Extended Data Fig. 8: Single-cell multiomics analysis of panicles at different developmental stages.

a, Schematic representation of panicles used in the study, highlighting their developmental stages and cell types. b, UMI counts for single cells across developmental stages of panicles. c, Proportion of each cell type across replicates for different stages. d, Scatter plots showing correlations between RNA and ATAC replicates across stages. e, Violin plots depicting Unique Molecular Identifier (UMI) counts for RNA and ATAC, along with TSS enrichment and nucleosome signal across replicates for each stage. f, Knee plots illustrating the distribution of cell counts across UMI thresholds, with dashed lines indicating the UMI cutoff. g, Examples of cell type marker genes validated using RNA in situ hybridization. Scale bar, 50 µm. Results were consistent across three independent biological replicates. h, Negative control for in situ hybridization validation of cell type marker genes using sense probes. Scale bar, 50 µm. i, Heatmaps showing gene expression (scRNA-seq) and chromatin accessibility (scATAC-seq) dynamics along pseudotime, transitioning from fm to ow (left), sta (middle), and fi (right). Each row represents a gene, with scRNA-seq data on the left and scATAC-seq data on the right. Only genes with chromatin accessibility preceding RNA expression are displayed. Motifs of the top three significant TFs are highlighted (upper right), along with GO enrichment analysis (bottom right) of genes in the heatmaps.