Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex
Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex
Single cell transcriptomics is revolutionizing our understanding of development and response to environmental cues1–3. Recent advances in single cell RNA sequencing (scRNA-seq) technology have enabled profiling gene expression pattern of heterogenous tissues and organs at single cellular level and have been widely applied in human and animal research4,5. Nevertheless, the existence of cell walls significantly encumbered its application in plant research. Protoplasts have been applied for scRNA-seq analysis, but mostly restricted to tissues amenable for wall digestion, such as root tips6–10. However, many cell types are resistant to protoplasting, and protoplasting may yield ectopic gene expression and bias proportions of cell types. Here we demonstrate a method with minimal artifacts for high-throughput single-nucleus RNA sequencing (snRNA-Seq) that we use to profile tomato shoot apex cells. The obtained high-resolution expression atlas identifies numerous distinct cell types covering major shoot tissues and developmental stages, delineates developmental trajectories of mesophyll cells, vasculature cells, epidermal cells, and trichome cells. In addition, we identify key developmental regulators and reveal their hierarchy. Collectively, this study demonstrates the power of snRNA-seq to plant research and provides an unprecedented spatiotemporal gene expression atlas of heterogeneous shoot cells.
Du Qingwei、Xu Mengxue、Tian Caihuan、Du Fei、Jiao Yuling
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences||University of Chinese Academy of SciencesState Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences||University of Chinese Academy of SciencesState Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of SciencesState Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences||University of Chinese Academy of Sciences
生物科学研究方法、生物科学研究技术植物学细胞生物学
Du Qingwei,Xu Mengxue,Tian Caihuan,Du Fei,Jiao Yuling.Single-nucleus RNA-seq resolves spatiotemporal developmental trajectories in the tomato shoot apex[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2020.09.20.305029.点此复制
评论