Subgenomic stability of progenitor genomes during repeated allotetraploid origins of the same grass Brachypodium hybridum.

Both homeologous exchanges (HEs) and homeologous expression bias (HEB) are generally found in most allopolyploid species. Whether HEs and HEBs differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our HE with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further HEB tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess HE with replacement in allopolyploids, thereby avoiding the detection of false HEs when using less related progenitor species genomes.