Extended Data Fig. 3: Characteristics of eQTL gbM genes.

(a-b) Ancestral methylation states of +eQTL^gbM, -eQTL^gbM, and NA^gbM genes using the Bonferroni (a) or FDR 0.05 (b) classification. Ancestral methylation states were determined by analyzing methylation states of Arabidopsis thaliana orthologs in Arabidopsis lyrata and Capsella rubella and retrieved from⁵¹. P values correspond to chi-squared test. (c-h) Plots show CG dinucleotide frequency (c and f), gene length (d and g), and gene expression (e and h) of Bonferroni (c-e) or FDR 0.05 (f-h) eQTL^gbM genes, NA^gbM (non-associated) genes, and genes with gbM in <10% of accessions. Different letters signify P < 0.001, one-way ANOVA, Dunn’s test. Numbers of genes within each group are indicated. (i-n) Methylation in the CG (i and l), CHG (j and m) and CHH (k and n) contexts within and adjacent to +eQTL^gbM, -eQTL^gbM and NA^gbM genes using the Bonferroni (i-k) or FDR 0.05 (l-n) classifications.