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

Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ. Overall design: Using a standardized nucleus extraction method, single-nucleus RNA seq was performed on whole Arabidopsis organs and tissues, including seeds, seedlings, rosettes, stems, flowers, and siliques, at ten developmental timepoints throughout the entire lifecycle of the plant. A minimum of four single-nucleus RNA-seq runs were performed per tissue and timepoint.