Fig. 4

Schematic representation of the comparisons performed during the analysis of differential cytosine methylation. Variation in DNA methylation at each individual cytosine was analyzed with a linear model according to a design with a single factor comprising all different experimental groups [14]. Specific groups were then compared with linear contrasts. Percentages of cytosines with significant (FDR < 0.001) differences in DNA methylation are given for each comparison (total number of cytosines tested: 994,696). In addition, there is a histogram with the differences in DNA methylation at the individual DMCs for each comparison (the sizes are not proportional to the number of DMCs found in the comparison). The x-axis of the histogram ranges from – 100% to + 100% and the vertical line is at 0. The orientation of the x-axis is such that a higher density in the left/right side of the histogram corresponds to higher methylation in the group at the left/right side of the arrow depicting the comparison. For example, almost all DMCs identified in the comparison “gametophyte vs sporophyte” have increased methylation levels in the sporophytes compared to the gametophytes. See Additional file: Figure S4 for differences in DNA methylation for each individual sequence and genomic feature context