Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Abstract Supergenes govern balanced polymorphisms in a wide range of systems. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S- locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown if hemizygosity is pervasive among distyly S -loci. Here we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue , followed by the identification of the S -locus using population genomic data. We show that hemizygosity and thrum-specific expression of S -linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S -locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S- linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes. The chromosome-level genome assembly and detailed characterization of the distyly S -locus in L. tenue will facilitate elucidation of molecular mechanisms underlying the different forms of flowers described by Darwin.