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

Summary Heterostyly is a polymorphic floral adaptation controlled by supergenes and maintained in populations by disassortative mating. The molecular basis of distyly has been investigated in several unrelated families. Previous studies have been limited to diploid species and have not included Rubiaceae, which has the highest number of heterostylous species. Here, we investigate the genetic architecture of tetraploid Schizomussaenda henryi (Rubiaceae) to identify candidate style-length genes, evidence for hemizygosity and the potential role of gene duplication in the evolution of the S -locus. Chromosome-level genome assemblies and transcriptomic approaches identified the S -locus region comprised of four hemizygous genes. The candidate gene SchzAUX22 may regulate style length and filament growth by acting in the auxin signaling pathway. Comparative studies of the two sub-genomes of S. henryi indicated strong similarities and no significant sub-genome dominance, as expected from autotetraploidy. Evidence from haplotype-resolved assemblies of a short-styled plant indicated that it possessed the ssSS genotype, consistent with autotetraploidy, which was estimated to have originated ∼3.6 Mya. Analysis of Ks values between S -locus genes and their paralogs indicated that the S -locus likely originated through stepwise duplication. Our study provides comprehensive genomic analysis of distyly in a polyploid and demonstrates that despite whole genome doubling the S -locus supergene remains intact and functional as an outbreeding mechanism. Our results contrast with many other heterostylous lineages where polyploidy is associated with breakdown of the polymorphism and transitions to self-fertilization.