expression changes during leaf maturation and drought adaptation, providing insight into how Arabidopsis modulates transcriptional responses under stress to regulate growth plasticity. 

https://www.biorxiv.org/content/10.1101/2025.02.24.639183v1

doi: https://doi.org/10.1101/2025.02.24.63918