Cell fate acquisition is a fundamental developmental process in all multicellular organisms. Yet, much is unknown regarding how a cell traverses the pathway from stem cell to terminal differentiation. Advances in single cell genomics¹ hold promise for unraveling developmental mechanisms^2-3 in tissues⁴, organs^5-6, and organisms^7-8. However, lineage tracing can be challenging for some tissues⁹ and integration of high-quality datasets is often necessary to detect rare cell populations and developmental states^10,11. Here, we harmonized single cell mRNA sequencing data from over 110,000 cells to construct a comprehensive atlas for a stereotypically developing organ with indeterminate growth, the Arabidopsis root. To test the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single cell resolution, shortroot and scarecrow. Although both transcription factors are required for early specification of cell identity¹², our results suggest the existence of an alternative pathway acting in mature cells to specify endodermal identity, for which SHORTROOT is required. Uncovering the architecture of this pathway will provide insight into specification and stabilization of the endodermis, a tissue analogous to the mammalian epithelium. Thus, the atlas is a pivotal advance for unraveling the transcriptional programs that specify and maintain cell identity to regulate organ development in space and time.

中文翻译：

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单细胞拟南芥根图谱揭示了野生型和细胞身份突变体的发育轨迹

在所有多细胞生物中，细胞命运的获取是一个基本的发展过程。然而，关于细胞如何横穿从干细胞到终末分化的途径，还有很多未知数。单细胞基因组学^1的发展有望为组织⁴，器官^5-6和生物体^7-8揭示发展机制^2-3。然而，沿袭追踪对于某些组织⁹可能是具有挑战性的，通常需要集成高质量的数据集以检测稀有细胞群体和发育状态^10,11。在这里，我们协调了来自110,000多个细胞的单细胞mRNA测序数据，以构建具有不确定生长的定型发育器官拟南芥根的综合图集。为了测试图集解释新数据集的效用，我们在单个细胞分辨率（短根和稻草人）上分析了两个关键转录调节因子的突变体。尽管两个转录因子都是早期确定细胞身份的必需条件¹²，但我们的研究结果表明，存在一种在成熟细胞中发挥作用以指定内胚层身份的替代途径，对此SHORTROOT是必须的。揭示该途径的结构将提供对真皮层（与哺乳动物上皮类似的组织）的规格和稳定性的了解。因此，该图集是揭开指定和维持细胞身份以调控时空器官发育的转录程序的关键进展。