Brachypodium distachyon Epigenomics. Brachypodium distachyon

DNA methylation is a common feature of eukaryotic genomes and especially common in noncoding regions of plants. Protein coding regions of plants are often methylated, too, but the extent, function and evolutionary consequences of gene-body methylation remain unclear. Here we investigate gene-body methylation using an explicit comparative evolutionary approach. We generated bisulfite sequencing (BS-seq) data from two tissues of Brachypodium distachyon and compared genic methylation patterns to those of rice (Oryza sativa ssp. japonica). Gene-body methylation was strongly conserved between orthologs of the two species and affected a biased subset of long, slowly-evolving genes. Because gene-body methylation is conserved over evolutionary time, it shapes important features of plant genome evolution, such as the bimodality of G+C content among grass genes. Our results superficially contradict previous observations of high cytosine methylation polymorphism within Arabidopsis thaliana genes, but reanalyses of these data are consistent with conservation of methylation within gene regions. Overall, our results indicate that the methylation level is a long-term property of individual genes, and therefore of both functional and evolutionary consequence.