In nature, plants have rich and vivid colors. Flower color can confer economic and ornamental value to ornamental plants, and is one of the target traits for current directed breeding. Therefore, it is essential to understand the molecular regulatory mechanisms behind flower color formation in ornamental plants. However, in Cosmos bipinnata Cav., one of the most important ornamental plants, the metabolic pathways and molecular regulatory mechanisms underlying the formation of different flower colors are not yet clear, which greatly restricts the molecular breeding of flower color varieties. We selected three varieties of Cosmos bipinnata Cav. with white, pink, and red flowers as research materials, and identified significantly different metabolites among them through ultra performance liquid chromatography mass spectrometry (UPLC-MS/MS) analysis and principal component analysis (PCA). Then, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and transcriptome sequencing analysis in different colors flowers were used to reveal that the differential metabolites were enriched in flavonoid metabolic pathways and related structural genes were differentially expressed. Furthermore, we identified differentially expressed members of the MYB and bHLH transcription factor families, which play key roles in regulating the anthocyanin biosynthesis. By constructing a phylogenetic tree and performing a joint analysis of transcriptome and metabolome data, we further elucidated the molecular regulatory network underlying the formation of flower colors in Cosmos bipinnata Cav. This study not only provides a theoretical basis and gene resources for color-oriented breeding and the creation of new color varieties, but also offers new insights into the molecular mechanisms of flower color formation in plants.

The precious aquatic plant Nymphaea hybrid, is valued for its ornamental and economic importance but is highly sensitive to environmental fluctuations. However, the interactive effects of light and temperature, two critical abiotic factors, on its photosynthetic performance and underlying structural basis remain poorly understood. In this paper, we conducted a two-factorial experiment in which N. hybrid plants were exposed to five light–temperature regimes for 9 days: control (T0, 800 μmol·m⁻²·s⁻¹ + 25/20 °C); low light–low temperature—LLLT (T1, 200 μmol·m⁻²·s⁻¹ + 15/10 °C); low light–high temperature—LLHT (T2, 200 μmol·m⁻²·s⁻¹ + 35/30 °C); high light–low temperature—HLLT (T3, 1400 μmol·m⁻²·s⁻¹ + 15/10 °C); and high light–high temperature—HLHT (T4, 1400 μmol·m⁻²·s⁻¹ + 35/30 °C). We systematically investigated changes in photosynthetic pigments, gas exchange, chlorophyll fluorescence, and leaf ultrastructure by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The results showed that: The HLLT treatment (T3) inflicted the most severe damage, triggering a rapid decline in net photosynthetic rate (Pn), maximal photochemical efficiency (F_v/F_m), and chlorophyll content, coupled with a significant increase in intercellular CO₂ concentration (Ci). Ultrastructurally, T3 caused stomatal closure, disintegration of thylakoid membranes, and accumulation of large osmophilic granules, indicating severe photo-oxidative stress. In contrast, the LLHT treatment (T2) demonstrated remarkable resilience, with physiological and structural parameters closely resembling the control. The HLHT treatment (T4) caused intermediate damage, primarily through non-stomatal limitations over time. Our findings demonstrate a significant light–temperature interaction in N. hybrid. The thermophilic nature of N. hybrid was evident: high temperature mitigated the negative effects of low light, whereas low temperature, especially in combination with high light, acted synergistically to cause catastrophic damage to the photosynthetic apparatus. This study provides a mechanistic understanding of N. hybrid’s environmental adaptability, offering critical insights for its cultivation management under changing climate conditions, especially in high altitude and high latitude areas.

Introduction: The vivid colors of color-leafed plants endow plants with unique ornamental value. At present, there are many researches focusing on the mechanism of flower color formation, while there is less interesting research on color-leafed plants. As an excellent color-leafed plant, Heuchera micrantha has only been studied for its pigment content and physiological characteristics, and the mechanism of color-leafed formation has not been characterized yet.Methods: In this study, we used two varieties of Heuchera micrantha with green and red leaves as materials, and employed a combination of metabolomics and transcriptomics to reveal the molecular mechanisms underlying the formation of different color leaves.Results: Through observation of phenotype, analysis of metabolomics and transcriptomics, and combined analysis of multi-omics, it was found that differential metabolites and differentially expressed genes were enriched in flavonoid metabolism and related pathways. Nine MYB and bHLH transcription-factor candidates implicated in flavonoid metabolism were selected and functionally annotated; five are predicted to act as activators and four as repressors of the flavonoid biosynthetic pathway.Discussion: In summary, this study provides important insights into the coloring mechanism of color-leafed plants and provides gene reserves for subsequent targeted breeding.

Fragrance lotus (Nymphaea hybrid) is a tropical interspecific cultivar characterized by large flowers and high scent intensity, offering dual potential for ornamental commerce and natural fragrance extraction. Floral scent determines both economic value and pollinator attraction, yet the biosynthetic organs and metabolic routes remain undocumented. To fill this gap, single flowers of the high-aroma cultivar ‘Eldorado’ at full anthesis were dissected into petal (PE), stamen (ST) and pistil (PI); each organ was subjected to untargeted LC-MS/MS metabolomics and Illumina RNA-seq. Organ-specific gene–metabolite co-expression networks were constructed by pairwise integration of transcript and metabolite matrices. All three organs formed distinct clusters in principal-component space. Compared with PE, 6221, 3352 and 5891 differentially expressed genes (DEGs) together with 30, 24 and 39 differentially accumulated metabolites (DAMs) were identified in ST, PI and PE, respectively. The phenylpropanoid biosynthesis pathway (map00940) was the only route simultaneously enriched at both transcript and metabolite levels; 59 DEGs mapped to this pathway co-linearly with three scent-related DAMs. ST contained the highest concentration of scent-active volatiles; phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL) and benzaldehyde reductase (BAR) were all significantly up-regulated in this organ, driving the accumulation of p-coumaric acid that is subsequently channeled into benzyl alcohol via side-chain cleavage and BAR-mediated reduction, thereby generating the characteristic fragrance of Nymphaea. This study provides the first organ-level resolution of scent biosynthesis and metabolic flux partitioning in fragrance lotus, furnishing molecular targets for directed aroma improvement and efficient natural fragrance extraction.