The ancestral crucifer karyotype and 22 conserved genomic blocks (CGBs) facilitate phylogenomic analyses in the Brassicaceae. Chromosomal rearrangements reshuffled CGBs of ancestral chromosomes during karyotype evolution. Here, we identify eight protochromosomes representing the common ancestral karyotype (ACBK) of the two Brassicoideae supertribes: Camelinodae (Lineage I) and Brassicodae (Lineage II). The characterization of multiple cascading fusion events allows us to infer evolutionary relationships based on these events. In the Camelinodae, the ACBK first evolved into the AKI genome, which remained conserved in the Cardamineae, whereas it was altered to tAKI by a reciprocal translocation that preceded the diversification of most Camelinodae tribes. The identified fusion breakpoints largely overlap with CGB boundaries, suggesting that CGBs are mainly disrupted by chromosome fusions. Our results demonstrate the stable inheritance of chromosome fusions and their importance for reconstructing evolutionary relationships. The chromosomal breakpoint approach provides a basis for ancestral state reconstruction based on chromosome-level genome assemblies.

CEITEC Central European Institute of Technology and Department of Experimental Botany Faculty of Science Masaryk University Brno Czech Republic

Key Laboratory for Bio resources and Eco environment and Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station College of Life Sciences Sichuan University Chengdu China

Missouri Botanical Garden St Louis MO USA

National Key Laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources Institute Chinese Academy of Tropical Agricultural Sciences Haikou China

School of Life Sciences North China University of Science and Technology Tangshan Hebei China

State Key Laboratory of Herbage Improvement and Grassland Agro ecosystem College of Ecology Lanzhou University Lanzhou China

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