The regulation of stomatal lineage cell development has been extensively investigated. However, a comprehensive characterization of this biological process based on single-cell transcriptome analysis has not yet been reported. In this study, we performed RNA sequencing on 12 844 individual cells from the cotyledons of 5-day-old Arabidopsis seedlings. We identified 11 cell clusters corresponding mostly to cells at specific stomatal developmental stages using a series of marker genes. Comparative analysis of genes with the highest variable expression among these cell clusters revealed transcriptional networks that regulate development from meristemoid mother cells to guard mother cells. Examination of the developmental dynamics of marker genes via pseudo-time analysis revealed potential interactions between these genes. Collectively, our study opens the door for understanding how the identified novel marker genes participate in the regulation of stomatal lineage cell development.

气孔谱系细胞发育的调控已被广泛研究。但是，尚未报道基于单细胞转录组分析的这种生物学过程的全面表征。在这项研究中，我们对5天大拟南芥子叶的12844个单个细胞进行了RNA测序幼苗。我们使用一系列标记基因鉴定了11个细胞簇，这些簇主要对应于特定气孔发育阶段的细胞。在这些细胞簇中具有最高可变表达的基因的比较分析显示，转录网络调节从间胚母细胞到保护母细胞的发育。通过伪时间分析检查标记基因的发育动力学揭示了这些基因之间的潜在相互作用。总体而言，我们的研究为了解已识别的新标记基因如何参与气孔谱系细胞发育的调控打开了大门。