Fig. 3.

Two-species clustering and visualization of scRNA-seq data between P. trichocarpa and E. grandis, T. aralioides, L. chinense, or Arabidopsis thaliana. A–C Two-species clustering of SDX single cells in P. trichocarpa and E. grandis (A), T. aralioides (B), or L. chinense (C). Single-species unsupervised K-means clustering (i–iv). Two-species graph-based cell clustering using orthologous genes (v–vii). In (i), (iii), and (v), black dots are SDX cells from P. trichocarpa and gold dots are cells from E. grandis, T. aralioides, and L. chinense. In (ii) and (iv), the colors of cell clusters for each species are based on their single-species cell clustering results. The cell clusters in two-species clustering (vi). In (vii), the colors of two-species clustering are derived from that of single-species clustering (see “Methods”). D Two-species clustering of SDX cells in P. trichocarpa and leaf cells in A. thaliana. Single-species unsupervised K-means clustering (i–iii). Two-species graph-based cell clustering using orthologous genes (iv–vii). In (i) and (v), black dots are SDX cells from P. trichocarpa. In (iii), (iv), (v), and (vii), gold dots are cells from A. thaliana. In (iv), gray dots represent the SDX cells from P. trichocarpa, and the xylem cells identified in previous Arabidopsis studies are in magenta. In (ii) and (vii), the colors of cell clusters are based on the single-species cell clustering results. The cell clusters in two-species clustering (vi)