Additional file 2: Figure S1. of Methylome evolution in plants

GMLs of different taxa measured by HPLC and WGBS-seq. Figure S2. Correlation between genome size and total number of repeats in the genome. (PDF 1044 kb

Additional file 3: of Methylome evolution in plants

Filtering of the methylomes used for the calculation of the mSFS. (DOCX 17 kb

Additional file 1: of Methylome evolution in plants

Plant species whose methylomes have been analyzed by whole-genome bisulfite sequencing (WGBS-seq) or by high-performance liquid chromatography (HPLC). (PDF 277 kb

Additional file 1 of METHimpute: imputation-guided construction of complete methylomes from WGBS data

Figures S1-S12. (PDF 1832 kb

Typical examples of chromatin profiles.

<p>(A) H3K4me3 peaks are absent in the TSS of MEG Smp_085840 (highlighted in yellow) while surrounding genes show characteristic peaks in all 4 samples. (B) Polycistronic genes Smp_038430, Smp_038420 and Smp_038410 (from right to left, highlighted in yellow) show an H3K4me3 peak only in the first gene. (C) Changes in chromatin structure in cercariae (left) and adults (right). On top predicted genes, below RNA-Seq based exon/intron structure, followed by H3K4Me3 (blue), H3K9Ac (green), H3K27Me3 (yellow) and H3K9Me3 (red), identical scale for cercariae and adults. Positions of TSS that were detected by RNA-Seq are indicated by a dotted line.</p

Comparison of EpiChIP profiles 2 kb upstream and 4 kb downstream of the TSS (average for 12,871 genes located on linkage groups that are assembled on chromosome level) between different histone isoforms in cercariae (left) and adults (right).

<p>TSS and direction of transcription indicated by an arrowhead. (A) methylation of H3K9 upstream of TSS and acetylation downstream, concentrated around TSS in cercariae and spanning the gene body (H3K9ac) and the intergenic region (H3K9me3) in adults, (B) methylation of H3K9 and H3K4 are mutually exclusive in adults but overlap in cercariae.</p

Detection of RNA synthesis by incorporation of EU by fluorescence microscopy.

<p>Top panel (blue) Hoechst 33342 staining of DNA, bottom panel (green) EU incorporation and detection with Alexa Fluor 488. White bar 20 μm.</p

Schematic representation of chromatin structure changes in tandem-repeat regions during metamorphosis of cercariae into adults.

<p>Autosomes 1–7 are labeled with numbers, sex chromosomes with letters. Repeat regions are indicated on each chromosome as inferred by alignment to the reference genome, or previously by FISH on the W-chromosome. Repeat class smr_3427 is presumably on chromosome 2 but the exact position is unknown (unpositioned contig).</p

MOESM4 of Epigenetic origin of adaptive phenotypic variants in the human blood fluke Schistosoma mansoni

Additional file 4. Primers used in this study

MOESM2 of Epigenetic origin of adaptive phenotypic variants in the human blood fluke Schistosoma mansoni

Additional file 2. TSA treatment results. This table contains results of all TSA experiments