Gapless pangenome analyses reveal fast <i>Brassica rapa</i> subspeciation

<i>Brassica rapa</i> (<i>Br</i>) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 <i>Br</i> accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with <i>Br</i> morphotypes and subspecies and <i>Brassica</i> species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among <i>Br</i> subspecies. Pangenome-wide association studies uncovered that the gene <i>BrLH1</i> controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of <i>Br</i> cultivation, providing invaluable resources for <i>Brassica</i> breeding.