Distribution of siRNA and DNA methylation frequencies across chromosomes and features of the genome. (A) Depicted here is chromosome 1 from C24 showing a representative pattern consistent across all chromosomes in both parents and hybrids (refer to Fig. S2). Cytosine DNA methylation and 24-nt siRNA densities were plotted by using a 50-kb window stepped in 25-kb increments. The heat maps show gene, TE, and repeat densities across the chromosome. Densely methylated regions correlate with higher levels of siRNAs, mainly around the pericentric region and associated with high TE densities. (B) A comparison of the C24-identified ^mC clusters between C24 and Ler parents. For Ler-identified clusters, refer to Fig. S3. (C) Additively and nonadditively methylated C24-identified ^mC clusters in the C24 x Ler hybrid. Arrows indicate statistical enrichment (red) or underrepresentation (blue) by using the Fisher exact test (P < 0.05). For Ler-identified cluster and Ler x C24 hybrid data refer to Fig. S3.

The frequency of additive and nonadditive ^mC levels in hybrids. Nonadditive methylation in the hybrids occurs more frequently when parental methylation levels are different. Represented here are the C24-identified clusters in the C24 x Ler hybrid. The C24 x Ler hybrid clusters were divided into 10 groups based on the similarity of methylation levels between parents (H, highly methylated; L/U, low or unmethylated; SH, semi-high; SL, semi-low—refer to Dataset S1, Table S5 for respective index scores). The methylation category of each parent (C24 v. Ler) and the number of clusters in each group are shown below each pie chart. The y axis separates groups on the overall parental methylation levels. The x axis separates groups based on the degree of difference in methylation levels between the parents. The Ler x C24 hybrid and Ler-identified clusters produced similar patterns (Dataset S2).

Changes to parental allelic methylation levels in the C24 x Ler hybrid. Permutation tables of all possible changes to parental allelic methylation levels in the hybrid. The majority of allelic methylation is stably inherited (gray), whereas the majority of nonadditive methylation occurs through TCM (red) and TCdM (blue). In the “parents similar” table, the parents were separated into high parent and low parent based on the minor differences of methylation levels.

Examples of altered allelic methylation in the hybrids through TCM or TCdM. Each locus has two parental graphs (C24 and Ler) and two hybrid graphs (C24 allele and Ler allele of the C24 x Ler hybrid). ^mCG (blue), ^mCHG (red) and ^mCHH (green) methylated residues are plotted along the x axis (each tick-mark equalling 100 nt) with the y axis representing the methylation level. The distribution and abundance of siRNA reads are plotted in red above each graph and are duplicated between the two alleles of the hybrids. Regions undergoing TCM and TCdM events are underlined in red and blue, respectively. For Ler x C24 hybrids, see Fig. S5.

Altered methylation levels in the hybrids associated with changes in gene expression. ^mC clusters located in or within ±1 kb of the listed genes. Gray histograms show average methylation level of the ^mC cluster (highlighted in yellow) and levels of gene expression obtained from a mRNA-seq dataset. The next set of graphs depict the distribution and abundance of siRNAs (red) and ^mC (blue) in both parents and each reciprocal hybrid. The six examples are of inverse correlations between ^mC and gene expression. Gene annotations are located at the bottom of each image with the arrows indicating orientation. Numbers at each extreme of the regions show genomic position. IC, insufficient coverage.