DNA methylation signatures of duplicate gene evolution in angiosperms

Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes through its association with gene expression. While this relationship is examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We apply a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis thaliana accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation is differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates are typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications are typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in partic..., , This dataset includes formatted genomes and annotations for use with code from: https://github.com/niederhuth/DNA-methylation-signatures-of-duplicate-gene-evolution-in-angiosperms.