Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle.

Crape myrtle () is a globally used ornamental woody plant and is the representative species of . However, studies on the evolution and genomic breeding of have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in following its divergence from . After resequencing 73 accessions of , the main parents of modern crape myrtle cultivars were found to be and . During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in . We constructed a high-density genetic linkage map with an average map distance of 0.33 cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains , , and associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of , with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified , , and . Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of .