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Genome Biol. 2016 Sep 27;17(1):194.

Widespread natural variation of DNA methylation within angiosperms.

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Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA.
Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA.
National Root Crops Research Institute (NRCRI), Umudike, Km 8 Ikot Ekpene Road, PMB 7006, Umuahia, 440001, Nigeria.
HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
Department of Genetics, University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.



DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angiosperm species.


By analyzing whole-genome bisulfite sequencing data in a phylogenetic context, it becomes clear that there is extensive variation throughout angiosperms in gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. The Brassicaceae have reduced CHG methylation levels and also reduced or loss of CG gene body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Furthermore, low levels of CHH methylation are observed in a number of species, especially in clonally propagated species.


These results reveal the extent of variation in DNA methylation in angiosperms and show that DNA methylation patterns are broadly a reflection of the evolutionary and life histories of plant species.

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