Extended Data Fig. 10: Genome-wide analysis of chromatin accessibility features in leaves of plantlet and non-plantlet plants.

a, K-means clustering analysis and heatmap showing differentially accessible chromatin regions during plantlet formation. Representative genes within each peak cluster are highlighted. b, GO enrichment analysis of biological processes associated with genes corresponding to K3-K8 peak clusters. K5 and K6 are significantly enriched for biological pathways related to embryonic development and meristematic activity regulation. Adjusted P values resulting from a one-sided hypergeometric test with subsequent Benjamini-Hochberg correction are shown. c, Volcano plot showing differential peaks between immature embryos and differentiated leaves (1st leaf) in A. thaliana. Peaks upregulated ≥ 2-fold, corresponding to 3,538 genes, were defined as highly accessible genes of embryogenesis (HAG-embryogenesis). d, GO enrichment analysis of biological pathways for the 3,538 HAG-embryogenesis genes. Adjusted P values resulting from a one-sided hypergeometric test with subsequent Benjamini-Hochberg correction are shown. e, Comparative analysis of chromatin openness intensity for HAG-embryogenesis genes versus background genes in immature embryo and shoot apex tissues in A. thaliana. f, Volcano plot showing differential peaks between shoot apices and differentiated leaves (1st leaf) in A. thaliana. Peaks upregulated ≥ 2-fold, corresponding to 1,421 genes, were defined as highly accessible genes of organogenesis (HAG-organogenesis). g, GO enrichment analysis of biological pathways for the 1,421 HAG-organogenesis genes. Adjusted P values resulting from a one-sided hypergeometric test with subsequent Benjamini-Hochberg correction are shown. h, Comparative analysis of chromatin openness intensity for HAG-organogenesis genes versus background genes in immature embryo and shoot apex tissues in A. thaliana. Regions encompassing the coding sequence, upstream -3.0 Kb, and downstream 3.0 Kb of each gene were calculated. TSS: Transcription Start Site, TES: Transcription End Site. The coding region is shaded yellow.