Genome-Wide Comparison of Soybean and Common Bean Methylomes

Common ancestor of soybean (Glycine max) and common bean (Phaseolus vulgaris) had experienced a shared paleopolyploidy event approximately 56.5 million years ago (MYA). After their divergence, only soybean has gone through another polyploidy event around 10 MYA, while common bean has not. Due to the independent whole genome duplication (WGD) in soybean, 75% of soybean genes are present as more than one copy, while 43% of common bean genes have multiple copies. Cytosine methylation is a common form of DNA modification in eukaryotes and plays an important role in the regulation of gene expression. Previous studies reported epigenetic re-patterning after polyploidization, but still little is known about the role of DNA methylation in regulation of duplicated genes. Using whole-genome bisulfite sequencing, we uncovered the soybean and common bean methylomes. Between paralogs and orthologs in both species, CG methylation in gene body was strongly conserved, while CHG and CHH methylation was not, indicating target loci of RNA-directed DNA methylation have been changed after the speciation and the duplication events. In addition, duplicated genes produced by WGD in both species showed higher level of gene expression, lower level of non-CG methylation and lower rate of TE insertion, suggesting a possible role of TE insertion and non-CG methylation regulating gene expression.