Fu, N.; Sun, P.; Liu, X.; Liu, T.-J.; Wang, Y.-B.; Li, W.-M.; Xiao, T.-W.; Li, X.-N.; Mi, Y.-Y.; Wang, Z.-F.; Rouard, M.; Ge, X.-J.; Huang, H.-R.; Wang, X.

The banana family (Musaceae) exhibits remarkable diversity in both karyotype structure and bract coloration, yet the evolutionary dynamics of chromosomes and the genomic and regulatory basis of color diversification remain poorly understood. Here, we present a telomere-to-telomere (T2T), gap-free genome assembly of Musa exotica, an ornamental species with brightly colored bracts occupying a basal position in sect. Callimusa (Musa L.). By integrating this high-quality genome with other Musaceae genomes, we reconstruct the ancestral Musaceae karyotype (AMK) for the first time, inferring a haploid chromosome number of n = 17. Comparative genomic analyses reveal that extant Musaceae lineages have undergone recurrent, lineage-specific inter-chromosome rearrangements, leading to stepwise reductions in chromosome number to n = 11, 10, and 9. Notably, closely related species share similar rearrangement patterns, indicating conserved evolutionary trajectories shaped by lineage-specific structural remodeling. Strikingly, rearrangement-associated regions are enriched in functionally important genes, particularly structural genes (CHS and F3H) and regulatory transcription factors (MYB and bHLH) involved in the anthocyanin biosynthesis pathway. Integrative transcriptomic and regulatory analyses demonstrate coordinated activation of anthocyanin biosynthetic genes (CHS, CHI, F3'5'H, and ANS) in bracts, with expression divergence largely decoupled from gene dosage and predominantly driven by transcriptional regulation. Co-expression analyses reveal extensive MYB- and bHLH-enzyme interactions, underscoring their central role in modulating pathway activity and bract coloration diversity. Together, our findings provide evidence linking genome structural evolution to trait diversification, offering a refined framework for understanding genome evolution and phenotypic diversification in Musaceae and other monocots.