Single-cell transcriptome sequencing reveals lineage trajectories of Arabidopsis stoma and leaves

Single-cell sequencing (single-cell sequencing) has now become one of the hottest technologies. Single-cell RNA sequencing (scRNA-Seq) is of great significance in observing single cells in multiple dimensions, revealing cellular heterogeneity and function, and studying the evolutionary paths of cell lineages during development.

In recent years, in the field of plant science, Chinese scientists have made important progress in scRNA-Seq, such as Wang Jiawei of the Center of Excellence for Molecular Plants of the Chinese Academy of Sciences [1,2], Sun Mengxiang of Wuhan University [3], and Sun Xuwu of Henan University [4] and other research groups All have published high-level articles related to scRNA-Seq, which shows the great potential of this emerging technology in plant research.

Stomata are tiny pores produced by plant leaf epidermal cells through asymmetric division. During this process, two cell types, pavement cells and guard cells, are created [5]. Guard cells are involved in regulating plant transpiration. and gas exchange with the environment [6]. However, the molecular mechanisms underlying cellular functional flexibility during stomatal lineage development and how cell fates in leaves are determined are currently unknown.

Recently, the research group of Professor Dominique C. Bergmann of Stanford University published a research paper entitled Single-cell resolution of lineage trajectories in the Arabidopsis stomatal lineage and developing leaf in Developmental Cell, using scRNA-Seq technology combined with molecular genetics and other methods A dynamic model of the differentiation of different types of cells in Arabidopsis leaf tissue was resolved.

Single-cell transcriptome sequencing reveals lineage trajectories in Arabidopsis stomata and leaves
Given that the previously published leaf scRNA-seq data are mainly mesophyll cells, the researchers used the Arabidopsis meristem layer ATML1 (MERISTEM LAYER 1) promoter to drive the reporter gene, combined with fluorescence-activated cell sorting (FACS) ) and the microfluidics of the 10X Genomics platform to obtain a more comprehensive and balanced cell type in leaves for subsequent analysis.

Further, using genes specifically expressed in different cell types, we defined clusters of vascular, mesophyll, and epidermal cells, and through comparative analysis of cell identities and trajectories, revealed the specific genetic programs of these cell types and leaf distance/proximity. Polar characteristics of the axial plane. To further explore the differentiation patterns of stomatal cell lineages, the researchers used the stomatal development gene TMM (TOO MANY MOUTHS) promoter to drive a reporter gene and obtained a stomatal lineage-specific scRNA-seq dataset in epidermal cells.

By analyzing 13,000 cells of stomatal lineage, the researchers identified differentiation trajectories that tended to either stomatal fates or fates previously characterized only by cell morphology. Pseudotime trajectories show that stomatal differentiation is achieved not by a single pathway but by multiple pathways.

The authors speculate that the choice of specific cell fates may be caused by rapid, local or even random events, rather than a quantitative to qualitative process. In addition, the study also found that the transcription factor SPEECHLESS (SPCH), which regulates cell development in the early stage, also plays a role in the late stage, and it cooperates with other transcription factors such as MUTE and FAMA to drive cell fate and promote the differentiation of guard cells.

Professor Bergmann received his Ph.D. in Molecular Biology from the University of Colorado in 2000, and then entered the Carnegie Institution for Science in the United States for postdoctoral research.

Currently, Professor Bergmann is working in the School of Biology, Stanford University, USA, and is mainly engaged in the work related to asymmetric cell division in stomatal development of Arabidopsis thaliana.


references: 1. Zhang T Q, Xu Z G, Shang G D, et al. A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root[J]. Molecular Plant, 2019, 12(5).2. Zhang T Q, Chen Y, Wang J W. A single-cell analysis of the Arabidopsis vegetative shoot apex[J]. Developmental Cell, 2021.3. Zhou X, Liu Z, Shen K, et al. Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos[J]. Nature Communications, 2020, 11(1):1366.4. Liu Z, Zhou Y, Guo J, et al. Global Dynamic Molecular Profiles of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing[J]. Molecular Plant, 2020.5. Lee L R, Wengier D L, Bergmann D C. Cell-type-specific transcriptome and histone modification dynamics during cellular reprogramming in the Arabidopsis stomatal lineage[J]. Proceedings of the National Academy of Sciences, 2019, 116(43):201911400.6. Am. H, Fi. W. The role of stomata in sensing and driving environmental change[J]. Nature, 2003, 424(6951):901-908.