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.

Loropetalum chinense var. rubrum is a common landscape plant. Because of the preference for the ‘red leaf’ trait, the ‘flower color’ trait was ignored in breeding, and the genetic diversity of L. chinense var. rubrum was replaced by a few genotypes. Therefore, the potential value of flower color traits was affected, and the genetic diversity was not fully exploited. In this study, we utilized a cultivar with mosaic-colored flowers and leaves and observed 15 phenotypic traits in its flower organs and its progeny, as well as a total of 60 different flower color materials. We analyzed the variation characteristics and diversity of flower colors, and qualitatively described and preliminarily classified flower colors using the ISCC-NBS and CIELab systems to explore the correlation with the flower color phenotype from the distribution and content of anthocyanins. The phenotypic diversity of the flower organs was enriched, and genetic differences in flower color were significant for the L.chinense var. rubrum, with most of the 15 phenotypic traits showing significant positive correlations, and the most critical phenotypes are sepal, petal and nectary color, as well as petal length. According to the CIELab color system and anthocyanin content and distribution characteristics, it is considered more accurate and convenient to classify the color phenotypes of L. chinense var. rubrum flowers into five categories. In this study, for the first time, the flower organ phenotype of L. chinense var. rubrum has been systematically analyzed, and it is explored as a reference method for breeding new cultivars of a diverse range of colors in L. chinense var. rubrum.

Challenges significantly hinder the sustainable cultivation of tea chrysanthemum, leading to imbalances in soil nutrients, the accumulation of allelopathic phenolic acids, reduced enzymatic activity, and disruptions in rhizosphere microbial communities. To explore potential mitigation strategies, this study systematically evaluated the integrative effects of exogenous methyl jasmonate (MeJA, 0–400 (μmol L⁻¹)) on both soil environmental parameters and plant growth performance under continuous cropping conditions. The results revealed that treatment with 100 (μmol L⁻¹) MeJA significantly enhanced plant height, canopy width, flower number, and fresh flower weight. Concurrently, it improved soil organic matter content, the available nitrogen levels, and redox stability while increasing the activity of key enzymes, including polyphenol oxidase, urease, and catalase. Notably, this treatment markedly reduced the accumulation of allelopathic phenolic acids, such as p-hydroxybenzoic acid and vanillic acid. High-throughput sequencing further demonstrated that 100 (μmol L⁻¹) MeJA optimized the composition of soil microbial communities, increasing the abundance of beneficial taxa, such as nitrogen-fixing and phosphate-solubilizing bacteria, while suppressing pathogenic fungi. Metabolomic analysis showed that this concentration of MeJA activated stress-resistance metabolic pathways involving flavonoids and terpenoids while downregulating degradation-related processes, thereby supporting enhanced plant resilience at the metabolic level. Collectively, these findings demonstrate that an appropriate concentration of exogenous MeJA can effectively alleviate continuous cropping obstacles in Chrysanthemum morifolium, providing both theoretical insights and practical guidance for its eco-friendly and efficient cultivation.

Wild orchid populations are declining with intensified habitat fragmentation posing severe challenges to germplasm conservation. As an important ornamental Orchidaceae species, Cymbidium ensifolium has abundant germplasm resources and frequent natural and artificial hybridization. Long-term natural evolution and anthropogenic disturbance have led to complex genetic backgrounds and ambiguous phylogenetic relationships hindering accurate germplasm identification, elite resource excavation, and selective breeding. As a distinctive variety, Cymbidium ensifolium var. susin has great breeding potential. Clarifying its phenotypic and genetic characteristics is crucial for accelerating breeding progress. In this study, phenotypic determination, Hyper-seq reduced-representation genome sequencing, SNP/InDel genotyping, genetic diversity analysis, and core collection construction were used to evaluate the genetic diversity, population differentiation, and core germplasm screening of 13 Cymbidium ensifolium var. susin accessions. The results showed significant phenotypic differences and rich genetic variation among tested materials. Based on highly weighted floral traits, accessions were divided into three major phenotypic groups. At the molecular level, 963,239 SNP and 182,399 InDel loci were identified and mainly distributed in intergenic regions, followed by introns and exons. A phylogenetic tree was constructed from SNP loci combined with principal component and phenotypic clustering analyses. This study preliminarily clarified the genetic structure of pure-heart Cymbidium ensifolium var. susin, showing a distinct geographical pattern: “high consistency in Fujian and Guangdong; strong differentiation in Southwest China; and a transitional gradient in Central China”. Meanwhile, six core germplasm accessions were screened in this study, which provides a solid theoretical basis and material support for the conservation of pure-heart Cymbidium ensifolium var. susin accessions, variety improvement, hybrid parent selection, and molecular marker-assisted breeding. This is of great significance for promoting the innovation of Chinese orchid germplasm resources and the high-quality development of the industry.

Wild orchid populations are declining with intensified habitat fragmentation, posing severe challenges to germplasm conservation. As an important ornamental Orchidaceae species, Cymbidium ensifolium has abundant germplasm resources and frequent natural and artificial hybridization. Long-term natural evolution and anthropogenic disturbance have led to complex genetic backgrounds and ambiguous phylogenetic relationships, hindering accurate germplasm identification, elite resource excavation, and selective breeding. As a distinctive variety, Cymbidium ensifolium var. susin has great breeding potential.Clarifying its phenotypic and genetic characteristics is crucial for accelerating breeding progress. In this study, phenotypic determination, Hyper-seq reduced-representation genome sequencing, SNP/InDel genotyping, genetic diversity analysis, and core collection construction were used to evaluate the genetic diversity, population differentiation, and core germplasm screening of 13 Cymbidium ensifolium var. susin accessions.The results showed significant phenotypic differences and rich genetic variation among tested materials. Based on highly weighted floral traits, accessions were divided into three major phenotypic groups. At the molecular level, 963,239 SNP and 182,399 InDel loci were identified, mainly distributed in intergenic regions, followed by introns and exons. A phylogenetic tree constructed from SNP loci, combined with principal component and phenotypic clustering analyses, clarified the genetic structure of pure-heart Cymbidium ensifolium var. Susin , showing a distinct geographical pattern: "high consistency in Fujian and Guangdong, strong differentiation in Southwest China, and a transitional gradient in central China".Meanwhile, six core germplasm accessions were screened in this study, which provides a solid theoretical basis and material support for the conservation of pure-heart Cymbidium ensifolium var. Susin accessions, variety improvement, hybrid parent selection, and molecular marker-assisted breeding. This is of great significance for promoting the innovation of chinese orchid germplasm resources and the high-quality development of the industry.

The Loropetalum chinense and Loropetalum chinense var. rubrum are typical and traditional ornamental and Chinese herbal medicine in Asia. However, more information is needed on the mechanisms underlying its flower coloring. Here, we profiled the flavonoid metabolome, full-length sequencing, and transcriptome analysis 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 and phenotypic of the petal were highly consistent with the petal color. Moreover, a total of 207 flavonoid components were identified. Of these, 12 flavonoid components were considered significantly different expression compounds among the four samples. Meanwhile, the first reference full-length transcriptome of L. chinense var. rubrum was being built, which had 171,783 high-quality non-redundant transcripts with correcting with next-generation sequencing (NGS). Among them, 52,851 transcripts were annotated in the seven database of NR, KOG, GO, NT, Pfam, Swiss-Port and KEGG. Combined with NGS analysis, the DETs involved in flavonoids and anthocyanins contributed greatest to the flower-coloring. Additionally, the different expressed of eight LcDFRs and four LcANS genes were positively correlated with flavonoid biosynthesis, and the four LcBZ1 and one Lc3Mat1 were positively correlated with the content of seven anthocyanins revealed by coupling with metabolomics and transcriptomics analysis. Together these results were used to mine candidate genes by analyzing flower coloring changes in a comprehensive metabolic and transcriptomic level in L. chinense and L. chinense var. rubrum.