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. 2018 Apr 9;9:1341. doi: 10.1038/s41467-018-03724-9

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — Independent Dnmt3 acquistion into K. nitens retrotransposons. a Maximum likelihood phylogenetic tree of eukaryotic DNMTs including K. nitens orthologs. b Distribution of DNMT classes in the viridiplantae, in red copy number of Dnmt3 found in K. nitens. c Structure of K. nitens retrotransposons that encode for DNMTs and domain architectures of the ORFs. The structure of repeats is the same as that of a DIRS retrotransposon, but the domain composition is typical of Gypsy retrotransposons. d Percentage of methylated cytosines in distinct sequence contexts in K. nitens MethylC-seq library. e Genome browser display showing the profile of cytosine methylation in CG, CHH and CHG contexts on KnitGypsy-Dnmt3 retrotransposons. rpm reads per million. f Methylation profiles in CG, CHH and CHG contexts on K. nitens genes and transposable elements. Line represents mean and pale shade represents standard error of the mean. TSS transcriptional start site, TES transcriptional end site, TE transposable element