Postembryonic organogenesis is critical for plant development. Underground, lateral roots (LRs) form the bulk of mature root systems, yet the ontogeny of the LR primordium (LRP) is not clear. In this study, we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis. Our analysis led to a model in which a single group of precursor cells, with a cell identity different from their pericycle origins, rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate. The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root. We did not detect cells resembling epidermis or root cap, suggesting that outer tissues may form later, preceding LR emergence. At this stage, some remaining initial precursor cells form the primordium flanks, while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged. Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR. Collectively, our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.

胚胎后器官发生对于植物发育至关重要。在地下，侧根 (LR) 形成了成熟根系的大部分，但 LR 原基 (LRP) 的个体发育尚不清楚。在本研究中，我们对拟南芥LR 形成的前四个阶段进行了单细胞 RNA 测序。我们的分析得出了一个模型，在该模型中，具有与其中柱鞘起源不同的细胞身份的单组前体细胞迅速重新编程并分裂成混合的基础组织/干细胞生态位命运和血管前体细胞命运。地面组织和干细胞生态位的命运很快就分开了，一部分更特化的血管细胞形成了蔗糖运输韧皮部细胞，这些细胞似乎与主根相连。我们没有检测到类似表皮或根冠的细胞，这表明外部组织可能在 LR 出现之前较晚形成。在此阶段，一些剩余的初始前体细胞形成原基侧翼，而其余的则形成多能细胞库，如果受损，这些细胞能够替代 LR。中央和外侧 LRP 区域的激光消融表明，剩余的细胞重新启动组织起始序列以形成 LR。总的来说，我们的研究揭示了 LR 形成的本体层次结构，其中主要根组织和干细胞的早期和连续分裂。