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

Abstract Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and the representative species of Lagerstroemia. However, studies on evolution genomic breeding L. indica were hindered by lack reference genome. Here, we assembled first high-quality genome using PacBio combined with Hi-C scaffolding to anchor 329.14 Mb assembly into 24 pseudochromosomes. We detected previously undescribed independent WGT event occurring 35.5 MYA in following its divergence from P. granatum. After resequencing 73 accessions Lagerstroemia, main parents modern crape cultivars found be fauriei. During process domestication, genetic diversity tended decrease many plants, but this was not observed indica. constructed high-density linkage map an average distance 0.33 cM. Furthermore, synthesized results QTL mapping BSA localized main-effect interval determining internode length (IL) chr1, which contains CDL15, CRG98, GID1b1 associated phytohormone pathways. Analysis gene expression red, purple white flower colour flavonoid pathways revealed that differential multiple genes determined indica, flowers having lowest expression. In addition, purple- green-leaved individuals populations performed, leaf loci mapped chr12 chr17. Within these intervals, identified MYB35, NCED, KAS1. Our provided foundation for investigating evolution, population structure differentiation Myrtaceae accelerated molecular