Genetic architecture of the S‐locus supergene revealed in a tetraploid distylous species

Summary Heterostyly is a polymorphic floral adaptation controlled by supergenes. The molecular basis of distyly has been investigated in diploid species from several unrelated families, but information is lacking for polyploid systems. Here, we address this knowledge gap in Schizomussaenda henryi, a tetraploid distylous species of Rubiaceae, the family with the greatest number of heterostylous species. Using chromosome‐level genome assemblies and transcriptome profiling, we characterized its tetraploid genome, identified the S‐locus region, and performed evolutionary analysis. The S‐locus contains four hemizygous genes in the S‐morph. SchzAUX22 emerged as a candidate gene potentially regulating both style length and filament growth via auxin signaling. Phylogenetic and k‐mer‐based analysis suggested a hybrid allopolyploid origin for S. henryi, while no subgenome dominance was detected. Results from the comparison of Ks values indicated that S‐locus formation likely occurred through stepwise duplications. This study provides the first comprehensive genomic analysis of distyly in a polyploid species and demonstrates that the S‐locus remains intact despite allopolyploidization resulting from hybridization. Our results indicated that polyploidization does not necessitate the breakdown of distyly, which occurs in several other heterostylous lineages.