A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

Travis A. Lee, Tatsuya Nobori, Natanella Illouz-Eliaz, Jiaying Xu, Bruce Jow, Joseph R. Nery, Joseph R. Ecker
bioRxiv (2023)


Extensive studies of the reference plant Arabidopsis have enabled deep understandings of tissues throughout development, yet a census of cell types and states throughout development are lacking. Here, we present a single-nucleus transcriptome atlas of seed-to-seed development employing over 800,000 nuclei, encompassing a diverse set of tissues across ten developmental stages, with spatial transcriptomic validation of the dynamic seed and silique. Cross-organ analyses revealed transcriptional conservation of cell types throughout development but also heterogeneity within individual cell types influenced by organ-of-origin and developmental timing, including groups of transcription factors, suggesting gatekeeping by transcription factor activation. This atlas provides a resource for the study of cell type specification throughout the continuum of development, and a reference for stimulus-response and genetic perturbations at the single-cell resolution.