Understanding the complex functions of plant leaves requires a thorough characterization of discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing cell subtypes has not been achieved yet. Here, we present scStereo-seq (single-cell spatial enhanced resolution omics sequencing) that enabled us to show the bona fide single-cell spatial transcriptome profiles of Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells have been successfully distinguished. Furthermore, we discovered cell-type-specific gene expression gradients from the main vein to the leaf edge, which led to the finding of distinct spatial developmental trajectories of vascular cells and guard cells. Our study showcases the importance of physical locations of individual cells for exerting complex biological functions in plants and demonstrates that scStereo-seq is a powerful tool to integrate single-cell location and transcriptome information for plant biology study.

了解植物叶子的复杂功能需要对离散细胞特征进行彻底的表征。尽管已经开发出单细胞基因表达谱技术，但它们在表征细胞亚型方面的应用尚未实现。在这里，我们展示了 scStereo-seq（单细胞空间增强分辨率组学测序），它使我们能够展示拟南芥的真实单细胞空间转录组谱树叶。已成功区分上表皮细胞和下表皮细胞之间微妙但显着的转录组差异。此外，我们发现了从主脉到叶缘的细胞类型特异性基因表达梯度，从而发现了维管细胞和保卫细胞的不同空间发育轨迹。我们的研究展示了单个细胞的物理位置对于在植物中发挥复杂生物学功能的重要性，并证明 scStereo-seq 是整合单细胞位置和转录组信息用于植物生物学研究的强大工具。