The Role of Gene Function on The Fate of Duplicated Genes in Soybean

Whole genome duplication (WGD) occurred repeatedly during plant evolution. Several models have been proposed to elucidate the evolution of duplicated genes. Most models assume that the duplicated genes evolve randomly and independently. Here, by studying soybean genome which has experienced two rounds of WGD ~13 and 59 MYA, we found that the fate of duplicated genes was highly influenced by their annotated functions. We found the functional categories are unevenly overrepresented in groups of genes with different duplication status. Non-syntenic single-copy genes were significantly enriched in many housekeeping functions, while high-copy (> 4 syntenic copies) genes were highly enriched in transcription regulation functions. There were fewer overrepresented categories in moderate-copy group (2-4 syntenic copies). These facts are consistent with the prediction of scaling laws in the functional content of genomes. We also found that the three gene groups showed dramatically different profiles in expression, DNA methylation and siRNA abundance. By analyzing presence–absence variations (PAVs) among 60 soybean accessions, we determined that 85% of PAV events were found in the non-syntenic group indicating ongoing evolution. Our results suggested that many factors may be involved in the evolution of duplicated genes and that a gene’s fate is discriminated by the nature of the gene. We propose that different requirements for complexity in different functional categories by evolutionary selection result in the phenomena of the scaling law of genome functional contents as well as the discriminated evolutionary fates of duplicated genes in different functional categories.