Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

Abstract

DNA methylation isa common feature ofeukaryotic genomes and is especially common in noncoding regions of plants. Protein coding regions ofplants are often methylated also, but the extent, function, and evolutionary consequences of gene body methylation remain unclear. Hereweinvestigate genebodymethylation usinganexplicit comparative evolutionary approach. We generated bisulfite sequencing 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 ofhigh 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 evolutionary consequence.