Genomics and adaptive divergence of the allopolyploid grass Brachypodium hybridum in a pangenotypic framework

The allotetraploid grass Brachypodium hybridum, a natural allopolyploid with multiple origins, serves as a valuable tool for examining genome evolution. Researchers analyzed whole-genome sequences from 307 accessions across the circum-Mediterranean region, alongside phylogenomics, population genomics, and comparative subgenomic analyses.

Three distinct allopolyploidization events were identified: one ancient event in Iberia around 1.78 million years ago, and two later events in the western and eastern Mediterranean, around 0.56 and 0.24 million years ago respectively. The nuclear and plastome phylogenies demonstrate that each subgenome (D and S) evolved independently from one another with limited recombination.

Both subgenomes in B. hybridum carry higher loads of deleterious mutations than their respective diploid progenitors, with the ancient Iberian lineage bearing a particularly heavy burden, especially in the S subgenome. Population structure identified three genetic groups, with the ancient lineage remaining isolated while recent lineages from the west and east exchanged migrants in the eastern Mediterranean contact zone.

This study illustrates how recurrent allopolyploidization, minimal subgenomic recombination, and environmental filtering combine to generate and maintain genetic diversity, highlighting B. hybridum as an exemplary model for polyploid evolution and ecological adaptation in grasses globally.