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 lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.

Chinese narcissus (Narcissus tazetta var. chinensis) was introduced to China 1300–1400 years ago, and has grown naturally in southeastern China. It is a popular Chinese traditional potted flower and a well-known flowering bulb cultivated worldwide with only two white-tepal triploid cultivars, ‘Jinzhan Yintai’ and ‘Yulinglong’. Recently, a mutant with yellow tepals was observed and promptly became popular. To clarify the key pigment for color difference and its molecular mechanism of accumulation, we conducted pigment metabolite analysis and comparative transcriptome analysis on ‘Jinzhan Yintai’ and the yellow-flowered mutant. The results showed that there was no significant difference in total flavonoid content between the mutant and ‘Jinzhan Yintai’, whereas the total carotenoid content of the mutant was more than 10-fold higher than that of ‘Jinzhan Yintai’. Based on the RNA-sequencing results, sixty-four unigenes, corresponding to 29 enzymes associated with the carotenoid biosynthesis pathway, were analyzed in detail. A comparative KEGG pathway enrichment analysis, in conjunction with quantitative real-time PCR data, revealed the opposite gene expression mode of the carotenoid biosynthesis pathway. Compared with ‘Jinzhan Yintai ’, PSY and PDS were up-regulated in the three mid-flowering stages of the mutant, whereas NCED genes were strongly down-regulated, which likely contributed to carotenoid accumulation in chromoplasts of the tepals in the mutant.

The Loropetalum chinense and Loropetalum chinense var. rubrum are typical as well as traditional ornamental and Chinese herbal medicines in Asia; however, more information is needed on the mechanisms underlying their flower coloring. Here, we profiled the flavonoid metabolome and carried out full-length sequencing in addition to transcriptome analyses to investigate the flavonoid biosynthesis and global transcriptome changes among different petal coloring cultivars of L. chinense and L. chinense var. rubrum. The total anthocyanins in addition to the RHSCC values and CIE 1976 L*a*b* values of petals were highly consistent with petal color. Moreover, a total of 207 flavonoid components were identified. Of these, 13 flavonoid compounds were considered significantly different expression compounds highly consistent with color information in the 4 samples. Meanwhile, the first reference full-length transcriptome of L. chinense var. rubrum was built, which had 171,783 high-quality nonredundant transcripts with correcting with next-generation sequencing (NGS). Among them, 52,851 transcripts were annotated in the seven databases of NR, KOG, GO, NT, Pfam, Swiss-Port, and KEGG. Combined with NGS analyses, the DETs involved in flavonoids and anthocyanins contributed greatest to the flower coloring. Additionally, the different expressions of eight LcDFRs and four LcANS genes were positively correlated with flavonoid biosynthesis, and the four LcBZ1 as well as one Lc3Mat1 were positively correlated with the content of seven anthocyanins revealed by coupling with metabolomics and transcriptomics analyses. Together, these results were used to mine candidate genes by analyzing flower coloring changes at comprehensive metabolic and transcriptomic levels in L. chinense and L. chinense var. rubrum.

The genus Lagerstroemia L. (Lythraceae), known for its exquisite flowers and prolonged flowering period, is commonly employed in traditional medicinal systems across Asian countries, where it has always been consumed as tea or employed to address ailments such as diabetes, urinary disorders, coughs, fevers, inflammation, pain, and anesthesia. Its diverse uses may be attributed to its rich active ingredients. Currently, at least 364 biological compounds have been identified from Lagerstroemia extracts, encompassing various types such as terpenes, flavonoids, phenolic acids, alkaloids, and phenylpropanoids. Extensive in vitro and in vivo experiments have examined the pharmacological activities of different extracts, revealing their potential in various domains, including but not limited to antidiabetic, anti-obesity, antitumor, antimicrobial, antioxidant, anti-inflammatory, analgesic, and hepatoprotective effects. Additionally, 20 core components have been proven to be associated with antidiabetic and hypoglycemic effects of Lagerstroemia. Overall, Lagerstroemia exhibit substantial medicinal potential, and the alignment between its traditional applications and contemporary pharmacological findings present promising opportunities for further investigation, particularly in food and health products, drug development, herbal teas, and cosmetics. However, evidence-based pharmacological research has largely been confined to in vitro screening and animal model, lacking clinical trials and bioactive compound isolations. Consequently, future endeavors should adopt a more holistic approach.

The plant hormone auxin plays an important role in cell division and the elongation of shoots to affect the plant architecture, which has a great impact on the plant yield, fruit quality and ornamental value; however, the regulatory mechanism of auxin controlling shoot growth is unclear in crape myrtle. In this study, two auxin/indole-3-acetic acid (Aux/IAA) genes and four small auxin upregulated RNA (SAUR) genes of auxin response gene families were isolated from dwarf and non-dwarf progenies of Lagerstroemia indica and then functionally characterized. Sequence alignment revealed that the six genes contain typical conserved domains. Different expression patterns of the six genes at three different tissue stages of two types of progenies showed that the regulation mechanism of these genes may be different. Functional verification of the six genes upon shoot growth of crape myrtle was performed via virus-induced gene silencing. When the LfiAUX22 gene was silenced, a short shoot phenotype was observed in non-dwarf progenies, accompanied by decreased auxin content. Therefore, we preliminarily speculated that LfiAUX22 plays an important role in the shoot growth of crape myrtle, which regulates the accumulation of indole-3-acetic acid (IAA) and the elongation of cells to eventually control shoot length.