Abstract
The role of transposable elements (TEs) in genome evolution and phenotypic diversification in Camellia remains poorly understood. Here, we present an integrated analysis of genome resequencing data from 237 Camellia accessions and 11 de novo genome assemblies representing all major floral colour types. We constructed a comprehensive phylogenetic framework for the genus and suggest that the most recent common ancestor likely had white flowers. Comparative genomic analyses reveal structural variants across species that overlap with numerous transposable elements and contribute to genome content divergence. Using a graph-based genome to characterise these structural variants, we find that lineage-specific TE amplifications drive the regulatory network rewiring, which modulates homoeologous gene expression, influencing flower colour diversification. Further experimental validation identifies a lineage-specific, high-frequency presence variation mediated by a TIR transposon that regulates MYB60 expression, suppressing anthocyanin biosynthesis and leading to large-scale floral colour divergence. Therefore, these findings highlight the central role of TE-mediated regulatory innovation in the evolution of flower colour in Camellia and offer broader insights into the molecular mechanisms driving phenotypic diversification in plants.