Self-organization of vascular strands drives their patterning in the Arabidopsis shoot apex

In plants, the development of the shoot vascular system is closely coordinated with lateral organ formation at the shoot apical meristem. Despite extensive studies on leaf initiation and vascular patterning, it remains unclear how vascular development relates to organogenesis. Current hypotheses emphasize PIN1-mediated polar auxin transport from the meristem surface in initiating and integrating new vascular strands into the existing vasculature. Using high-resolution 3D imaging of auxin reporters and genetic analysis, we show that vascular strands form within the vascular cylinder independently of surface-derived auxin, yet their organization reflects the phyllotactic pattern of leaf primordia. To resolve this paradox, we developed a computational model based on repulsive interactions between strands, which reproduces the dynamic spatial arrangement of strands observed in planta. Our findings reveal a biphasic development of the shoot vascular system, governed by self-organizing principles that determine its patterning.