Abstract
BackgroundDNA 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.ResultsBy 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.ConclusionsThese 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1059-0) contains supplementary material, which is available to authorized users.
Highlights
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression
Symmetry is a comparison of per-site DNA methylation levels at cytosines on the Watson versus the Crick strand for the symmetrical CG and CHG contexts (Additional file 1: Figures S2 and S3)
As chromomethylase 3 (CMT3) is responsible for maintaining the symmetrical DNA methylation of CHG sites [27], we can use A. thaliana cmt3 mutants to establish thresholds with which to identify sites as symmetrical or asymmetrical and [58] quantify the asymmetry of mCHG sites (Additional file 1: Figure S4)
Summary
DNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Biological diversity is established at multiple levels This has focused on studying the contribution of genetic variation. Epigenetic variations manifested in the form of DNA methylation [1,2,3], histones and histone modifications [4], which together make up the epigenome, might contribute to biological diversity. These components are integral to proper regulation of many aspects of the genome; including chromatin structure, transposon silencing, regulation of gene expression, and recombination [5,6,7,8]. Significant amounts of epigenomic diversity are explained by genetic variation [2, 3, 9,10,11,12,13], a large portion remains unexplained and in some cases these variants arise
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