The Arabidopsis Shoot Apex Cell Atlas

Abstract

Plant stem cell niches are embedded within an organized group of dividing cells known as the meristem. The shoot apical meristem allows for reiterative development and the formation of new aerial structures throughout the life cycle of a plant. As in animals, plant stem cells possess the capacity to self-renew and at the same time to differentiate into lateral organs through transit-amplifying cells. Here, we use single-cell RNA sequencing to define the cellular taxonomy of the Arabidopsis vegetative shoot apex at the transcriptome level. We find that the shoot apex is composed of highly heterogeneous cells, which can be partitioned into 7 broad populations with 23 transcriptionally distinct cell clusters. We delineate cell cycle continuums and developmental trajectories of epidermal cells, vascular tissue and leaf mesophyll cells, and infer transcription factors and gene expression signatures associated with cell fate decisions. Moreover, panoramic integration analysis of shoot and root apical meristem cell populations reveals common vascular cell types and uncovers shoot-specific parenchymatous bundle sheath cell cluster. Our results thus provide a molecular definition of the cell populations making up the shoot apex, and offer an unprecedented opportunity to investigate conserved principles underlying cell division and differentiation in multicellular organisms at single-cell resolution.