A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges

We describe four ancient polyploidy events where the descendant taxa retain many more duplicated gene copies than has been seen in other paleopolyploidies of similar ages. Using POInT (the Polyploidy Orthology Inference Tool), we modeled the evolution of these four events, showing that they do not represent recent independent polyploidies despite the rarity of shared gene losses. We find that these events have elevated rates of interlocus gene conversion and that these gene conversion events are spatially clustered in the genomes. Regions of gene conversion also show very low synonymous divergence between the corresponding paralogous genes. We suggest that these genomes have experienced a delay in the return to a diploid state after their polyploidies. Under this hypothesis, homoeologous exchanges between the duplicated regions created by the polyploidy persist to this day, explaining the high rates of duplicate retention. Genomes with these characteristics arguably represent a new class of paleopolyploid taxa because they possess evolutionary patterns distinct from the more common and well-known paradigm of the rapid loss of many of the duplicated pairs created by polyploidy.