Extended Data Fig. 9: Gene ontology (GO) enrichment terms for hypo-DMR-associated genes and association of CG methylation with non-additive gene expression in allotetraploids.
From: Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids
a, The first two columns show CG DMR (A-T) levels (difference threshold > 0.5) of homologous genes in A. thaliana (Ler4, T) and A. arenosa (Aar/Ath) and in A. suecica (Asu). The remaining four columns indicate expression levels (TPM) of these genes in Aar/Ath (Ler4 and Aar) and Asu, respectively. b, Correlation between expression fold changes of shared differentially expressed genes (DEGs) between Aar and Ath (Wang et al., 2016) (y axis) and methylation differences (x axis). c, Correlation between expression fold changes of shared DEGs between Allo738 and MPV (Wang et al., 2016) (y axis) and methylation differences between A (red) and T (blue) subgenomes in Allo738 against Aar/Ath (x axis). The red dashed line indicates 0.2 value of methylation difference; the percentage statistics indicates the fraction of genes with more than 0.2 methylation differences in each quadrant. The genes used in (b) and (c) were the shared DEGs of Aar vs. Ler4 and Allo738 vs. MPV. d, GO term overrepresentation for the genes showing conserved (red), convergent (blue), and other (grey) CG hypo-DMRs between sA of A. suecica and A. arenosa (Aar, A). Dashed line indicates onefold enrichment.
