Fig. 2

Validation of cluster-specific marker genes and comparison of root cell clusters of rice, Arabidopsis and wheat. a–d Relative expression of defense-related genes between root tips of radicles and root border cells. Means are calculated based on three independent biological replicates. Expression of Actin7 was used as the endogenous control. JAZ10 is the wheat homolog of JASMONATE-ZIM-DOMAIN PROTEIN 10;PDR8 that represents the homologs of PLEIOTROPIC DRUG RESISTANCE 8; PRN2 that represent the homologs of PIRIN2. Asterisks indicate significant difference between the root tips of radicles and root border cells in Student’s t test (** p-value < 0.01). e–h RNA in situ hybridization assays to confirm the expression pattern of marker genes in root tips. DAR2 homologs are the marker genes of companion cell (e); XCP1 homologs are the marker genes of protoxylem (f). WAT1 homologs are the marker genes of provascular cells (cluster 5) (g); G-H2AX homologs are the marker genes of proximal meristem (h). The zones labeled by two dashed white lines are the corresponding regions for provascular cells and proximal meristem, respectively. i Pairwise correlations of Arabidopsis (left) and wheat (top) root cell clusters. Dots indicate statistically significant correlations. j Pairwise correlations of rice (top) and wheat (left) root cell clusters. Dots indicate statistically significant correlations. k Sankey diagram showing that wheat shares a high degree of similarities in epidermal cell (root hair and no root hair), meristem, phloem (phloem, companion cell and sieve element), and xylem with rice and Arabidopsis. The number of overlapped orthologous genes for each cell type is given on the right of each cluster