RT Journal Article
SR Electronic
T1 Widespread natural variation of DNA methylation within angiosperms
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 045880
DO 10.1101/045880
A1 Chad E. Niederhuth
A1 Adam J. Bewick
A1 Lexiang Ji
A1 Magdy S. Alabady
A1 Kyung Do Kim
A1 Justin T. Page
A1 Qing Li
A1 Nicholas A. Rohr
A1 Aditi Rambani
A1 John M. Burke
A1 Josh A. Udall
A1 Chiedozie Egesi
A1 Jeremy Schmutz
A1 Jane Grimwood
A1 Scott A. Jackson
A1 Nathan M. Springer
A1 Robert J. Schmitz
YR 2016
UL http://biorxiv.org/content/early/2016/03/27/045880.abstract
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.