The Primula edelbergii S‐locus is an example of a jumping supergene

Abstract Research on supergenes, non‐recombining genomic regions housing tightly linked genes that control complex phenotypes, has recently gained prominence in genomics. Heterostyly, a floral heteromorphism promoting outcrossing in several angiosperm families, is controlled by the S ‐locus supergene. The S ‐locus has been studied primarily in closely related Primula species and, more recently, in other groups that independently evolved heterostyly. However, it remains unknown whether genetic architecture and composition of the S ‐locus are maintained among species that share a common origin of heterostyly and subsequently diverged across larger time scales. To address this research gap, we present a chromosome‐scale genome assembly of Primula edelbergii , a species that shares the same origin of heterostyly with Primula veris (whose S ‐locus has been characterized) but diverged from it 18 million years ago. Comparative genomic analyses between these two species allowed us to show, for the first time, that the S ‐locus can ‘jump’ (i.e. translocate) between chromosomes maintaining its function in controlling heterostyly. Additionally, we found that four S ‐locus genes were conserved but reshuffled within the supergene, seemingly without affecting their expression, thus we could not detect changes explaining the lack of self‐incompatibility in P. edelbergii . Furthermore, we confirmed that the S ‐locus is not undergoing genetic degeneration. Finally, we investigated P. edelbergii evolutionary history within Ericales in terms of whole genome duplications and transposable element accumulation. In summary, our work provides a valuable resource for comparative analyses aimed at investigating the genetics of heterostyly and the pivotal role of supergenes in shaping the evolution of complex phenotypes.