Genetic and Epigenetic Divergence of Duplicate Genes in Two Legume Species.

Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a polyploidy event similar to 59MYA, followed by a Glycine-specific whole genome duplication (WGD) similar to 8-13MYA. Duplicated genes were classified into five categories: singletons, dispersed, proximal, tandem, or WGD/segmental and found strong correlations between gene category and functional annotation. Photosynthesis and transcriptional regulation-related Gene Ontology terms were significantly over-represented in singletons and WGD genes, respectively, aligning with the gene balance hypothesis. We found that the divergence of gene expression and DNA methylation between WGD-derived paralogs increased with age and that WGD genes, initially retained via dosage constraints, subsequently underwent expression divergence, associated with other factors such as DNA methylation. Genes derived from different modes of duplication differed in breadth, level, and specificity of expression in both species. Orthologous genes and ungrouped genes (genes not in an ortholog group) differed in expression patterns. The protein divergence rates of WGD paralog pairs containing an ungrouped gene were higher than those for which both copies had orthologs. We propose that many ungrouped genes are derived from divergent and redundant gene copies, concordant with the neofunctionalization hypothesis. Tandemly duplicated genes were distinct from WGD-derived genes, indicating that mode of duplication contributes to the evolutionary fate of duplicated genes. We present a comprehensive study of multiple -omics data sets to understand mechanisms underlying the evolution of duplicated genes following whole genome duplications (WGDs) in two legume species Glycine max (soybean) and Phaseolus vulgaris (common bean). Soybean and common bean share a polyploidy event similar to 59MYA, followed by a Glycine-specific WGD similar to 8-13MYA, a useful system to study the evolution of duplicated genes following multiple WGD events. Comparing and contrasting genomic features among different duplication categories, as well as between the two species, we found that the fate of duplicated genes did not fit a single predictive hypothesis of how genes evolve postduplication. Rather, the postduplication evolution of gene function and their fate post is a complex process where duplication mode was an important factor affecting evolutionary trajectories of gene expression, methylation, and function.