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 Hui Li;Xinren Dai;Xiong Huang;Mengxuan Xu;Qiao Wang;Xiaojing Yan;Ronald R.Sederoff;Quanzi Li

作者机构：State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijing 100091China Research Institute of ForestryChinese Academy of ForestryBeijing 100091China Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNC 27695USA 

出 版 物：《Journal of Integrative Plant Biology》 (植物学报（英文版）)

年 卷 期：2021年第63卷第11期

页      面：1906-1921页

核心收录：

学科分类：0907[农学-林学] 08[工学] 0829[工学-林业工程] 09[农学] 

基　　金：This work was supported by grants from Fundamental Research Funds of Chinese Academy of Forestry(CAFYBB2018ZY001-5 and CAFYBB2017ZY001) the National Natural Science Foundation of China(31670667) 

主　　题：differentiating trajectory differentiating xylem marker genes Populus alba×Populus glandulosa single-cell RNA-seq wood formation 

摘      要：High-throughputsingle-cellRNAsequencing(sc RNA-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 sc RNA-seq profiled9,798 cells, which were grouped into 12 *** 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 pseudotime 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 developmental 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.