Fig. 3: Transcriptome dynamics at the transition stage during endosperm differentiation.

a Visualization of five endosperm cell types by UMAP plots at each time point, colored according to cell clusters. b Bar charts showing the ratio of cell number of different cell clusters at 6 and 7 DAP, colored as in (a). c Differential gene-expression analysis showing 6 DAP and 7 DAP marker genes across all 12 clusters. 6 DAP marker genes are indicated in milky white, while 7 DAP marker genes are indicated in blue. d Expression levels of selected marker genes at 6 and 7 DAP from bulk RNA-seq. milky white and blue represent genes with the highest expression at 6 DAP and 7 DAP, respectively. e Trajectories of the developmental “pseudotime” in each cell cluster mapped onto the same UMAP plot depicted in (a); the differentiation score is calculated based on the stage-specific genes identified from bulk RNA-seq. f Raincloud plot showing the cell differentiation score of 6 and 7 DAP. n = 2898 cells in 6 DAP, n = 12,698 in 7 DAP. ****, P < 0.0001. Two-tailed student’s t-test. No adjustments were made for multiple comparisons test. Box plots indicating median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers) as well as all data (single points). g tSNE plots of the SE and AL developmental trajectory depicting cell types (right) and pseudotime (left) using CytoTRACE. h Box plots showing CytoTRACE values for clusters 0, 1, 3, 4, 5, 6, 7 and 8. n = 2043 cells in cluster 0, n = 1644 cells in cluster 1, n = 1358 cells in cluster 3, n = 1216 cells in cluster 4, n = 732 cells in cluster 5, n = 1,161 cells in cluster 6, n = 968 cells in cluster 7. Box plots indicate median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers) as well as all data (single points). i–k Expression of selected genes in the pseudotime trajectory using CytoTRACE. i FL3; j AL9; k 1d038865. Gradient from blue to red represents low to high expression levels.