Supergenes are sets of loci that can maintain adaptive combinations of traits, because they are inherited as a unit. They are responsible for a wide range of balanced polymorphisms in nature, yet our understanding of their origin and evolution remains incomplete. An improved understanding of supergene evolution is of broad significance, as it can contribute to resolving fundamental questions regarding the causes and consequences of suppressed recombination. Here, we aim to use the latest advances in genomic technologies to investigate the evolution of a classic supergene, the distyly S-locus. Distyly is a balanced floral polymorphism that has attracted the attention of many generations of biologists, including Darwin. It has long been known that distyly is governed by a supergene, yet we still know surprisingly little about the molecular genetics and evolution of the distyly S-locus. We aim to sequence and characterize the evolution of the distyly supergene in Linum (wild flaxseed species), a classic system for the study of distyly. To do so, we will use high-quality genomic data and a comparative genomic approach. Our main aim is to test whether distyly S-locus exhibits similarities to sex chromosomes with respect to recombination suppression, genetic degeneration and gene expression evolution. We will further investigate the role of inversions, insertions and other types of structural genomic changes at the S-locus. We are specifically interested in whether structural changes at the S-locus represent a cause vs. a consequence of suppressed recombination, and whether introgression has contributed to the origin and evolution of the S-locus in Linum. To address these questions, we will first combine de novo genome assembly of long-read data with genetic analyses to identify S-linked regions. We will then build on this knowledge to investigate structural variation, test for an effect of recombination suppression on the efficacy of selection, and test for introgression at the S-locus, in a comparative genomic framework. Finally, we will investigate the genetic causes and population genetic consequences of recurrent loss of distyly in Linum. The high-quality genome assemblies produced during this project will pave the way for future studies of the molecular basis of adaptive floral differences first identified by Darwin. The results from this project are important for an improved understanding of the processes that govern supergene evolution and the origins of coadapted gene complexes.