Gene expression with respect to DMRs and their direction.

<p>A) A graph of the distribution of gene expression when a DMR is located within a gene and hypermethylated in the Leaf or Floral Bud, or when there is no DMR in the gene (None). For the 25 genes hypermethylated in leaf, we predicted positive values on the <i>y</i>-axis, signaling higher expression in floral bud, but no bias was detected. For the 19 genes hypermethylated in floral bud, we predicted negative values on the <i>y</i>-axis, signaling higher expression in leaf, but again no bias was detected. B) The same graph of differential expression when the gene contains a DMR in its a promoter region. Again, there are no detectable biases in the direction of gene expression relative to genes that do not contain a DMR in their promoter region. C) A graph of differential gene expression when the TE nearest to a gene has a DMR that is hypermethylated in leaf, flower or no (None) DMR. For all graphs, the box plots represent the median, first, and third quartile. The whiskers represent the minimum and maximum, The numbers above the graph refer to sample size in each category.</p

Methylation patterns within promoters and its relationship to gene expression.

<p>Graphs A,B and C present the level of CG, CHG and CHH methylation, respectively, in terms of distance from the Transcription Start Site. Graphs D, E and F compare methylation contexts, as measured by <i>prop</i> statistics in a log scale, within leaf tissue. Floral bud comparisons are not shown but are visually identical. Panels G, H and I compare differential gene expression [log2fold (FKPM_Flower/FKPM_Leaf)] vs. the difference in <i>prop</i> between floral bud and leaf tissue. The correlation values for G and H are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150002#pone.0150002.t003" target="_blank">Table 3</a>.</p

The number of potential methylation sites, DMSs and CMSs in each of three sequence contexts (CG, CHG and CHH) throughout the entire <i>brachypodium</i> genome and also for three features separately (Genes, Promoters and TEs).

<p>The number of potential methylation sites, DMSs and CMSs in each of three sequence contexts (CG, CHG and CHH) throughout the entire <i>brachypodium</i> genome and also for three features separately (Genes, Promoters and TEs).</p

Methylation patterns within genes.

<p>A) The correlation between <i>prop</i>_CG and <i>prop</i>_CHG between genes for leaf tissue (<i>r</i> = 0.5977; <i>p</i> < 2.2e-16); floral bud tissue is not shown but the relationship is essentially identical. Methylation is plotted on a log scale. B) A comparison of propCG, on a log scale, and gene expression (FPKM) on a log2 scale within leaf (<i>r</i> = 0.2867; <i>p</i> <2.2e-16); again, floral bud tissue is not shown but essentially identical. C) A comparison of differential gene expression [log2fold (flower/leaf)] vs. the difference in <i>prop</i>_CG between leaf and floral bud tissue.</p

Spearman correlation coefficients between <i>prop</i> values within a tissue.

<p>Spearman correlation coefficients between <i>prop</i> values within a tissue.</p

Spearman correlations between the difference in <i>prop</i> values between tissues and the log2 fold change in gene expression.

<p>Spearman correlations between the difference in <i>prop</i> values between tissues and the log2 fold change in gene expression.</p

The inferred number of DMSs and DMRs between replicates.

<p>A) The upper matrix reports the number of DMSs between two BSseq replicates. The lower matrix reports the percentage of DMSs that map to the same location as the 500,245 DMSs inferred from the combined data sets. B) A neighbor-joining phylogeny representing the relationship among the six BSseq samples, based on distances defined by the lower matrix in A. C) The upper matrix reports the number of DMRs between two BSseq replicates. The lower matrix provides the percentage of DMRs that overlap with the 448 DMRs inferred from the combined data set. D) A neighbor-joining phylogeny representing the relationship among the six BSseq samples, based on distances defined by the lower matrix in C.</p

Context, direction, and regions of CMSs and DMSs.

<p>A) The number of sites in the correct context for methylation throughout the genome (Total Cs), along with the number of CMSs and DMSs in context. B) The proportion of CMSs relative to cytosines in the correct context for Genes, Promoters, TEs and the Whole Genome. C) The proportion of DMSs relative to cytosines in the correct context for Genes, Promoters, TEs and the Whole Genome. Note the difference in the scale of the <i>y</i>-axis between panels B and C. D to F) The graphs show the CMS, DMS, gene and TE density along chromosome 1. Density was measured within a 50kb sliding window for smoothing. H) Differential gene expression plotted along the physical length of chromosome 1. The other chromosomes are represented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150002#pone.0150002.s002" target="_blank">S2 Fig</a>.</p

Pairwise comparisons between accessions for: a) TE hits; b) 22 nt siRNA hits per RPKM_TE and c) 24 nt siRNA hits per RPKM_TE.

<p>For all the cases the <i>x</i>- and <i>y</i>-axis indicate accessions under comparison (B73, PT or OAXA). Each dot represents a TE subfamily, with the regression (<i>y</i>) and correlations (<i>r²</i>) between accessions indicated. The solid line represents the regression fit, while the dashed line represents the null hypothesis. The color of the dots represents significance: red dots are significant differences between accessions at a FDR of <i>q</i><0.001, based on the χ²_Corr in panel a and the χ²_Prop for panels b and c. Blue dots are not significant.</p

The number of significantly differences in pairwise comparisons between genotypes for TE, 22

a<p>The standard χ² test based on a 2×2 table of the relative proportions of hits.</p>b<p>The χ² corrected by the coverage to the FGS.</p>c<p>The χ² test of proportionality; see text and Supplement <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004298#pgen.1004298.s007" target="_blank">Text S1</a>.</p