Gene duplications have greatly shaped the gene content of plants. Multiple factors, such as the epigenome, can shape the subsequent evolution of duplicate genes and are the subject of ongoing study. We analyze genic DNA methylation patterns in 43 angiosperm species and 928 Arabidopsis thaliana ecotypes to finding differences in the association of whole-genome and single-gene duplicates with genic DNA methylation patterns. Whole-genome duplicates were enriched for patterns associated with higher gene expression and depleted for patterns of non-CG DNA methylation associated with gene silencing. Single-gene duplicates showed variation in DNA methylation patterns based on modes of duplication (tandem, proximal, transposed, and dispersed) and species. Age of gene duplication was a key factor in the DNA methylation of single-gene duplicates. In single-gene duplicates, non-CG DNA methylation patterns associated with silencing were younger, less conserved, and enriched for presence-absence variation. In comparison, DNA methylation patterns associated with constitutive expression were older and more highly conserved. Surprisingly, across the phylogeny, genes marked by non-CG DNA methylation were enriched for duplicate pairs with evidence of positive selection. We propose that DNA methylation has a role in maintaining gene-dosage balance and silencing by non-CG methylation and may facilitate the evolutionary fate of duplicate genes.
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