An evolutionary landscape of sesame: chromosomal variation, allopolyploid speciation and metabolic specialization

Sesame ( Sesamum indicum ) is one of the earliest domesticated oilseed crops and is valued for antioxidant lignans that stabilize oil quality. However, the genomic and evolutionary history of the genus Sesamum , including the origin of its allotetraploid relative S. radiatum and the diversification of lignan metabolism, remains poorly understood owing to limited chromosome-scale genomic resources. Here we present chromosome-level genome assemblies for three wild Sesamum species, two Ceratotheca species and a Japanese sesame cultivar to reconstruct genome and karyotype evolution across the Sesamum–Ceratotheca complex. Comparative analyses show that the derived x =16 lineage originated from an ancestral x =13 karyotype through chromosome fission, fusion and translocation, whereas another x =13 lineage underwent extensive restructuring associated with retrotransposon expansion. Phylogenomics places Ceratotheca within the x =16 Sesamum clade and reveals that S. radiatum originated through hybridization involving a C. sesamoides -like ancestor. The antioxidative lignan gene CYP92B14 was reintroduced via the BB progenitor, linking hybridization with restoration of oil-stabilizing metabolism during sesame evolution.