Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus

• 作 者: Hui Li Xinren Dai Xiong Huang Mengxuan Xu Qiao Wang Xiaojing Yan Ronald R.Sederoff Quanzi Li
• 机 构: State Key Laboratory of Tree Genetics and Breeding,Chinese Academy of Forestry,Beijing 100091,China
• 出 处: 植物学报（英文版）
• 发表日期: 2021年11期
• 关键词: differentiating trajectory differentiating xylem marker genes Populus alba × Pop

High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudo-time analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during devel-opmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.