Fig. 1

Xylem anatomy and cell type annotation. A–C Schematics of a woody plant (A), the cambium (fusiform and ray initials) on the transverse section (B), and the tangential section (C) of the stem. D Xylem cell morphologies via axial and radial systems. Vessel elements (labeled as vessel) and libriform fibers (labeled as fiber) both derived from fusiform initials. Ray parenchyma cells derived from ray initials. E Debarking and differentiating xylem protoplast isolation. F Anatomical analyses during stem debarking of four previous studies (shown as Tung et al. 2023 [6], Chen et al. 2021 [10], Li et al. 2021 [9], and Xie et al. 2022 [8]). The anatomical data is not available in Xie et al. G Annotated cell types on stem after debarking of four previous studies. H Schematics of laser capture microdissection (LCM) procedure to harvest three cell types for in situ cell transcriptomes, including libriform fiber (red area), vessel element (blue area), and ray parenchyma cell (pink area). I The correlation was obtained by the following two steps: (i) first round correlation analyses between the in situ cell transcriptomes and scRNA-seq transcriptomes. For each cell in scRNA-seq, a correlation coefficient was obtained. (ii) Second round correlation analyses between the results from (i) and the transcript abundance of each marker gene in each cell. The correlation (shown as LCM vs marker genes) were illustrated as the results from second round correlation analyses. F, libriform fibers. V, vessel elements. R, ray parenchyma cells. One, two, and three asterisks represent Student’s t-test p < 0.05, 0.01, and 0.001, respectively. ns, no significant difference. J Inconsistent xylem cell type annotations (shown as black area) (Chen et al. for vessel elements; Li et al. for vessel elements; Xie et al. for libriform fibers, vessel elements, and ray parenchyma cells)