A pan-genome framework reveals structural variation and small RNA regulation underlying heterodichogamy in Pterocarya

Heterodichogamy, characterized by reciprocal timing of male and female flowering, promotes disassortative mating yet remains poorly understood at the genomic level. Here, we investigated this mating system in Pterocarya, a genus within Juglandaceae, using a low-input pan-genome framework that integrates phased assemblies with population resequencing. We identified a deeply divergent 78-kb locus associated with mating morphs in P. stenoptera, marked by repeat-rich structural variants and containing a FAF-like gene linked to floral development. This region also produces small RNAs that potentially regulate key floral and hormonal pathways, suggesting pleiotropic trans-regulatory effects. Comparative analyses reveal that although the loci controlling heterodichogamy in Juglans, Carya, and Pterocarya are non-homologous, they appear to share convergent evolutionary solutions involving tandem repeats or transposable element (TE) insertions. Our study uncovers the genomic basis of heterodichogamy in Pterocarya and underscores the utility of pan-genome approaches for dissecting structural variation-associated traits.