Abstract

Chromosomal variation underlies species evolution, but reconstructing its large-scale dynamics remains challenging, obscuring its adaptive significance. Here, we introduce GouMang, a framework that mines conserved genic section compositions across diverse species to trace karyotype evolution. In grasses, applied to 818 highly varied chromosomes spanning eight subfamilies, GouMang resolved a shared karyotype evolution path of 9-to-18 ({rho} whole genome duplication, {rho}WGD)-to-12 chromosomes, followed by lineage specific rearrangements or WGDs. Genes retained from the early {rho}WGD are linked to cold/light adaptation, supporting a key biomass expansion event that impacted subsequent global ecological pattern and human agricultural civilization, in which K-Pg global cooling and subsequent forest degradation drove early understory grasses to sun plants. Parallel analysis in Brassicaceae reconstructed karyotype evolution as well as {beta}WGD which unlinked to cold/light adaptation, reflecting a divergent biogeographic history compared to grasses. Together, GouMang depicts a widespread plant evolutionary pattern where karyotype constantly diversified with WGDs recurrently fueling adaptation.