Fig. 3: h3.3ko;HTR5 K4A shares transcriptional similarity with sdg2.

a PCA plot of Col, h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2 showing transcriptome differences determined by RNA-seq. PC1 covers the highest amount of variance between samples, PC2 covers most of the remaining variance. Three biological replicates were performed for each line. b Volcano plots of differentially expressed genes (DEGs). The y-axis values correspond to -log₁₀ (P-adjust: a false discovery rate adjusted P value), and the x-axis values correspond to log₂ (fold change). Genes with at least two-fold expression changes and P-adjust less than 0.05 are considered misexpressed. The numbers of transcript level increased and decreased genes were indicated at the top right and left corners, respectively. c Correlation of changes in transcript levels of significantly misexpressed genes in h3.3ko;HTR5 K4A and sdg2 compared to Col. The R value represents the Pearson correlation coefficient, and the P value was derived from the t-distribution to assess the significance of the correlation. d Venn diagrams of transcript level significantly increased and decreased genes in h3.3ko;HTR5 K4A and sdg2 compared to Col. P values were calculated with hypergeometric test. e Heatmap showing transcript levels of GA biosynthetic genes determined by RNA‐seq. f Genome browser view of H3K4me3 accumulation levels at AtKAO2, GA20ox1, GA20ox2 and GA3ox1 in Col, h3.3ko;HTR5, h3.3ko;HTR5 K4A and sdg2.