Search Results (329)

Safflower (Carthamus tinctorius L.) is an important medicinal plant widely used as a source of natural pigments. Flower color is a key trait affecting both ornamental and commercial value; however, the roles of long non-coding RNAs (lncRNAs) in safflower flower coloration remain largely unclear. In this study, strand-specific RNA sequencing was performed on three safflower varieties with distinct flower colors at different floral developmental stages. A total of 4851 lncRNAs were identified, including 940 natural antisense transcript (NAT) pairs. Among them, lncRNA MSTRG.28365 was identified as a natural antisense transcript paired with CtCHS.7, a chalcone synthase-like gene potentially involved in flavonoid biosynthesis. Expression analysis revealed that CtCHS.7 was highly expressed in the red-flowered variety, whereas MSTRG.28365 exhibited an opposite expression pattern, suggesting a potential regulatory association. Co-expression analysis further indicated that CtCHS.7 was associated with genes putatively involved in flavonoid modification, including UDP-glycosyltransferases and cytochrome P450 enzymes. Functional assays showed that the recombinant CtCHS.7 protein could catalyze the production of downstream flavonoid-related metabolites, although the detected product differed from canonical naringenin chalcone. These findings suggest that lncRNAs may participate in flower color variation and flavonoid biosynthesis-related processes in safflower. This study provides candidate regulatory elements for future functional validation of safflower flower coloration mechanisms. Full article

Methylated flavonoids are abundant phytochemicals in Eucalyptus and are of interest because methylation can alter flavonoid diversity, bioactivity, and stability. However, the enzymes responsible for flavonoid methylation in eucalypts remain largely uncharacterised. We used comparative leaf transcriptomics of two species with contrasting flavanone profiles, together with protein-structure-guided candidate selection, to identify prospective O-methyltransferases involved in methylated flavonoid biosynthesis. Five candidate methyltransferases from E. eugenioides were cloned, heterologously expressed, and assayed against a panel of flavonoids and a chalcone precursor. The enzymes showed distinct substrate preferences and regioselectivities. EeOMT1 acted as a broad 7-O-methyltransferase, whereas EeOMT3–EeOMT5 preferentially methylated B- and C-ring hydroxyl groups, with differing capacities for sequential methylations at different sites. EeOMT2 was of particular interest because it methylated pinocembrin chalcone to alpinetin chalcone more efficiently than it converted the flavanone pinocembrin to alpinetin. Expression–metabolite analyses across E. eugenioides genotypes were consistent with roles for EeOMT2 and EeOMT1 in the in planta accumulation of 5-O- and 7-O-methylated flavanones, respectively. These findings support a revised model in which alpinetin biosynthesis proceeds, at least in part, through methylation of a chalcone precursor before flavanone formation. This work provides a foundation for elucidating flavonoid methylation pathways in plants and for engineering the production of tailored methylated flavonoids. Full article

Spatholobus suberectus is a traditional edible, ornamental, and medicinal vine with an abundant flavonoid content in its dried stems. An integrated metabolomic and transcriptomic analysis was conducted on its vegetative organs to identify flavonoid biosynthesis pathways. The results showed that: (1) a total of 268 flavonoids could be identified among all the vegetative organs, and stems accumulated most of them; (2) a total of 449,569,220 clean reads were retained from all the vegetative organs (many genes related to key enzymes of flavonoid biosynthesis and transcription factors were found in all the compared groups between different organs; among them, 77 genes showed high correlations with key flavonoids in different pathways); and (3) PAL (encoding phenylalanine ammonia-lyase), 4CL (encoding 4-coumarate: CoA ligase), C4H (encoding cinnamate-4-hydroxylase), CHS (encoding chalcone synthase), DFR (encoding dihydroflavonol 4-reductase) and others showed positive correlations with L-phenylalanine and various flavonoids, while FLS (encoding flavonol synthase) showed negative correlations with many flavonols and flavonoids, as revealed through integrated analysis. This study reveals the flavonoid biosynthesis characteristics in S. suberectus and provides new insights into the utilization of its biological resources. Full article

Verticillium wilt (VW), caused by the soil-borne phytopathogen Verticillium dahliae, is a devastating vascular disease that severely threatens global cotton production and causes substantial economic losses. Jasmonic acid (JA) signaling plays a crucial role in plant innate immunity; however, the molecular mechanisms governing JA biosynthesis during cotton defense responses to V. dahliae infection remain largely elusive. In this study, we identified that GhAOS1 (allene oxide synthase 1), a key rate-limiting enzyme-encoding gene in the JA biosynthetic pathway, was rapidly and significantly induced by V. dahliae infection and exclusively localized in chloroplasts. Functional analysis in GhAOS1-silenced cotton and overexpressing Arabidopsis plants demonstrated that GhAOS1 positively regulates resistance to V. dahliae. Transcriptome analysis of GhAOS1-silenced cotton plants showed that DEGs are significantly enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and α-linolenic acid metabolism pathways. Consistent with these findings, silencing GhAOS1 significantly reduced endogenous JA levels and suppressed the expression of defense-related genes and JA biosynthetic genes in cotton. Furthermore, we identified that the transcription factor GhWRKY70 directly binds to the W-box cis-acting element in the GhAOS1 promoter through Y1H, LUC, and EMSA, which activated GhAOS1 transcription. Silencing GhWRKY70 in cotton significantly enhanced plant susceptibility to V. dahliae and suppressed the expression of JA signaling pathway-related genes. Collectively, our results elucidate that GhWRKY70 positively regulates cotton resistance to VW by activating GhAOS1-mediated JA biosynthesis, revealing a novel GhWRKY70-GhAOS1 regulatory module that integrates JA signaling to coordinate cotton immune responses against V. dahliae. This study provides new insights into the molecular mechanism of JA-mediated defense and offers potential targets for molecular breeding of VW-resistant cotton. Full article

Extracellular DNA (eDNA) has gained attention as a danger signal between organisms because of the ecological implications of this mechanism and its great potential as a biological modulator in agriculture. Self-DNA and non-self DNA have been evaluated earlier, both as plant immune system elicitors. Here we show the effect of eDNA extracted from the bacterial phytopathogen Clavibacter michiganensis applied to tomato plants in different concentrations (50, 100 and 150 µg mL⁻¹). Monitoring morphology of the plants, spectrophotometric determinations and RT-qPCR assays showed a dose-dependent effect on plant growth and root development, activation of antioxidant enzymes such as catalase and superoxide dismutase, biosynthesis of secondary metabolites, including phenolic compounds and flavonoids, and differential expression of genes related to plant stress response, such as chalcone synthase and phenylalanine ammonia-lyase. Lower concentration treatments showed an increment in the variables as beneficial responses for agricultural practices, and the higher concentration (150 µg mL⁻¹) showed reduced or no effects on the evaluated variables. This work represents a step forward in the development of effective and more sustainable agricultural technology in crop production. Full article

The genus Cymbopogon comprises neocosmopolitan grasses widely used as medicinal plants and in the perfume, pharmaceutical and herbal product industries. Despite their economic relevance, these species are still considered orphan crops, with limited phytotechnical, genomic and evolutionary studies within the Poaceae family. In this study, we investigated the evolutionary relationships of Cymbopogon flexuosus and Cymbopogon winterianus, with a focus on differences in gene expression associated with the biosynthesis of secondary metabolites. De novo transcriptome assembly yielded 25,576 transcripts in C. flexuosus and 42,250 in C. winterianus. A total of 5318 and 8631 more informative differentially expressed transcripts (DETs) were identified in each mapping, among which 76 and 94 were associated with secondary metabolism pathways. When mapping the libraries against related species, the highest percentages of mapped reads per transcriptome and per gene (depth) were observed in Andropogon gerardi, Sorghum bicolor, Saccharum officinarum, Miscanthus sinensis, Miscanthus lutarioriparius and Zea mays. These results indicate A. gerardi, S. bicolor and Z. mays as the most promising genomic models for future studies within the genus Cymbopogon. Comparison of the expression of transcripts that are homologous to the precursor enzymes of terpenoids, phenylpropanoids, flavonoids and other secondary metabolites revealed a complex and non-linear interaction between the metabolic pathways in each species and it was not possible to predict the predominance of greater expression of a class of metabolites on a given species. Full article

The flower color of Rhododendron is primarily determined by anthocyanin biosynthesis, with cytochrome P450 CYP75 family members, particularly flavonoid 3′,5′-hydroxylase (F3′5′H), playing a central role. However, the composition and functional characterization of CYP75 genes in Rhododendron remain insufficiently explored. This study performed genome-wide identification of the CYP75 gene family using the Rhododendron simsii reference genome and functionally characterized the corresponding F3′5′H homolog cloned from Rhododendron × hybridum petals (red cultivar and pink cultivar). Seven RsCYP75 genes were identified, categorized into two subfamilies: RsCYP75A (A1–A5) and RsCYP75B (B1–B2), with a prominent cluster on chromosome 13. All encoded proteins contained a conserved cytochrome P450 domain and typical heme-binding motifs. Among these, RhCYP75A2 showed the highest expression level in red petals at full blooming period and was designated as RhF3′5′H. RhF3′5′H encodes a basic membrane protein with the characteristic F3′5′H motif, with its transcript most abundant in flowers. Transient overexpression of RhF3′5′H in red R. × hybridum petals resulted in a 9.74-fold increase in its transcript levels and a 1.25-fold increase in anthocyanin content compared to that in the control accompanied by the up-regulation of CHS, F3H, DFR and ANS. Conversely, RhF3′5′H silencing reduced anthocyanin accumulation but increased CHS and F3H transcript levels, suggesting a compensatory transcriptional response in the upstream anthocyanin pathway. Moreover, RhF3′5′H was heterologously expressed in E. coli Rosetta as an MBP fusion protein, purified, and identified by LC-MS/MS and ELISA. The protein showed the ability to promote anthocyanin accumulation. Molecular docking analysis demonstrated that RhF3′5′H can bind to naringenin and dihydrokaempferol. These results confirm that RhF3′5′H is a functional F3′5′H-type CYP75A enzyme and a positive regulator of anthocyanin accumulation in Rhododendron petals. This work enriches the CYP75 gene catalog in Rhododendron and provides candidate genes for future studies on flower color regulation and molecular breeding. Full article

Cadmium (Cd) contamination is widely recognized as a major risk factor affecting the security and quality of crop production. Watermelon (Citrullus lanatus) is a globally cultivated fruit that is susceptible to Cd stress. 24-Epibrassinolide (EBR), an active brassinosteroid, is essential for plant growth and abiotic stress responses. However, its protective role in watermelon under Cd stress remains unclear. This study elucidates the physiological and molecular processes underlying EBR-mediated alleviation of Cd toxicity in watermelon seedlings. The results showed that exogenous EBR application effectively mitigated Cd-induced growth inhibition through decreased Cd deposition, reduced the accumulation of reactive oxygen species (ROS), lowered membrane lipid peroxidation, and increased antioxidant capacity in watermelon leaves under Cd treatment. Transcriptome (RNA-Seq) analysis revealed that EBR triggered substantial reprogramming of gene expression patterns, identifying 530 differentially expressed genes (DEGs) in Cd + EBR co-treatment compared with Cd treatment alone, including 204 down-regulated genes and 326 up-regulated genes. These DEGs are vital for controlling several physiological processes, including phenylpropane metabolism, phenylpropanoid biosynthesis, endoplasmic reticulum’s protein production, cell wall organization, and others. Further physiological assays confirmed that EBR increased the activities of PAL and 4CL, the core enzymes driving phenylpropanoid biosynthesis, leading to a significant accumulation of total phenols and flavonoids. Together, the above results give concrete proof of the powerful functions of 24-EBR, acting as an enhancer of plant performance under Cd stress by enhancing the antioxidant system and by activating the phenylpropanoid pathway and its derived metabolic networks. Full article

Liver diseases, including fatty liver, hepatitis, and cirrhosis, remain major global health challenges due to their disruption of metabolic homeostasis and detoxification processes. Redox imbalance plays a central role in liver disease progression by promoting inflammation, hepatic stellate cell activation, mitochondrial dysfunction, and fibrogenesis. Although flavonoids have historically been considered direct reactive oxygen species (ROS) scavengers, emerging evidence indicates that their biological effect at physiological concentrations are primarily mediated through modulation of intracellular redox signalling rather than simple radical neutralisation. This review highlights flavonoids as redox-modulating agents capable of restoring hepatic redox homeostasis through coordinated regulation of molecular pathways. Mechanistically, flavonoids activate the Nrf2-Keap1 axis to enhance endogenous antioxidant defences, including heme oxygenase-1 and glutathione biosynthesis enzyme, while suppressing NF-κB-mediated pro-inflammatory signalling and modulating MAPK and PI3K/Akt pathways. They also regulate mitochondrial redox balance, supporting mitophagy, metabolic adaptation, and cellular resilience to oxidative stress. In addition, flavonoid biotransformation by the gut microbiome improves intestinal barrier integrity, reduces endotoxin-driven hepatic inflammation, and contributes to gut–liver crosstalk. Collectively, these mechanisms position dietary flavonoids as multi-target redox modulators with promising therapeutic potential in chronic liver disease, although further studies are needed to improve their bioavailability and clinical translation. Full article

Vitamin D3 deficiency is a common concern in dermatology and aging, yet its topical supplementation is restricted in the EU, and direct precursors are unstable. Stimulating the skin’s endogenous vitamin D3 biosynthesis using phytochemicals represents a promising alternative. This research reveals the potential of a natural Passiflora edulis (passion fruit) extract to stimulate vitamin D3 synthesis in the skin epidermis. An in silico screening of phytochemicals using molecular docking and Molecular Mechanics/Poisson–Boltzmann Surface Area (MM/PBSA) analysis was performed to identify compounds with affinity for the vitamin D receptor (VDR) and lathosterol oxidase, a key enzyme in the vitamin D3 biosynthesis pathway. While several flavonoids showed high predicted vitamin D receptor affinity, genistein, which has been reported to occur in P. edulis fruit extracts, exhibited favorable docking scores and was predicted to interact with the active site of lathosterol oxidase. Subsequent in vitro experiments on HaCaT keratinocytes and an ex vivo human skin model demonstrated that the P. edulis extract significantly increased vitamin D3 amount, both under UVB irradiation and, notably, in its absence. The P. edulis extract significantly increased vitamin D3 level in HaCaT keratinocytes by up to 274.04% without UVB exposure and demonstrated a synergistic effect with UVB, enhancing production by a further 61.41% compared to UVB alone (p < 0.001). In the ex vivo model, the extract alone increased vitamin D3 levels by 153.31%, and its combination with UVB resulted in a 54.82% higher yield compared to the UVB control (p < 0.01). These findings highlight the promising potential of P. edulis fruit extract as a natural cosmeceutical ingredient for enhancing cutaneous vitamin D3 synthesis, offering a novel approach to supporting skin health through dermatocosmetics. Full article

The ripe fruits of blackcurrant (Ribes nigrum L.) are rich in vitamin C, anthocyanins, and flavonoids. Besides being consumed fresh, the fruits can be processed into fruit juices, jams, wines, and other products, exhibiting considerable economic and nutritional value. Flavonoids are a class of important plant secondary metabolites with antioxidant, anti-inflammatory, and anti-cancer properties. Although previous studies have confirmed the involvement of multiple structural genes and transcription factors in flavonoid biosynthesis, the specific role of the dihydroflavonol 4-reductase (DFR) gene in regulating flavonoid accumulation during fruit development of blackcurrant remains to be clearly elucidated. In this study, we identified an RnDFR gene located in the nucleus and cytoplasm, which has the same expression trend as flavonoid content in fruit development stages. Overexpression of RnDFR improved the flavonoid accumulation and upregulated the expression levels of related structural genes (4CL, CHS, LDOX, ANR, and UFGT) in tomato. Transiently overexpressing RnDFR in blackcurrant fruit also increased the content of flavonoids and DFR enzyme activity, whereas silencing RnDFR resulted in the opposite effect. In addition, overexpression of RnDFR in tomato seedlings improved cold and drought tolerance by increasing flavonoid accumulation, reducing membrane lipid peroxidation damage and enhancing the activities of antioxidant enzymes. This study systematically reveals the key role of RnDFR in flavonoid biosynthesis and the enhancement of cold and drought tolerance, and offers an important theoretical basis for future efforts to optimize flavonoid content in blackcurrant and improve fruit nutritional quality. Full article

The ‘Pingguoli’ pear (Pyrus pyrifolia cv. Pingguoli) has a cultivation history spanning nearly one hundred years. Bud mutation selection is an important breeding method for the ‘Pingguoli’ pear. In this study, high-throughput sequencing technology (RNA-Seq) and non-targeted metabolomics (LC-MS/MS) were used to analyze the large-fruited bud mutation line (LFS) and normal type (NTF) of the ‘Pingguoli’ pear during the cell division (G1), rapid growth (G2), and mature stages (G3) of the fruit. The results showed that LFS exhibited a 46.32% increase in average single fruit weight (383.01 ± 54.72 g vs. 261.76 ± 10.79 g, p < 0.01) and a 19.10% decrease in soluble solids content (12.70 ± 0.94% vs. 15.40 ± 2.06%, p < 0.05) compared to NTF. Compared with the NTF, the content of total phenols and total flavonoids and the activity of antioxidant enzymes in the LFS fruits were significantly higher, while the contents of soluble sugar, reducing sugar, and soluble protein were significantly lower. Transcriptome analysis revealed that key metabolic pathways—including pentose and glucuronate interconversions, starch and sucrose metabolism, and cutin, suberine, and wax biosynthesis—were significantly enriched between NTF and LFS. These pathways may contain the specific differentially expressed genes (e.g., those involved in sugar metabolism and wax biosynthesis) identified as potential regulators of fruit size, appearance, and nutritional quality in the LFS. LC-MS/MS analysis identified key differentially accumulated metabolites, including L-arginine, caffeic acid, L-cysteine, pyridoxamine 5′-phosphate, adenosine-5′-phosphosulfate, neopentolactone D, chlorogenic acid, and gluconic acid, which are directly associated with the nutritional and antioxidant differences between LFS and NTF. The genes most related to metabolites in the three different developmental periods of the LFS and NTF were identified through combined analysis. These results provide insights for further research on bud mutation breeding and the quality formation mechanism of ‘Pingguoli’ pears. Full article

Background: Nymphaea atrans exhibits a gradual flower color transition from nearly white to rose-red during anthesis, yet the molecular mechanisms of this phenomenon remain unclear. In the present study, transcriptomic and metabolomic analyses were performed to systematically investigate anthocyanin accumulation patterns and regulatory mechanisms during the color transition of N. atrans. Methods: Petals were collected at three flowering stages: day 1 (D1), day 3 (D3), and day 5 (D5). Targeted metabolomics was performed using UPLC-ESI-MS/MS to profile anthocyanin and other flavonoid metabolites. Transcriptome analysis was conducted via RNA-seq. Differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) were identified, followed by functional enrichment and integration analysis. Results: The results revealed significant accumulation of seven anthocyanins, including cyanidin-3-O-arabinoside, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, cyanidin-3-O-(6″-O-acetyl)-glucoside, at stages D3 (day 3 after flowering, light pink petals) and D5 (day 5 after flowering, deep pink petals), accompanied by the upregulation of key enzyme-encoding genes, chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, di-hydroflavonol 4-reductase, and anthocyanidin synthase in the anthocyanin biosynthetic pathway. Genes involved in JA biosynthesis and key regulatory genes in the JA signaling pathway were significantly up-regulated, indicating that the JA signaling pathway may play an important regulatory role in the synthesis of anthocyanins in N. atrans. Conclusions: This study unravels the metabolic and molecular underpinnings of flower color transition in N. atrans, thereby establishing a theoretical basis for the targeted regulation of floral pigmentation and molecular breeding of ornamental water lilies. Full article

Epimedium brevicornu is an important medicinal plant in China, whose main bioactive components are flavonoid glycosides. UDP-glycosyltransferases (UGTs) play key roles in flavonoid glycosylation and metabolic diversification. In this study, transcriptome data from four representative production regions in Gansu Province were used to systematically identify and analyze the UGT gene family in E. brevicornu. A total of 359 UGT members were identified, and 168 homologous genes with clear expression evidence were obtained from four geographical populations. Molecular evolutionary analysis showed that most UGT genes were under purifying selection, whereas UGT2, UGT52, UGT57, UGT241, UGT269, and UGT271 exhibited significant signals of positive selection in specific lineages (p < 0.05). Protein interaction analysis indicated that many UGT proteins were closely associated with key enzymes involved in flavonoid biosynthesis, including CHS (TT4), CHI (TT5), F3H, FLS, and DFR, suggesting their potential involvement in flavonoid metabolism. Promoter analysis further revealed a high enrichment of ERF (11,169 occurrences) and MYB (7673 occurrences) transcription factor binding sites in the upstream regions of UGT genes. In addition, UGT57 and UGT241 showed significantly higher expression levels in the QLH population. Molecular docking analysis indicated relatively strong binding affinities with quercetin, with binding energies of −7.23 kcal/mol and −4.62 kcal/mol, respectively. These results suggest that the sequence variation and differential expression of UGT genes may be associated with flavonoid glycosylation and ecological adaptation in Epimedium. This study provides a basis for understanding the evolutionary characteristics and expression patterns of the UGT gene family and offers candidate genes for future studies on flavonoid metabolism. Full article

Naked oat (Avena nuda L.) is an important dual-purpose crop for grain and forage in cold regions; however, its high fatty acid content renders seeds prone to deterioration during storage. This study aimed to investigate the protective effects of zinc oxide nanoparticles (ZnO NPs) on artificially aged naked oat seeds and elucidate the underlying molecular mechanisms. Non-aged seeds (Naged) were subjected to artificial aging at 45 °C and 100% relative humidity for 24 h (Aged), followed by priming with 30 mg L⁻¹ ZnO NPs for 6 h (Daged). Antioxidant enzyme activities were determined spectrophotometrically, and transcriptome sequencing was performed on an Illumina platform to identify differentially expressed genes (DEGs) and enriched pathways. We found that ZnO NPs increased catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) activities by 3–4-fold, restored germination rate from 75% to 98%, and enhanced seed vigor index. A total of 21,403 DEGs were detected, with 15,841 stably expressed in response to nano-priming. Reactive oxygen species (ROS) burst rapidly induced up-regulation of AP2/EREBP transcription factor family members, which subsequently activated antioxidant enzyme genes to maintain cellular redox homeostasis. Metabolic pathway analysis demonstrated that the phenylpropanoid pathway was reprogrammed, characterized by down-regulated lignin biosynthesis and up-regulated flavonoid production, thereby enhancing ROS scavenging capacity. Additionally, the pentose phosphate pathway was activated to provide additional NADPH for antioxidant defense, and up-regulated ADP-glucose pyrophosphorylase (AGPase) facilitated starch accumulation. Notably, the 40S ribosomal protein S13 exhibited the highest connectivity in protein–protein interaction networks, was up-regulated 2.1-fold, and was enriched in post-translational modification processes. These findings suggest that nano-priming with ZnO NPs represents a promising biotechnological strategy for enhancing seed vigor and storability in naked oat, with potential applications in sustainable agriculture and the seed industry. Full article