J Integr Plant Biol. ›› 2021, Vol. 63 ›› Issue (11): 1906-1921.DOI: 10.1111/jipb.13159

Special Issue: Biotechnology

• Cell and Developmental Biology • Previous Articles     Next Articles

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

Hui Li1†, Xinren Dai1†, Xiong Huang1,2, Mengxuan Xu1, Qiao Wang1,2, Xiaojing Yan1, Ronald R. Sederoff3 and Quanzi Li1*   

  1. State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
    2 Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
    3 Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA

    These authors contributed equally to this work.
    *Correspondence: Quanzi Li (liqz@caf.ac.cn)
  • Received:2021-05-18 Accepted:2021-08-02 Online:2021-08-04 Published:2021-11-01

Abstract: 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 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.

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