The southern African endemic tree genus Greyia Hook. & Harv. (Francoaceae, Geraniales) comprises three species distinguished by striking variation in trichome morphology and floral architecture, yet the genomic and regulatory basis of these traits has remained largely unexplored. Here, we present chromosome-scale genome assemblies for all recognized Greyia species, namely Greyia radlkoferi, Greyia sutherlandii, and Greyia flanaganii, providing the first high-quality genomic resources for Geraniales. Phylogenomic analyses placed Geraniales as sister to Crossosomatales, with divergence at ~103 million years ago (Mya), and indicated that Greyia diversified recently during the Quaternary (~1.39 Mya). Comparative genomics revealed a Greyia-specific whole-genome triplication event dated to ~86.9 Mya, generating extensive gene duplication which has been retained. Transcriptomic analyses linked divergence in trichome morphology to regulatory subfunctionalization of the conserved MYB-bHLH-WD40 (MBW) complex, including transcriptional silencing of GL1 and shifts in GL3/EGL3 expression in G. sutherlandii. In addition, analyses of flower and inflorescence identified expansion of MADS-box transcription factor families and species-specific cis-regulatory divergence in LFY and FT. Notably, predicted AGL6 binding sites are retained in the LFY and FT promoters of G. radlkoferi and G. sutherlandii but absent in G. flanaganii, which aligns with differences in inflorescence density among species. Together, these results demonstrate how polyploidy and regulatory divergence of conserved developmental pathways have shaped morphological diversification in Greyia.
