Figure S1. RACE mapped transcription starts and polyA signals of Ogre CL5 and Ogre CL5del and putative splice site of Ogre CL5 and Ogre CL5del in Silene latifolia genome. (a) Multiple sequence alignment of Ogre CL5 5‘ LTR and 5‘ RACE clones. First dinucleotide of LTR (TG), putative GC box, TATA box and transcription start site are indicated. (b) Multiple sequence alignment of Ogre CL5 3‘ LTR and 3‘ RACE clones. Putative poly A signal CATAAA is indicated. (c) Gel electrophoresis of PCR and RT-PCR products of primers Ogre-F1 and Ogre-R1 (Table S1b). Full-length 2227 bp long product is present in both cDNA (RT) and genomic DNA (G) as well as 627 bp long product of Ogre CL5 splicing or Ogre CL5del transcription. RT- indicates negative control without reverse transcription step. (d) Schematic representation of pairwise similarities of Ogre CL5 and Ogre CL5del. Red arrows indicate positions of primers Ogre-F1 and Ogre-R1 used for amplification of the splice site. (e) Multiple sequence alignment of Ogre CL5 genomic copies (within BAC clones 77L4, 277C14 and 78D8) and PCR products on genomic DNA and cDNA. Putative splice site is indicated by black arrows. Numbers indicate the first and the last nucleotide of intron aligned onto full-length Ogre element copy within BAC clone 277C14. Fig. S1

Figure S2. Chronogram showing divergence times estimated in BEAST based on sequences of four genes in species of genus Silene. Time scale is in millions of years. Error bars at each node show 95% high probability densities for node age. Values above each branch show Bayesian posterior probability for the corresponding clade, values above 0.9 are shown. The arrows point to the nodes used in the ancestral state reconstruction. Fig. S2

Figure S3. Chronograms showing divergence times estimated in BEAST – species of genus Silene. Time scale is in millions of years. Values on the right of branches show divergence times for the corresponding clade. (a) Chronogram based on Cyp sequences. (b) Chronogram based on DD44 sequences. (c) Chronogram based on XY4 sequences. Fig. S3

Figure S4. Linear regression of X-Y split time in millions of years and percentage of synonymous substitutions in Silene latifolia. Fig. S4

Fig. S5 Figure S5. The spatial distribution and abundance of 24-nucleotide (24-nt) small RNAs (smRNAs) along four genomic copies of Ogre elements in Silene latifolia. The distribution of 24-nt sRNAs along four TE families in leaves (first row), pistils (second row) and pollen (third row). Blue and red dots represent reads in male and female leaves libraries respectively. Violet and green dots represent reads in unfertilized and fertilized pistils respectively. Sense and antisense reads matching TEs are marked by coloured dots above or below the x-axis respectively. Position of dots along Y-axis reflects number of sRNA reads in respective libraries after normalization to the size of respective library and TE copy number. TEs are schematically represented below graphs. Blue boxes represent long terminal repeats (LTRs) and yellow boxes represent protein-coding sequences or central domains of retrotransposon genes gag, protease, reverse transcriptase, RNaseH and integrase.

Fig. S6 Figure S6. Microview of CHH methylation of the right LTR in TE Ogre CL5 in Silene latifolia. Vertical bar plots show the level of cytosine methylation in CHH context in three different tissues. (a) leaves, (b) sperm cells, (c) vegetative cells. Y-axis represents the percentage of CHH along three parts of Ogre CL5 LTR. (d) Distribution of 24-nucleotide (24-nt) RNAs alongside the tested parts of the right LTR in pollen. Y-axe represents normalized count of small RNAs (sRNAs). Dot plot represents a detected transcription start. (e) Difference in CHH methylation level between sperm and vegetative cells.

Fig. S7 Figure S7. The detailed view of the spatial distribution of 24-nucleotide (24-nt) small RNAs (sRNAs) along LTRs of Retand and Ogres (first three rows) in Silene latifolia. The bottom row shows the transcript level along LTRs. The peaks of sRNAs production colocalize with the peaks of transcript level. Interestingly, Ogre CL5 shows the highest transcript level at the beginning of the LTR in pollen.