Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [RNA-Seq]

Plants can regenerate entire organs from somatic cells, offering a powerful system to uncover fundamental principles of cellular reprogramming and self-organization. Unlike animals, depending on pre-existing stem cell niches, plants re-establish pluripotency de novo. Although current understanding emphasizes hormonal control and external environmental cues, a unifying framework that explains how millions of cells coordinate fate decisions across space and time remains elusive. Here, we construct a million-cell spatial transcriptomic atlas of plant regeneration, achieving mesoscale resolution observation for all stages of tomato callus development. This atlas reveals a tripartite stem cell niche architecture: an outer signaling layer, intermediate plastic zone, and a quiescent core, features reminiscent of animal regenerative niches. We uncover a fundamental Inducer-Maintainer-Trigger (IMT) triad model, wherein PI-2 (Inducer) establishes a stem cell activating microenvironment, DCL2/22-nt siRNAs (Maintainer) safeguard pluripotency through post-transcriptional regulation, and EPFL8 (Trigger) initiates stem cell niche establishment. This triad model unifies niche signaling, small RNA-mediated plasticity, and metabolic-state-dependent activation, drawing parallels between plant and animal regeneration. Beyond resolving key questions in plant biology, our findings highlight deep evolutionary convergence in regenerative logic across multicellular life, offering new blueprints for engineering regeneration in synthetic biology, crop science, and tissue engineering.