Evolutionary Patterns of Genic DNA Methylation Across a Broad Taxonomic Sample of Land Plants

Little is known about patterns of genic DNA methylation across the plant kingdom or about the evolutionary processes that shape them.  To characterize gene body methylation within exons, we have gathered single-base resolution methylome data that span the phylogenetic breadth of Land Plants.  We find that a basal land plant, Marchantia polymorpha, lacks any evident signal of gene body methylation within exons; in contrast, conifers have high levels of both CG and CHG methylation in expressed genes.  To begin to understand the evolutionary forces that shape gene body methylation, we first tested for correlations in methylation levels across orthologs.  Genic CG methylation levels are correlated across orthologs for species as distantly related as ferns and angiosperms, which diverged ~400 million years ago.   Hence, CG methylation is a long-held property of individual genes.  We also find that gene body methylation levels in the CHG context correlate with genome size, suggesting that the host response to transposable elements also affects genes.  Altogether, our data indicate that the evolutionary forces acting on DNA methylation vary substantially across species, genes and methylation contexts.