Extended Data Fig. 8: Identification of TF motifs and TEs associating with epidermal cell divergence.

a, TF motif enrichment tests were performed in species-specific ACRs per species pair using O. sativa as the baseline (See Methods: Binomial test-based motif enrichment analysis). The TF motif with a q value more than 0.05 was indicated by filling them with a white color. b, This panel utilized the same method as panel a to conduct TF motif enrichment tests in syntenic and non-syntenic ACRs in the O. sativa-to-Z. mays species pair (The results from other species pairs were shown in Supplementary Table 24). The ‘-Log10 (q value)’ of each TF family was calculated by averaging ‘-Log10 (q value)’ across all individual TF motifs within this family. TF family names were marked besides each dark dot, while the PLINC, HD-ZIP, SBP, and WRKY family were highlighted using blue color. The x-axis indicates the number of TF motifs detected to be enriched (q value < 0.05) in the relative TF family. c, TF motif enrichment tests were performed in species-specific ACRs neighboring Z. mays ortholog exhibiting higher expression levels in L1 cell based on Binomial test (See Methods: Binomial test-based motif enrichment analysis). Significance testing in violin plot was performed using the one-tailed t-test (alternative = ‘greater’). The center line indicates the median; the box limits indicate the upper and lower quartiles; the whiskers indicate 1.5 times the IQR; the dots represent the outliers. A total of 166 orthologous genes between Z. mays and O. sativa were used for the box plot analysis. d, GO enrichment test was performed in Z. mays orthologous genes. e, Enrichment of TE family on ACRs within non-syntenic regions relative to those in syntenic regions. Significance testing was performed using Fisher’s exact test (alternative = ‘greater’). The TE with a p value more than 0.05 was indicated by filling them with a white color. f, TF motif enrichment tests were performed on the epidermis specific ACRs overlapping with LTR Gypsy TEs based on Binomial test (See Methods: Binomial test-based motif enrichment analysis). The TE with a p value more than 0.05 was indicated by filling them with a white color. g, A screenshot of OsNCED5 accessibility in O. sativa and NCED3 accessibility in Z. mays L1-derived cells which contains four H3K27me3-broad ACRs and two O. sativa epidermal specific and species-specific ACRs with three ZHD1 motif sites.