A Complete Reference Genome Reveals Genetic Landscape of Brassica Centromeres

Centromeres are essential regions of chromosome. Yet, their composition and evolutionary dynamics in higher plants remain poorly understood. This challenge is particularly evident in Brassica crops, whose genomes are highly repetitive and polyploid, making their centromeres especially difficult to characterize. Here, we present the first complete chromosome-level assembly of the Brassica napus genome and provide a comprehensive analysis of the sequence composition, three-dimensional organization, and evolutionary trajectories of Brassica centromeres. We identify the core satellite repeats that constitute centromeric regions and uncover pronounced sequence polymorphism among subgenomes. Notably, we report the first observation of rDNA-enriched pericentromeres in Brassica, likely resulting from rDNA relocations driven by chromosome fission-fusion events during the evolutionary transition from ancestral karyotypes to the modern Brassica genome. Our analyses further demonstrate that polyploidization in Brassica markedly influences long terminal repeat (LTR) retrotransposon removal efficiency across subgenomes and reveal a dynamic, cyclic model of centromere evolution driven by interactions between LTR retrotransposons and satellite repeats. These findings provide key insights into genome stability and adaptive mechanisms following polyploidization in plants.