Comprehensive characterization of the R2R3-MYB gene family in Liquidambar formosana reveals LifMYB047 as a key regulator of flavonol biosynthesis

MYB transcription factors play pivotal regulatory roles in plant secondary metabolism. However, the MYB gene family in Liquidambar formosana , an ecologically and ornamentally important tree species, remains insufficiently characterized. In this study, 120 R2R3-MYB family members were systematically identified using whole-genome data, and their evolutionary features and potential functions were comprehensively analyzed. Integrated analysis revealed that segmental duplication is the primary mechanism driving the expansion of this gene family. Throughout evolution, these genes have formed structurally conserved yet functionally differentiated subgroups, enabling them to meet the regulatory demands of diverse biological processes. Phylogenetic analysis classified the LifR2R3-MYBs into 32 subgroups, Furthermore, combined with the enriched distribution of cis‑regulatory elements related to hormone signaling and stress responses in their promoter regions, these genes can be categorized into four functional modules: metabolic regulation, defense response, developmental control, and differentiation processes. Notably, subgroup S17 exhibited potential regulatory roles in flavonoid metabolism. Integrated transcriptomic and metabolomic analyses revealed that the expression of LifMYB047 , a member of this subgroup, was positively correlated with the accumulation of flavonoids, such as kaempferol and quercetin. Its expression trend closely mirrored of key flavonol biosynthetic genes, including LifCHS3 , LifCHI3 , LifF3H , and LifFLS1 . Yeast one-hybrid assays further confirmed LifMYB047 's direct binding and activation capabilities on the promoters of its target genes. This study offers new insights into the evolutionary dynamics of the R2R3-MYB gene family in L. formosana and elucidates the molecular mechanisms by which it regulates foliar coloration through secondary metabolism. These findings lay a theoretical foundation for unraveling secondary metabolic networks in woody plants and provide a basis for improving ornamental traits. • First genome-wide analysis of R2R3-MYB genes functional diversity in L. formosana. • LifMYB047 identified as key regulator of flavonol biosynthesis. • Clarify MYB047 's molecular mechanism, offer target genes for breeding colorful trees.