A complete reference genome reveals genetic landscape of Brassica centromeres

Abstract Centromeres are essential for chromosome segregation, yet their organization and evolution remain poorly understood in polyploid crops. We present the first complete telomere-to-telomere reference genome of Brassica napus cultivar Zhongshuang11 and characterize centromere architecture and evolution. We identify core satellite repeats that define centromeres and reveal extensive sequence polymorphism and structural divergence between subgenomes associated with polyploidization and domestication. We further uncover rDNA-enriched pericentromeres generated by recurrent chromosome rearrangements and propose a centromere evolutionary cycle model that explains how satellite repeats and transposons jointly shape centromere evolution.