Fig. 6: Genome-wide analysis of H3K9bhb in U. virens-infected (IF) and uninfected (CK) rice spikelets at 1 dpi.

a β-Hydroxybutyrate concentration assay in IF and CK rice spikelets using liquid chromatography-tandem mass spectrometry. Data from three independent experiments are shown as mean ± SD. P-value was calculated by a two-tailed, paired Student t test. b Analysis of H3K9bhb and H3K9ac levels in IF rice spikelets compared with CK rice spikelets by immunoblotting. The histone modification antibodies used in the tests are indicated on the left. The immunoblot signals were quantified using ImageJ. Relative signals (with the CK rep1 signal set at 1.00) are indicated below the bands. Images shown are representative of two independent experiments. c Ridge plots of H3K9bhb levels in CK and IF rice spikelets. d Cumulative density plots of H3K9bhb levels in IF and CK rice spikelets. e Scatter plot of ChIP-seq data showing the differential occupancy of H3K9bhb in IF relative to CK rice spikelets. Peaks with fold changes >1.5 and FDR values <0.05 were considered upregulated or downregulated. f GO enriched pathways of H3K9bhb significantly upregulated genes. g Volcano plots of differential transcript levels in IF relative to CK rice spikelets. h GO pathway analysis of the genes (n = 2135) that were upregulated in IF rice spikelets in comparison to CK. i Correlation analysis of expression changes and H3K9bhb changes in IF versus CK rice spikelets. Person correlation coefficient is shown. P-values were determined by a two-tailed, paired Student’s ttest. j Cumulative density plots of H3K9bhb levels for genes significantly upregulated in (g) in CK and IF rice spikelets. k Venn diagrams showing the overlap between hyper-H3K9bhb genes and transcriptionally upregulated genes in IF versus CK rice spikelets. P-value was calculated by Fisher’s exact test. l GO-enriched pathways of genes (n = 238) that are both H3K9bhb and transcriptionally upregulated in IF versus CK rice spikelets. The P-value in (d, j) were calculated using a two-sample Kolmogorov–Smirnov test. The read counts in (c, d, and j) were normalized using the DESeq2 size factor normalization method. Source data are provided as a Source Data file.