Most plants are polyploid due to whole-genome duplications (WGD) and can thus have duplicated genes.Following a WGD,paralogs are often fractionated (lost) and few duplicate pairs remain.Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes.Using high-resolution methylation maps of accessions of domesticated and wild soybean,we show that in soybean,a recent paleopolyploid with many paralogs,DNA methylation likely contributed to the elimination of genetic redundancy of polyploidy-derived gene paralogs.Transcriptionally silenced paralogs exhibit particular genomic features as they are often associated with proximal transposable elements (TEs) and are preferentially located in pericentromeres,likely due to gene movement during evolution.Additionally,we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean,and within populations.