PT  - JOURNAL ARTICLE
AU  - Chad E. Niederhuth
AU  - Adam J. Bewick
AU  - Lexiang Ji
AU  - Magdy S. Alabady
AU  - Kyung Do Kim
AU  - Justin T. Page
AU  - Qing Li
AU  - Nicholas A. Rohr
AU  - Aditi Rambani
AU  - John M. Burke
AU  - Josh A. Udall
AU  - Chiedozie Egesi
AU  - Jeremy Schmutz
AU  - Jane Grimwood
AU  - Scott A. Jackson
AU  - Nathan M. Springer
AU  - Robert J. Schmitz
TI  - Widespread natural variation of DNA methylation within angiosperms
AID  - 10.1101/045880
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 045880
4099  - http://biorxiv.org/content/early/2016/03/27/045880.short
4100  - http://biorxiv.org/content/early/2016/03/27/045880.full
AB  - DNA methylation can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of 34 diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing 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. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species.