Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations.

KEY MESSAGE: We provided a study on homeologous gene evolution of homeologous genes by comparing Brassica genomes. Polyploidy has played fundamental roles during the evolution of plants. Following polyploidization, many duplicated genes are diversified or lost in a process termed diploidization. Understanding the retention and diversification of homeologs after polyploidization will help elucidate the process of diploidization. Here, we investigated the evolution of homeologous genes in Brassica genomes and observed similarly asymmetrical gene retention among different functional groups and consistent retention after recurrent polyploidizations. In the comparative analysis of Brassica diploid genomes, we found that preferentially retained genes show different patterns on sequence and expression divergence: genes with the function of 'biosynthetic process' and 'transport' were under much stronger purifying selection, while transcriptional regulatory genes diverged much faster than other genes. Duplicate pairs of the former two functional groups show conserved high expression patterns, while most of transcriptional regulatory genes are simultaneously lowly expressed. Furthermore, homeologs in diploids and allotetraploids showed similar loss and retention patterns: duplicates in progenitor genomes were more likely to be retained and accumulated fewer substitutions. However, transcriptional regulation is also enriched in the genes that do not have any non-synonymous mutations in the Brassica allotetraploids, indicating that some of these genes were under strong purifying selection. Overall, our study provided insight into the evolution of homeologs genes during diploidization process.