Karyotype reconstruction provides new insights into polyploid evolution in grasses (Poaceae)

Chromosomal rearrangements following whole-genome duplication (WGD) shape the diversity of genome structures in Poaceae. An accurate karyotype construction based on high-quality genomes of extant species will facilitate a deeper understanding of the origin and evolution of Poaceae. Here, we determine ancestral karyotypes for the BOP and PACMAD clades (ABPK, n  = 12) and further infer ancestral karyotypes for subfamilies and tribes with distinct chromosome structures. Evolutionary trajectories from ancestral karyotypes to modern genomes are reconstructed for 29 species across 7 subfamilies through the characterization of multiple cascading fusion events. Our results reveal that subfamily-specific fusions contribute to the divergence and establishment of distinct subfamilies, while shared fusions among closely related species within each subfamily reflect the stable inheritance of karyotypic architecture. Based on the comparative karyotype analysis, we elucidate that Cenchrus purpureus and C. fungigraminus share two diploid progenitors contributing to their respective subgenomes A and B, and that Paleotetraploid S. maritimus and S. alterniflorus share the first allotetraploid WGD (WGD1) but experience independent second WGD (WGD2) events. Our results highlight the importance of chromosome fusion in descending dysploidy after recurrent polyploidization and shed light on the polyploidization and karyotype evolution across the Poaceae family.