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

作者：Yang Zhou, Tangchun Zheng, Ming Cai, Lu Feng, Xiufeng Chi, Ping Shen, Xin Wang, Zhiting Wan, Cunquan Yuan, Man Zhang, Yu Han, Jia Wang, Huitang Pan, Tangren Cheng, Qixiang Zhang · 发表于：Horticulture Research · 年份：2023 · DOI：10.1093/hr/uhad146 · 被引用次数：38 · 研究领域：Horticultural and Viticultural Research、Forest Insect Ecology and Management、Plant and animal studies

Abstract Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica 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 L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. 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 CDL15, CRG98, and GID1b1 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 L. indica, with white flowers having the ...