A Comparative Metabolomics Study of Flavonoids in Radish with Different Skin and Flesh Colors (Raphanus sativus L.)

Different responses of canopy and shrub leaves to canopy nitrogen and water addition in warm temperate forest

Introduction

Understanding the effects of nitrogen deposition and increased rainfall on plants is critical for maintaining forest ecosystem services. Although previous studies primarily examined the effects of environmental changes on leaf functional traits, the underlying physiological and metabolic processes associated with these traits remain poorly understood and warrant further investigation.

Methods

To address this knowledge gap, we evaluated the influence of canopy nitrogen (25 kg ha-1 yr-1) and water (30% of the local precipitation) addition on leaf functional traits, diversity, and associated physiological and metabolic processes in the dominant species of tree and shrub layers.

Results

Only the interaction between nitrogen and water significantly reduced the functional richness (FRic) of the community. The other treatments had no notable effects on functional diversity. Importantly, the physiological processes of trees and shrubs showed different regulatory strategies. In addition, there were significant changes in 29 metabolic pathways of the tree, whereas only 18 metabolic pathways were significantly altered in shrub. Among the identified metabolic pathways, four were annotated multiple times, with amino acid metabolism being the most active.

Discussion

These regulatory processes enable the leaves to withstand external disturbances and maintain their relative stability under changing environmental conditions. The study findings underscore the limitations of previous research, which often relied on the direct application of treatments to the understory and so failed to accurately assess the effects of nitrogen and water on leaf functional traits. Future studies should adopt canopy-level nitrogen and water addition to better simulate the impacts of global environmental change.

Changes in Quality and Metabolites of Pickled Purple Radish During Storage

This study investigated the changes in the physicochemical properties and metabolites of pickled purple radish during storage. Pickles of purple radish ('Boraking') prepared by the addition of acetic acid and sugar were stored in the dark at 4 °C for 60 days. The color of the pickled purple radish changed from purple to pink, while the pickling solution changed from pink to purple. During storage, sucrose content gradually decreased, while glucose and fructose levels increased. LC-ESI-QToF-MS metabolomic analysis indicated that metabolites, including organic acids, amino acids, sulfur-containing compounds, lysophosphatidylcholine, lysophosphatidylethanolamine, and anthocyanins, were identified. The antioxidant capacity and color meter of pickled purple radish may undergo changes due to the altered levels of non-volatile compounds (cyanidins, adenosine, and amino acids) during storage. Anthocyanins had negative correlations with the color of pickled purple radish. The radical scavenging activity and ferric-reducing antioxidant power of pickled purple radish declined during storage. These findings emphasized the need for further research to develop processing and storage methods that enhance the bioactivity and stability of pickled purple radish.

Comparison of the characteristics of phenolic compounds in Se-enriched kiwifruit and conventional kiwifruit

While selenium (Se) fortification significantly influences plant secondary metabolism, there has been limited research on its effects on the phenolic profile of kiwifruit. This study aimed to characterize and compare the phenolic profile of Se-enriched and conventional kiwifruit. A total of 463 phenolic compounds were identified. Among these, nine common differential metabolites, including six flavonoids, two phenolic acids, and one lignan (massoniresinol), were identified between Se-enriched and conventional kiwifruit of the same variety. Further comparative analysis of diverse varieties indicated that massoniresinol was the sole differential metabolite. This metabolite was found to be significantly up-regulated in Se-enriched kiwifruit compared to conventional kiwifruit. In addition, correlation analysis showed that the total Se, phenol, and flavonoids content were highly significantly positively correlated with antioxidant activities in kiwifruit. These findings enhance our understanding of the phenolic composition in Se-enriched and conventional kiwifruit and provide a potential biomarker for distinguishing Se-enriched from conventional kiwifruit.

Effect of degrees of milling on the volatile compounds of cooked fragrant Simiao rice: differential volatiles obtained by GC-MS-based untargeted metabolomics

BACKGROUND

Alterations in the degrees of milling (DOM) could significantly influence the odor of rice. A gas chromatography-mass spectrometry (GC-MS)-based untargeted metabolomics method has been effectively employed to identify the differential volatiles among rice from various origins or varieties, although it has not been utilized to identify the differential volatiles among cooked rice with different DOM.

RESULTS

Fifty volatile compounds were detected in cooked brown rice (CBR), cooked medium-milled rice (CMMR) and cooked well-milled rice (CWMR) of the four fragrant Simiao rice by GC-MS. A comprehensive GC-MS-based untargeted metabolomics analysis revealed 25 differential volatiles among CBR, CMMR and CWMR. Among them, seven differential volatiles, namely hexanal, octanal, decanal, (E,E)-2,4-decadienal, vanillin, acetoin and pentanol, as well as one differential volatile (dibutyl phthalate), were determined as volatile markers for CBR and CMMR, respectively. Moreover, acetoin was identified to distinguish among CBR, CMMR, and CWMR of fragrant Simiao rice.

CONCLUSION

GC-MS-based untargeted metabolomics could be effectively applied to screen differential volatiles in cooked rice with different DOM. The 25 differential volatiles identified could significantly contribute to the distinctive odor in cooked fragrant Simiao rice with different DOM. © 2024 Society of Chemical Industry.

Analysis of rabbiteye blueberry metabolomes and transcriptomes reveals mechanisms underlying potassium-induced anthocyanin production

Environmental factors play an important role in anthocyanin biosynthesis, and potassium, an essential nutrient for blueberry growth, can act as an enzyme activator. However, few reports exist on the transcriptional and anthocyanin metabolic changes in blueberries regulated by potassium. The results indicated that potassium treatment significantly increased the contents of malvidin, petunidin, and delphinidin in blueberry fruits and accelerated early color development, particularly favoring the accumulation of darker pigments such as malvidin, petunidin, and delphinidin when applied at the young fruit stage. Transcriptome analysis identified 102 glucose metabolism-related genes and 12 differential potassium transport genes potentially involved in potassium-mediated anthocyanin synthesis and accumulation, with AKT1 and KUP potassium transporters being upregulated under potassium fertilization. In the anthocyanin biosynthesis pathway, 13 genes, including UFGT, F3H, CHI, HCT, C12RT1, DFR, and F3'5'H, were closely linked to flavonoid and anthocyanin metabolite synthesis regulated by potassium. Furthermore, potassium treatment markedly enhanced the activities of key enzymes, F3H, F3'5'H, and UFGT, in the anthocyanin synthesis pathway of blueberry fruits. Overall, these findings elucidate the influence of potassium application timing on anthocyanin synthesis and provide valuable insights into the molecular mechanisms governing anthocyanin biosynthesis in blueberries.

Exploring the Effects of Gracilaria lemaneiformis Polysaccharides on the Fecal Microbiota and Fecal Metabolites of Fattening Pigs Based on 16S rDNA and Metabolome Sequencing

Sixty Duroc × (Landrace × Yorkshire) castrated male finishing pigs were randomly divided into negative control (NC) and gracilaria lemaneiformis polysaccharides (GLP) groups to study the effects of GLP on the fecal microbiota and fecal metabolites of fattening pigs. The NC group was fed a basic diet, and the GLP group was fed a basic diet supplemented with 0.1% GLP. The diversity of the species and the fecal metabolites were analyzed using 16S rDNA sequencing and metabolome sequencing, respectively. The serum immune and antioxidant indices were analyzed using the ELISA assay. The abundances of hazardous bacteria such as Proteobacteria at the phylum level and Shigella at the genus level were extremely significantly decreased (p < 0.01) and those of beneficial bacteria such as Firmicutes at the phylum level (p < 0.01), Clostridium at the genus level (p < 0.01), and Lactobacillus at the genus level (p < 0.05) were significantly increased in the GLP group compared with the NC group. A total of 41 differentially expressed metabolites were identified. The expression of anti-inflammatory and antioxidant active substances, such as methyl cinnamate, protopanaxatriol, and isovanillic acid, was elevated in the GLP group. The ELISA assay showed increased GSH-Px activity (p < 0.01), T-AOC (p < 0.01), IgG (p < 0.01), IgA (p < 0.05), and IgM (p < 0.05) in the GLP group. These results indicate that dietary GLP supplementation can improve the antioxidant ability, anti-inflammatory ability, and immune level of fattening pigs by regulating fecal flora and metabolites and could be used as a functional feed additive.

Integrated Transcriptomic and Metabolomic Analysis Revealed Regulatory Mechanisms on Flavonoids Biosynthesis in the Skin of Passion Fruit (Passiflora spp.)

Passion fruit is one of the most famous fruit crops in tropical and subtropical regions due to its high edible, medicinal, and ornamental value. Flavonoids, a class of plant secondary metabolites, have important health-related roles. In this study, a total of 151 flavonoid metabolites were identified, of which 25 key metabolites may be the main contributors to the purple phenotype. Using RNA sequencing, 11,180 differentially expressed genes (DEGs) were identified. Among these, 48 flavonoid biosynthesis genes (PAL, 4CL, C4H, CHS, CHI, F3H, DFR, ANS, and UFGT) and 123 transcription factors were identified. Furthermore, 12 distinct modules were identified through weighted gene coexpression network analysis, of which the brown module displays a robust positive correlation with numerous flavonoid metabolites. Overexpression of PeMYB114 significantly promoted flavonoids accumulation in tobacco leaves. Our study provided a key candidate gene for molecular breeding to improve color traits in passion fruit.

Why the adventitious roots of poplar are so colorful: RNAseq and metabolomic analysis reveal anthocyanin accumulation in canker pathogens-induced adventitious roots in poplar

MAIN CONCLUSION

This study revealed a substrate-level synthesis of pigment cyanidin-3-O-glucoside and the redirection of metabolomic flux in the flavonoid/anthocyanin biosynthesis pathway in poplar adventitious roots (ARs) induced by stem canker pathogens. Recently, we observed a novel allometry on poplar stems, with copious colorful adventitious roots (ARs) induced by fungal canker pathogens. Here, we reveal chemical, physiological, and molecular mechanisms of AR coloration in poplar-pathogens (Valsa sordida/Botrosphaeria dothidea) interaction system using our phloem girdling-inoculation system. Light-induced coloration in ARs: red/rosy under sunlight, and milky white under shading. Chemical and metabolomic analyses indicated that numerous (93 in all 110) and high relative intensities/contents of flavonoids metabolites (mainly including flavonols, flavones, and anthocyanins class) accumulate in red ARs, some flavones and anthocyanins metabolites all contribute to the color of poplar ARs, and cyanidin-3-O-glucoside is the most abundant colorant. Integrated analysis of metabolomic and transcriptomic analysis suggested that sunlight exposure redirected the metabolomic flux from the flavonoid biosynthesis pathway to the flavonols and flavones branch pathways, induced by the upregulation of FLS (flavonol synthase/flavanone 3-hydroxylase) and other structural genes. The anthocyanins metabolomic analysis and the downregulation of the ANS (anthocyanin synthase) gene illustrated a retard of metabolomic flux from leucoanthocyanidins to anthocyanidins. Metabolomic results and the upregulation of the gene BZ1 (Bronze 1, anthocyanin 3-O-glucosyltransferase) illustrated that sunlight triggered a rapid biosynthesis of anthocyanin metabolites in poplar ARs, which based on the substrate level of anthocyanidins. Transcriptomic and RT-qPCR analyses showed that transcriptional factor MYB113, HY5 (Elongated hypocotyl 5), and COP1 (Ring-finger protein CONSTITUTIVE PHOTOMORPHOGENIC1) genes positively regulated the expression of the flavonoid/anthocyanin biosynthesis structural genes (such as the BZ1, FLS and LAR gene) in both sunlight-exposed red ARs and white ARs after light-exposure, suggesting sunlight induces anthocyanins biosynthesis through the interaction between "MBW" complex and COP1-HY5 module. Moreover, one SPL gene (squamosa promoter-binding-like protein gene, target of miR156, and one component of miR156-SPL module) was down-regulated in sunlight-exposed poplar ARs, implying the biosynthesis flavonoid/anthocyanin be regulated at the posttranscriptional level. This study provides a potential AR experimental system for research on flavonoid/anthocyanin biosynthesis in tree species.

The Effect of Seasonal and Annual Variation on the Quality of Polygonatum Cyrtonema Hua Rhizomes

This study aims to reveal the interannual and seasonal variations in functional components in Polygonatum cyrtonema Hua. rhizomes and evaluate whether the variations significantly affect the quality of rhizomes as a traditional Chinese herbal medicine. The interannual and seasonal variations in total flavonoid content and total saponin content were analyzed. The global dynamic variation in secondary metabolites in the rhizomes during a five-year growth period and in two traditional harvesting seasons were investigated based on metabolomics method. Results clearly showed that the functional components in P. cyrtonema rhizomes exhibited a significant increase in accumulation during the one- to four-year growth period and a significant decrease in accumulation during the four- to five-year growth period. The most active accumulation occurred during the three- to four-year growth period. Drastic variations in functional components occurred from spring to autumn. The significant interannual variation and drastic seasonal variation were strongly associated with the enrichment in some pathways related to the biosynthesis of secondary metabolites and the metabolisms of amino acids. The interannual and seasonal variations in functional components significantly affected the quality of P. cyrtonema rhizomes. The four-year-old rhizomes had the most superior quality due to their higher content of functional components and much more newly formed components. The rhizomes harvested in spring or autumn had unequal quality because of their significant differences in composition and content of functional components. Specifically, the rhizomes from spring contained more flavonoids, alkaloids, and phenolic acids, while those from autumn comprised more steroids. In conclusion, this study reveals that the interannual and seasonal variations in functional components can significantly affect the quality of P. cyrtonema rhizomes as a traditional Chinese herbal medicine. This study provides foundational insights and theoretical guidance for determining an optimal cultivation period to obtain medicinal rhizomes with superior quality. It also offers a strategy for harvesting medicinal rhizomes in two different seasons to achieve unequal quality.

Integrated metabolomics and transcriptomics analysis provides insights into biosynthesis and accumulation of flavonoids and glucosinolates in different radish varieties

Radish is an important vegetable worldwide, with wide medicinal functions and health benefits. The quality of radish, strongly affected by phytochemicals like flavonoids and glucosinolates, are quite different depending on the radish varieties. However, the comprehensive accumulation profiles of secondary metabolites and their molecular regulatory mechanisms in different radish cultivars remain unclear thus far. Herein, we comprehensively analyzed the secondary metabolite and gene expression profiles of the flesh and skin of four popular radish varieties with different flesh and/or skin colors, using UPLC-MS/MS-based metabolomics and transcriptomics approach combined with RT-qPCR. The results showed that altogether 352 secondary metabolites were identified in radish, of which flavonoids and phenolic acids accounted for 60.51% of the total. The flesh and skin of each variety exhibited distinct metabolic profiles, making them unique in coloration, flavor, taste, and nutritional quality. The differential metabolites were mostly enriched in flavonoid biosynthesis, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and glucosinolate biosynthesis pathway. Further, 19 key genes regulating the differential accumulation of flavonoids among different radish varieties were identified, such as RsCHS, RsCCOAMT, RsF3H, RsFLS, RsCYP75B1, RsDFR, and RsANS that were significantly upregulated in red-colored radish tissue. Also, 10 key genes affecting the differential accumulation of glucosinolates among different varieties were identified, such as RsCYP83B1, RsSUR1, and RsST5a that were significantly increased in the skin of green radish. Moreover, systematical biosynthetic pathways of flavonoids and glucosinolates and co-expression networks between genes and metabolites were constructed based on integrative analysis between metabolomics and transcriptomics. Our findings provide a novel insight into the mechanisms of radish quality formation, thereby providing a molecular basis for breeding and cultivation of radish with excellent nutritional quality.

A Comparative Metabolomics Study of the Potential Marker Compounds in Feces from Different Hybrid Offspring of Huainan Pigs

As a notable native Chinese genetic population, the Huainan pig has an exceptional meat quality but a low percentage of lean meat and subpar genetic performance. To better exploit the superior genetic traits of the Huainan pig and address knowledge gaps regarding the optimization of its hybrid offspring, this study used Huainan pigs as the maternal line and bred them with Yorkshire, Landrace, and Berkshire sires. This approach produced three hybrid combinations: Yorkshire × Huainan (YH), Landrace × Huainan (LH), and Berkshire × Huainan (BH). The body size, fat ratio, and average backfat thickness of these hybrid progeny were evaluated under the same feeding management and nutritional circumstances. The results revealed that the average backfat thickness of YH was significantly lower than that of LH and BH. In order to better understand the causes of these variations, fecal samples were taken from three pigs in each group for metabolomic analysis. A total of 2291 metabolites were identified, including benzene derivatives (16.6%), amino acids and their metabolites (14.5%), and organic acids (13.4%), with pyruvaldehyde and norethindrone acetate elevated in YH compared to LH and BH. In addition, the three hybrid pig groups commonly exhibited differences in the "glycerophospholipid metabolism" pathway. This variation may also contribute to differences in their fat ratio and backfat thickness. Our findings provide a novel perspective on the role of hybrid vigor in advancing the genetic population of Huainan pigs, while also revealing the unique metabolic characteristics of the YH with regard to fat deposition. This study is expected to enhance the conservation and effective utilization of genetic resources within the Huainan pig population.

Transcriptomics and metabolomics revealed the molecular basis of the color formation in the roots of Panax notoginseng

Panax notoginseng is a traditional Chinese medicine rich in many pharmacological components. The root of the 'Miaoxiang Sanqi No. 2' is yellow or greenish yellow, while a novel cultivar-'Wenyuan Ziqi No. 1' shows purple root and is thought to have high medicinal value. Little information is available about the anthocyanin biosynthesis in P. notoginseng root. In this study, we compared the 'Miaoxiang Sanqi No. 2' and 'Wenyuan Ziqi No. 1' in morphological, transcriptional and metabolic levels. The results showed that purple rich in the periderm, rhizome and phloem around cambium of the 'Wenyuan Ziqi No. 1' root and cyanidin 3-O-galactoside was the main anthocyanin causing purple. Moreover, 'Wenyuan Ziqi No. 1' highly accumulated in 155 metabolites, including flavones, phenylpropanoids and lipids. Transcriptome data showed that phenylpropanoid biosynthesis pathway genes are highly expressed in 'Wenyuan Ziqi No. 1'. Conjoint analysis showed that anthocyanin biosynthesis pathway substances were highly accumulated in 'Wenyuan Ziqi No. 1', and the expression level of structural genes involved in anthocyanin biosynthesis pathway was higher in 'Wenyuan Ziqi No. 1'. Meanwhile, eight R2R3-MYB genes that might be involved in anthocyanin biosynthesis were identified. The comprehensive analysis of two cultivars provides new insights into the understanding of root coloration in P. notoginseng.

Traditional Processing Can Enhance the Medicinal Effects of Polygonatum cyrtonema by Inducing Significant Chemical Changes in the Functional Components in Its Rhizomes

The aims of this study were to explore the significant chemical changes in functional components induced by the traditional processing method and evaluate whether this method based on nine cycles of steaming and drying can effectively enhance the medicinal effects of Polygonatum cyrtonema rhizome. A global analysis on dynamic changes in secondary metabolites during nine processing cycles was performed, and the significantly differentially accumulated secondary metabolites were initially identified based on the secondary metabolome. Unsupervised principal component analysis (PCA), hierarchical clustering analysis (HCA), and orthogonal partial least squares discriminant analysis (OPLA-DA) on secondary metabolites clearly showed that processing significantly increased the global accumulation of secondary metabolites in processed P. cyrtonema rhizomes compared to unprocessed crude rhizomes. The first six processing cycles induced drastic changes in the accumulation of functional components, while the last three did not induce further changes. The accumulations of most functional components were significantly enhanced after the first three cycles and stabilized after six cycles; meanwhile, the first three cycles also led to numerous new components. However, the enhancing effects were unavoidably reversed or weakened under continued processing lasting 6-9 cycles. Furthermore, continued processing also reduced the contents of a small number of original components to undetectable levels. Processing induced some significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, among which the first three processing cycles enhanced the synthesis of various secondary metabolites and significantly affected the metabolisms of amino acids. In conclusion, this study not only reveals that processing can effectively enhance the medicinal effects, by two main mechanisms including enhancing chemical synthesis and inducing structural transformation of functional components, but also provides theoretical guidance for the optimization of the traditional processing method based on nine cycles of steaming and drying for achieving optimal effects on enhancing the medicinal effects of P. cyrtonema rhizome.

Investigation of the Functional Components in Health Beverages Made from Polygonatum cyrtonema Rhizomes Provides Primary Evidence to Support Their Claimed Health Benefits

This study aims to understand the functional component compositions of traditional herbal health beverages made from Polygonatum cyrtonema rhizomes and to reveal the pharmacodynamic chemical basis for their claimed health benefits. Two traditional methods, rhizome decoction and rhizome infusion, were used to make health herbal beverages, including "Huangjin" tea and "Huangjin" wine, respectively. The secondary metabolites of "Huangjin" beverages were investigated and compared by widely targeted metabolomics. The results clearly showed that the major functional components in "Huangjin" beverages were phenolic acids, flavonoids, and alkaloids. The "Huangjin" wine has a greater variety of flavonoids and alkaloids than "Huangjin" tea, and the functional components in "Huangjin" wine were more abundant than those in "Huangjin" tea. Homoisoflavones and amide alkaloids were the dominating flavonoids and alkaloids in "Huangjin" wine, respectively. Continuous rhizome infusion could not increase the content of functional components in "Huangjin" wine. In conclusion, this study not only provides primary evidence to support the claimed health benefits of "Huangjin" beverages but also suggests that making traditional herbal beverages by rhizome infusion has superior health benefits than making them by rhizome decoction, which is attributed to the higher yields of functional components extracted by Chinese liquor than hot water. Therefore, Chinese liquor shows advantages in its use as a superior binary ethanol-water solvent in making herbal health beverages to enhance the solubility of poorly water-soluble functional components.

Characterization of flavor and taste profile of different radish (Raphanus Sativus L.) varieties by headspace-gas chromatography-ion mobility spectrometry (GC/IMS) and E-nose/tongue

A comprehensive study of the overall flavor and taste profile of different radishes is lacking. This study systematically compared the volatile profile of six radish varieties using HS-GC-IMS and their correlation with the E-nose analysis. Organic acids and amino acids were quantified, and their association with the E-tongues analysis was explored. A total of 73 volatile compounds were identified, with diallyl sulfide and dimethyl disulfide being the primary sulfides responsible for the unpleasant flavor in radish. Compared to other varieties, cherry radishes boast a significantly higher concentration of allyl isothiocyanate, which likely contributes to their characteristic radish flavor. Moreover, oxalic acid was identified as the most abundant organic acid in radish, accounting for over 97% of its content, followed by malic acid and succinic acid. In conclusion, the distinct flavor and taste characteristics of different radish varieties partially explain their suitability for diverse culinary preferences.

Widely Targeted Metabolomics Provides New Insights into Nutritional Profiling and Reveals the Flavonoid Pathway of Pea (Pisum sativum L.)

To learn more about the nutritional composition and health benefits for human consumers of peas, we used a widely targeted metabolomics-based approach to reveal the metabolite components from three main varieties, and a total of 1095 metabolites were identified. A comparison of 487 differentially accumulated metabolites shared among three varieties of fresh and dried peas found most of the amino acids and derivatives were downregulated and most of the lipids and flavonoids were upregulated in dried peas. Furthermore, comparing the main nutrient profiles exclusively showed that there were few differences in free fatty acids, sugars, vitamins, and alkaloids between dried and fresh peas. Peas are especially enriched with B-group vitamins. Through detailed identification and classification, the flavonoid pathway of peas was revealed; a variety of glycosylated derivatives from kaempferol, quercetin, and luteolin were confirmed to be abundant in peas. It was also found that isoflavones are richer in peas than in many other plants, and putatively the isoflavone synthesis pathway originates from liquiritigenin and naringenin. Our study not only offers guidance for understanding the nutritional components of peas, but also provides the basis for healthy diet analysis of the edible value and health benefits of peas.

Chemical composition analysis and transcriptomics reveal the R2R3-MYB genes and phenol oxidases regulating the melanin formation in black radish

Melanins are dark-brown to black-colored biomacromolecules which have been thoroughly studied in animals and microorganisms. However, the biochemical and molecular basis of plant melanins are poorly understood. We first characterized melanin from the black radish (Raphanus sativus var. niger) 'HLB' through spectroscopic techniques. p-Coumaric acid was identified as the main precursor of radish melanin. Moreover, a joint analysis of transcriptome and coexpression network was performed for the two radish accessions with black and white cortexes, 'HLB' and '55'. A set of R2R3-type RsMYBs and enzyme-coding genes exhibited a coexpression pattern, and were strongly correlated with melanin formation in radish. Transient overexpression of two phenol oxidases RsLAC7 (laccase 7) or RsPOD22-1 (peroxidase 22-1) resulted in a deeper brown color around the infiltration sites and a significant increase in the total phenol content. Furthermore, co-injection of the transcriptional activator RsMYB48/RsMYB97 with RsLAC7 and/or RsPOD22-1, markedly increased the yield of black extracts. Spectroscopic analyses revealed that these extracts are similar to the melanin found in 'HLB'. Our findings advance the understanding of structural information and the transcriptional regulatory mechanism underlying melanin formation in radish.

Accumulation mechanism of metabolite markers identified by machine learning between Qingyuan and Xiushui counties in Polygonatum cyrtonema Hua

Polygonatum cyrtonema Hua is a traditional Chinese medicinal plant acclaimed for its therapeutic potential in diabetes and various chronic diseases. Its rhizomes are the main functional parts rich in secondary metabolites, such as flavonoids and saponins. But their quality varies by region, posing challenges for industrial and medicinal application of P. cyrtonema. In this study, 482 metabolites were identified in P. cyrtonema rhizome from Qingyuan and Xiushui counties. Cluster analysis showed that samples between these two regions had distinct secondary metabolite profiles. Machine learning methods, specifically support vector machine-recursive feature elimination and random forest, were utilized to further identify metabolite markers including flavonoids, phenolic acids, and lignans. Comparative transcriptomics and weighted gene co-expression analysis were performed to uncover potential candidate genes including CHI, UGT1, and PcOMT10/11/12/13 associated with these compounds. Functional assays using tobacco transient expression system revealed that PcOMT10/11/12/13 indeed impacted metabolic fluxes of the phenylpropanoid pathway and phenylpropanoid-related metabolites such as chrysoeriol-6,8-di-C-glucoside, syringaresinol-4'-O-glucopyranosid, and 1-O-Sinapoyl-D-glucose. These findings identified metabolite markers between these two regions and provided valuable genetic insights for engineering the biosynthesis of these compounds.

Identification strategy of Fructus Gardeniae and its adulterant based on UHPLC/Q-orbitrap-MS and UHPLC-QTRAP-MS/MS combined with PLS regression model

Fructus Gardeniae (FG) is the desiccative and ripe fruits of Gardenia jasminoides Ellis in the Rubiaceae family, which is a commonly used in traditional Chinese medicine (TCM) for clearing away heat, detoxification, relieving restlessness, and eliminating blood stasis. At the same time, it has also been announced as the first batch of TCM with homology of medicine and food. Fructus Gardeniae Grandiflorae (FGG), the fruit of Gardenia jasminoides Ellis var. grandiflora Nakai (Rubiaceae), is a common counterfeit herbal medicine of FG, which still appears in the TCM market, and causes a certain degree of confusion. In order to effectively distinguish FG and its adulterant, the compounds in these two species were thoroughly characterized firstly by ultrahigh-performance liquid chromatography/quadrupole-orbitrap mass spectrometry (UHPLC/Q-Orbitrap MS). Furthermore, a pseudo-targeted metabonomics method with 60 targeted ion pairs was established based on UHPLC-triple quadrupole-linear ion trap mass spectrometry (UHPLC-QTRAP-MS) for discrimination. Multivariate statistical analysis showed that FG and FGG were clustered obviously, and 13 significantly differential markers were screened out by variable importance for projection (VIP) > 1 and p < 0.05 for the construction of the partial least squares (PLS) regression prediction model. The validation of the model proved that its prediction ability was quite satisfactory. Moreover, based on the absolute quantitative analysis of these 13 characteristics, the quality control standards of FG and FFG were established. In summary, an integral method of pseudo-targeted metabonomics combined with chemometrics analysis and a PLS regression model was proposed to provide an effective identification strategy for discrimination FG and FGG.

Flavonoids‑targeted metabolomic analysis following rice yellowing

Flavonoids are the main metabolites responsible for yellowing of rice. However, the accumulation pattern of flavonoids and the metabolic basis of flavonoid biosynthesis during rice yellowing remain unclear. Thus, flavonoid-targeted metabolomics was used to investigate the composition and concentration of flavonoids in rice during yellowing. The results indicated the differential flavonoids at Month 3 and Month 5 of storage were more in composition and concentration with higher antioxidant capacity. Accumulated flavonoids were mainly flavones, flavonols, isoflavones, and anthocyanidins, of which rutin, farrerol, naringenin, cyanidin 3-rutinoside, and diosmetin were the indicators of rice yellowing. Metabolic association among flavonoids demonstrated the formation of yellow pigments was jointly induced by flavones, flavonols, isoflavones, and anthocyanidins metabolism. Examination of flavonoid metabolism presented in this study enhanced current understanding of the relationship between flavonoid metabolites and development of rice yellowing. It also offers a theoretical basis for targeted prediction of rice yellowing in the future.

A comparative metabolomics study of polyphenols in highland barley (Hordeum vulgare L.) grains with different colors

Highland barley (HB) grains are gaining increasing popularity owing to their high nutritional merits. However, only limited information is available on the metabolic profiles of HB grains polyphenols, especially the difference of polyphenols in different colors of HB. In this study, we determined the metabolic profiles of black, blue, and white HB grains via an ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based metabolomics. A total of 402 metabolites were identified, among which 198, 62, and 189 metabolites displayed different accumulation patterns in the three comparison groups (WHB vs. BKHB, WHB vs. BEHB, BEHB vs. BKHB), respectively. In particular, flavonoids and phenolic acids contents displayed considerable differences among the three HB cultivars. The phenolics content of black HB was relatively high. Additionally, "Flavonoid biosynthesis" and "flavone and flavonol biosynthesis" were the significantly enriched pathways. In conclusion, this study provides comprehensive insights into the adequate utilization and development of novel HB-based functional foods.

The Chemical Composition and Transcriptome Analysis Reveal the Mechanism of Color Formation in Tea (Camellia sinensis) Pericarp

To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. Jinxuan), and Baitangziya (Camellia sinensis L. var. Baitang). Results of biochemical analysis revealed that low chlorophyll content and low chlorophyll/carotene ratio may be the biochemical basis for albino characteristics in the 'Zhongbaiyihao' pericarp. The differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, including DFR, F3'5'H, CCoAOMT, and 4-coumaroyl-CoA, were highly expressed in the purple 'Baitangziya' pericarp. In the chlorophyll synthesis of white pericarp, GUN5 (Genome Uncoupled 5) and 8-vinyl-reductase both showed high expression levels compared to the green one, which indicated that albino 'Zhongbaiyihao' pericarp had a higher chlorophyll synthesis capacity than 'Jinxuan'. Meanwhile, chlorophyllase (CLH, CSS0004684) was lower in 'Baitang' than in 'Jinxuan' and 'Zhongbaiyihao' pericarp. Among the differentially expressed transcription factors, MYB59, WRKY41-like2 (CS ng17509), bHLH62 like1 (CS ng6804), and bHLH62-like3 (CSS0039948) were downregulated in Jinxuan pericarp, suggesting that transcription factors played a role in regulating tea pericarp coloration. These findings provide a better understanding of the molecular mechanisms and theoretical basis for utilizing functional components of tea pericarp.

Metabolomics analysis reveals the differences between Abrus cantoniensis Hance and Abrus mollis Hance

BACKGROUND

Abrus cantoniensis Hance. (Ac) and Abrus mollis (Am), two edible and medicinal plants with economic value in southern China, belong to the Abrus genus. Due to its growth characteristics, Am often replaces Ac in folk medicine. However, the latest National Pharmacopeia of China only recommends Ac. The differences in the metabolite composition of the plants are directly related to the differences in their clinical efficacy.

RESULTS

The difference in metabolites were analyzed using an untargeted metabolomic approach based on ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC‒ESI‒MS/MS). The roots (R), stems (S) and leaves (L) of the two varieties were examined, and 635 metabolites belonging to 8 classes were detected. A comparative study revealed clear variations in the metabolic profiles of the two plants, and the AmR group had more active ingredients (flavonoids and terpenoids) than the AcR group. The metabolites classified as flavonoids and triterpene saponins showed considerable variations among the various samples. Both Ac and Am had unique metabolites. Two metabolites (isovitexin-2''-xyloside and soyasaponin V) specifically belong to Ac, and nine metabolites (vitexin-2"-O-galactoside, ethyl salicylate, 6-acetamidohexanoic acid, rhein-8-O-glucoside, hederagenin-3-O-glucuronide-28-O-glucosyl(1,2)-glucoside, methyl dioxindole-3-acetate, veratric acid, isorhamnetin-3-O-sophoroside-7-O-rhamnoside, and isorhamnetin-3-O-sophoroside) specifically belong to Am.

CONCLUSIONS

The metabolite differences between Ac and Am cause the differences in their clinical efficacy. Our findings serve as a foundation for further investigation of biosynthesis pathways and associated bioactivities and provide guidance for the clinical application of traditional Chinese medicine.

Integrated Transcriptome and Metabolome Analysis Revealed the Causal Agent of Primary Bud Necrosis in 'Summer Black' Grape

Primary bud necrosis of grape buds is a physiological disorder that leads to decreased berry yield and has a catastrophic impact on the double cropping system in sub-tropical areas. The pathogenic mechanisms and potential solutions remain unknown. In this study, the progression and irreversibility patterns of primary bud necrosis in 'Summer Black' were examined via staining and transmission electron microscopy observation. Primary bud necrosis was initiated at 60 days after bud break and was characterized by plasmolysis, mitochondrial swelling, and severe damage to other organelles. To reveal the underlying regulatory networks, winter buds were collected during primary bud necrosis progression for integrated transcriptome and metabolome analysis. The accumulation of reactive oxygen species and subsequent signaling cascades disrupted the regulation systems for cellular protein quality. ROS cascade reactions were related to mitochondrial stress that can lead to mitochondrial dysfunction, lipid peroxidation causing damage to membrane structure, and endoplasmic reticulum stress leading to misfolded protein aggregates. All these factors ultimately resulted in primary bud necrosis. Visible tissue browning was associated with the oxidation and decreased levels of flavonoids during primary bud necrosis, while the products of polyunsaturated fatty acids and stilbenes exhibited an increasing trend, leading to a shift in carbon flow from flavonoids to stilbene. Increased ethylene may be closely related to primary bud necrosis, while auxin accelerated cell growth and alleviated necrosis by co-chaperone VvP23-regulated redistribution of auxin in meristem cells. Altogether, this study provides important clues for further study on primary bud necrosis.

Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV)

Recently, a novel poplar mosaic disease caused by bean common mosaic virus (BCMV) was investigated in Populus alba var. pyramidalis in China. Symptom characteristics, physiological performance of the host, histopathology, genome sequences and vectors, and gene regulation at the transcriptional and posttranscriptional levels were analyzed and RT-qPCR (quantitative reverse transcription PCR) validation of expression was performed in our experiments. In this work, the mechanisms by which the BCMV pathogen impacts physiological performance and the molecular mechanisms of the poplar response to viral infection were reported. The results showed that BCMV infection decreased the chlorophyll content, inhibited the net photosynthesis rate (Pn) and stomatal conductance (Gs), and significantly changed chlorophyll fluorescence parameters in diseased leaves. Transcriptome analysis revealed that the expression of the majority of DEGs (differentially expressed genes) involved in the flavonoid biosynthesis pathway was promoted, but the expression of all or almost all DEGs associated with photosynthesis-antenna proteins and the photosynthesis pathway was inhibited in poplar leaves, suggesting that BCMV infection increased the accumulation of flavonoids but decreased photosynthesis in hosts. Gene set enrichment analysis (GSEA) illustrated that viral infection promoted the expression of genes involved in the defense response or plant-pathogen interaction. MicroRNA-seq analysis illustrated that 10 miRNA families were upregulated while 6 families were downregulated in diseased poplar leaves; moreover, miR156, the largest family with the most miRNA members and target genes, was only differentially upregulated in long-period disease (LD) poplar leaves. Integrated transcriptome and miRNA-seq analyses revealed 29 and 145 candidate miRNA-target gene pairs; however, only 17 and 76 pairs, accounting for 2.2% and 3.2% of all DEGs, were authentically negatively regulated in short-period disease (SD) and LD leaves, respectively. Interestingly, 4 miR156/SPL (squamosa promoter-binding-like protein) miRNA-target gene pairs were identified in LD leaves: the miR156 molecules were upregulated, but SPL genes were downregulated. In conclusion, BCMV infection significantly changed transcriptional and posttranscriptional gene expression in poplar leaves, inhibited photosynthesis, increased the accumulation of flavonoids, induced systematic mosaic symptoms, and decreased physiological performance in diseased poplar leaves. This study elucidated the fine-tuned regulation of poplar gene expression by BCMV; moreover, the results also suggested that miR156/SPL modules played important roles in the virus response and development of viral systematic symptoms in plant virus disease.

FtbZIP85 Is Involved in the Accumulation of Proanthocyanidin by Regulating the Transcription of FtDFR in Tartary Buckwheat

As a drought-tolerant crop, Tartary buckwheat survives under adverse environmental conditions, including drought stress. Proanthocyanidins (PAs) and anthocyanins are flavonoid compounds, and they participate in the regulation of resistance to both biotic and abiotic stresses by triggering genes' biosynthesis of flavonoids. In this study, a basic leucine zipper, basic leucine zipper 85 (FtbZIP85), which was predominantly expressed in seeds, was isolated from Tartary buckwheat. Our study shows that the expressions of FtDFR, FtbZIP85 and FtSnRK2.6 were tissue-specific and located in both the nucleus and the cytosol. FtbZIP85 could positively regulate PA biosynthesis by binding to the ABA-responsive element (ABRE) in the promoter of dihydroflavonol 4-reductase (FtDFR), which is a key enzyme in the phenylpropanoid biosynthetic pathway. Additionally, FtbZIP85 was also involved in the regulation of PA biosynthesis via interactions with FtSnRK2.6 but not with FtSnRK2.2/2.3. This study reveals that FtbZIP85 is a positive regulator of PA biosynthesis in TB.

Metabolic Composition and Quality Traits of Polygonatum cyrtonema Hua from Different Germplasms and Age Sections Based on Widely Targeted Metabolomics Analysis

Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values of rhizomes, the metabolic composition and quality traits of rhizomes from different germplasms and age sections of P. cyrtonema were analysed by widely targeted metabolomics, and the molecular mechanism of triacylglycerol synthesis was explored. The results showed that the different germplasms and age sections of P. cyrtonema were rich in different nutritional and medicinal components. Of these, the broad-leaved green stem (GK) germplasm is rich in polysaccharides, alkaloids, and lipids; the pointed-leaved green stem (JL) germplasm is rich in flavonoids, steroids, and amino acids, while the pointed-leaved purple stem (JZ) germplasm contains more phenolic acids. The one-year (AT) age section is rich in polysaccharides, steroids, organic acids, and lipids; the three years (CT) age section contains more flavonoids, alkaloids, and amino acid metabolites. Lipids were significantly enriched in the broad-leaved green stem germplasm and the one-year age section. Interestingly, the highest accumulation of triacylglycerols, an important component of lipids, was also found in the GK germplasm and the AT age section. Nineteen, 14, and 13 members of the glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferase (LPAT), and diacylglycerol acyltransferase (DGAT) gene families, respectively, involved in triacylglycerol synthesis were also identified. The quantitative real-time PCR (qRT-PCR) results further suggested that the differentially expressed PcDGAT1, PcDGAT2.4, PcGPAT9.1, PcLPAT2.9, and PcLPAT4.3 genes may play important roles in triacylglycerol synthesis in P. cyrtonema. Therefore, this study provides a new theoretical reference for product development and the breeding of new varieties of Polygonatum species.

Combined widely targeted metabolomics and transcriptomics analysis reveals differentially accumulated metabolites and the underlying molecular bases in fleshy taproots of distinct radish genotypes

Radish is an important taproot crop with medicinal and edible uses that is cultivated worldwide. However, the differences in metabolites and the underlying molecular bases among different radish types remain largely unknown. In the present study, a combined analysis of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) and RNA-Seq data was conducted to uncover important differentially accumulated metabolites (DAMs) among radish accessions with green, white and red taproot flesh colours. A total of 657 metabolites were identified and 138 DAMs were commonly present in red vs. green and red vs. white accessions. Red accessions were rich in phenolic compounds, while green and white accessions had more amino acids. Additionally, 41 metabolites and 98 genes encoding 37 enzymes were enriched in the shikimate and phenolic biosynthesis pathways. CHS is the rate-limiting enzyme determining flavonoid differences among accessions. A total of 119 candidate genes might contribute to red accession-specific accumulated metabolites. Specifically, one gene cluster consisting of 16 genes, including one RsMYB1, RsMYBL2, RsTT8, RsDFR, RsANS, Rs4CL3, RsSCPL10, Rs3AT1 and RsSAP2 gene, two RsTT19 and RsWRKY44 genes and three RsUGT genes, might be involved in anthocyanin accumulation in red radish fleshy taproots. More importantly, an InDel marker was developed based on an RsMYB1 promoter mutation, and the accuracy reached 95.9% when it was used to select red-fleshed radishes. This study provides comprehensive insights into the metabolite differences and underlying molecular mechanisms in fleshy taproots among different radish genotypes and will be beneficial for the genetic improvement of radish nutritional quality.

Evaluation of the Efficacy of Antioxidant Extract from Lemon By-Products on Preservation of Quality Attributes of Minimally Processed Radish (Raphanus sativus L.)

The aim of this work was to enhance the use of a food-grade antioxidant extract obtained from lemon processing byproducts (peel, pulp and seeds) to extend the shelf life of minimally processed radishes. The extract (LPE) was previously characterized in terms of total phenolic (6.75 ± 0.34 mg GAE g-1 d.w.) and flavonoid content (2.04 ± 0.09 mg CE g-1 d.w.) and antioxidant activity, and eriocitrin and hesperidin were identified as the most prevalent phenolic compounds by a UHPLC system. The effects of different dipping aqueous solutions (UCR, DRa, DRb) and alginate-based edible coating formulations (CRc, CRd) with and without the antioxidant extract were studied on the quality parameters of minimally processed radishes, characterized regarding their microbiological and physicochemical characteristics for up to 14 days at 3 °C. The coating formulated with LPE delayed the radish respiration process, as well as resulting in less color variation (ΔE < 3) and reduced mesophilic aerobic count values (4.49 ± 1.43 log CFU g-1), proving the effectiveness of LPE as a value-added ingredient in developing post-harvest strategies to prolong the shelf life of minimally processed vegetables. Indeed, coated samples without the extract showed a clear development of rotting, which led to the end of their shelf life on their 7th day of storage.

Analysis of flavonoid-related metabolites in different tissues and fruit developmental stages of blackberry based on metabolome analysis

Blackberry is an economically important shrub species of Rubus in the Rosaceae family. It is rich in phenolic compounds, which have many health effects and pharmaceutical value. The utilization of metabolites from various blackberry tissues is still in the primary stage of development, so investigating the metabolites in various tissues is of practical significance. In this study, nontargeted LC - MS metabolomics was used to identify and measure metabolites in the roots, stems, leaves and fruits (green, red, and black fruits) of blackberry "Chester". We found that 1,427 and 874 metabolites were annotated in the positive and negative ion modes (POS; NEG), respectively. Differentially abundant metabolites (DAMs) between the leaf and root groups were the most abundant (POS: 249; NEG: 141), and the DAMs between the green and red fruit groups were the least abundant (POS: 21; NEG: 14). Moreover, the DAMs in different fruit development stages were far less than those in different tissues. There were significant differences in flavonoid biosynthesis-related pathways among the comparison groups. Trend analysis showed that the profile 10 had the largest number of metabolites. This study provides a scientific basis for the classification and efficient utilization of resources in various tissues of blackberry plants and the directional development of blackberry products.

Discovery of metabolic markers for the discrimination of Helwingia species based on bioactivity evaluation, plant metabolomics, and network pharmacology

RATIONALE

Helwingia japonica (HJ), a traditional medicinal plant, is commonly used for the treatment of dysentery, blood in the stool, and scald burns. Three major HJ species, Helwingia japonica (Thunb.) Dietr. (QJY), Helwingia himalaica Hook. f. et Thoms. ex C. B. Clarke, and Helwingia chinensis Batal., share great similarities in both morphology and chemical constituents. The discrimination of medicinal plants directly affects their pharmacological and clinical effects. Here, we solved the taxonomy uncertainty of these three HJ species and explored the discrimination and study of other traditional medicines (TMs).

METHODS

First, the anti-inflammatory effects of the three HJ species were compared using lipopolysaccharide (LPS)-induced inflammatory responses in mouse leukemia cells of monocyte macrophage (RAW) 264.7 cells. Then, plant metabolomics were performed in 48 batches of samples to discover chemical markers for discriminating different HJ species. Finally, network pharmacology was applied to explore the linkages among constituents, targets, and signaling pathways.

RESULTS

In vitro experiments showed that the QJY exhibited the most potential anti-inflammatory activities. Meanwhile, 172 compounds were tentatively identified and eight metabolites with higher relative content in QJY were designated as chemical markers to distinguish QJY and the other two species. According to the property of absorbed in vivo, threonic acid, arginine, and tyrosine were selected to construct a component-target-pathway network. The network pharmacology analysis confirmed that the chemotaxonomy differentiation was consistent with the bioactive assessment.

CONCLUSIONS

The present study demonstrates that bioactivity evaluation integrated with plant metabolomics and network pharmacology could be used as an effective approach to discriminate different TMs and discover the active compounds.

Metabolomics study of flavonoids in Coreopsis tinctoria of different origins by UPLC-MS/MS

To analyze the flavonoids in Coreopsis tinctoria and compare the differences in flavonoids among C. tinctoria of different origins, the chemical composition of C. tinctoria capitulum was analyzed by ultra-high-performance liquid chromatography-tandem quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and the flavonoid metabolites were analyzed and identified based on their retention time, mass-to-charge ratio and fragment ions in the UPLC-QTOF-MS matrix. Capitulum samples of C. tinctoria were collected from three locations in the Xinjiang region at different altitudes. A total of 204 flavonoid compounds were identified, and 31 different flavonoid metabolites were then identified from flowers of C. tinctoria of different origins. Further analysis of these 31 significantly accumulated metabolites identified seven flavonoid metabolites, namely, homoplantaginin, kaempferol, quercetin, isorhamnetin, avicularin, quercetin 3-O-(6'-galloyl)-β-D-galactopyranoside and isorhamnetin 3-O-glucoside, with high accumulation only in sample collected from Tashkurgan Tajik (TX) and low expression in sample collected from Yutian County (YT) and Shaya County (SY). Moreover, 7,4'-dihydroxyflavone and 4,4'-dimethoxychalcone showed high accumulation only in SY, and afzelin was specifically highly accumulated in YT. In addition, the identified flavonoid metabolites were annotated using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and key pathways that might regulate the biosynthesis of these flavonoid compounds were analyzed. These findings provide key information for research on flavonoids and their biosynthesis in C. tinctoria and will provide a theoretical basis for studying the herbal quality and origin of C. tinctoria.

Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole

Background

Insufficient low temperatures in winter and soil residues caused by paclobutrazol (PBZ) application pose a considerable challenge for mango floral induction (FI). Gibberellin inhibitors SPD (compound of mepiquat chloride, prohexadione-calcium and uniconazole) had a significant influence on enhancing the flowering rate and yield of mango for two consecutive years (2020-2021). Researchers have indicated that FI is regulated at the metabolic level; however, little is known about the metabolic changes during FI in response to SPD treatment.

Methods

Here, ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based widely targeted metabolomic analysis was carried out to assess the metabolic differences in the mango stem apex during different stage of mango FI (30, 80, 100 days after SPD/water treatment).

Results

A total of 582 compounds were annotated and 372 metabolites showed two-fold differences in abundance (variable importance in projection, VIP ≥ 1 and fold change, FC≥ 2 or≤ 0.5) between buds at 30, 80, 100 days after SPD/water treatment or between buds under different treatment. Lipids, phenolic acids, amino acids, carbohydrates, and vitamins were among metabolites showing significant differences over time after SPD treatment. Here, 18 out of 20 lipids, including the lysophosphatidylethanolamine (12, LPE), lysophosphatidylcholine (7, LPC), and free fatty acids (1, FA), were significantly upregulated from 80 to 100 days after SPD treatment comared to water treatment. Meanwhile, the dormancy release of mango buds from 80 to 100 days after SPD treatment was accompanied by the accumulation of proline, ascorbic acid, carbohydrates, and tannins. In addition, metabolites, such as L-homocysteine, L-histidine, and L-homomethionine, showed more than a ten-fold difference in relative abundance from 30 to 100 days after SPD treatment, however, there were no significant changes after water treatment. The present study reveals novel metabolites involved in mango FI in response to SPD, which would provide a theoretical basis for utilizing SPD to induce mango flowering.

Metabolomics and proteomics reveal the molecular basis of colour formation in the pericarp of Chinese wild rice (Zizania latifolia)

Chinese wild rice (Zizania latifolia) is rich in flavonoids and the characteristic colour of its pericarp is attributed to the flavonoids. In this study, the molecular basis of the colour change in the pericarp of Chinese wild rice was studied using metabolomics and proteomics. Whole seeds in three developmental stages (10, 20, and 30 days after flowering) were characterised based on phenolic contents, free amino acids (FAAs), and the expression level and activities of enzymes critical in flavonoid biosynthesis. The total phenolic and proanthocyanidin contents of Chinese wild rice increased gradually, whereas total flavonoid and FAA contents decreased during seed development. Metabolomic analysis revealed gradual upward trends for 57 flavonoids (sub classes 1, 3, and 10) related to colour change in the pericarp. Proteomic analysis showed that the phenylpropanoid biosynthesis metabolic pathway was enriched with differentially expressed proteins and was associated with flavonoid biosynthesis. Proteomic data suggested that leucoanthocyanidin reductase and WD40 repeat protein may be involved in flavonoid biosynthesis in Chinese wild rice, which was also verified by real-time quantitative PCR. Our results provide new insights into the understanding of the colour formation in the pericarp of Chinese wild rice.

Root Vegetables-Composition, Health Effects, and Contaminants

Root vegetables are known all over the world, but they are being less and less consumed by individuals. The main purpose of this article was to summarize the benefits, health effects, and threats associated with the consumption of carrot, celery, parsley, beetroot, radish, turnip, and horseradish. They are characterized by high nutritional value due to their richness in dietary fiber, vitamins, and minerals. One of their most important features is their high content of bioactive compounds, such as polyphenols, phenols, flavonoids, and vitamin C. These compounds are responsible for antioxidant potential. Comparison of their antioxidant effects is difficult due to the lack of standardization among methods used for their assessment. Therefore, there is a need for a reference method that would allow for correct interpretation. Moreover, root vegetables are characterized by several health-promoting effects, including the regulation of metabolic parameters (glucose level, lipid profile, and blood pressure), antioxidant potential, prebiotic function, and anti-cancer properties. However, due to the type of cultivation, root vegetables are vulnerable to contaminants from the soil, such as toxic metals (lead and cadmium), pesticides, pharmaceutical residues, microplastics, and nitrates. Regardless, the low levels of toxic substances present in root vegetables do not pose health risks to the average consumer.

Identification of Medicinal Compounds of Fagopyri Dibotryis Rhizome from Different Origins and Its Varieties Using UPLC-MS/MS-Based Metabolomics

Fagopyrum dibotrys, being native to southwest China, is widely distributed in Yunnan, Guizhou Provinces and Chongqing City. However, the quality of medicinal materials growing in different origins varies greatly, and cannot meet the market demand for high-quality F. dibotrys. In this study, 648 metabolites were identified, and phenolic compounds of F. dibotrys from different origins were clearly separated by principal component analysis (PCA). Our results suggested that the medicinal differences of F. dibotrys from different origins can be elucidated via the variations in the abundance of the phenolic and flavonoid compounds. We found that the epicatechin, total flavonoids and total tannin content in Yunnan Qujing (YQ) and Yunnan Kunming (YK) were higher than those in Chongqing Shizhu (CS), Chongqing Fuling (CF) and Guizhou Bijie (GB), suggesting that Yunnan Province can be considered as one of the areas that produce high-quality medicinal materials. Additionally, 1,6-di-O-galloyl-β-D-glucose, 2,3-di-O-galloyl-D-glucose and gallic acid could be used as ideal marker compounds for the quality control of F. dibotrys from different origins caused by metabolites, and the F. dibotrys planted in Yunnan Province is well worth exploiting.

Flavonoid Metabolic Profiles and Gene Mapping of Rice (Oryza sativa L.) Purple Gradient Grain Hulls

Rice (Oryza sativa L.) grain hull color is an easily observable trait and regarded as a crucial morphological marker in rice breeding. Here, a purple gradient grain hull mutant (pg) was found from natural mutations of a straw-white grain hull rice variety IARI 6184B (Orzya sativa L. subsp. indica). The color of the mutant grain hulls changed from straw-white to pink, then purple, and finally brownish-yellow. Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) identified 217 flavonoids, including 18 anthocyanins, among which cyanidin O-syringic acid had the highest concentration in pink (66.2 × 10⁶) and purple (68.0 × 10⁶) grain hulls. The relative contents of hesperetin O-malonyl-hexoside, apigenin derivatives, genistein derivatives, and kaempferol 3-O derivatives were consistently downregulated during pg grain hull development. Conversely, 12 anthocyanins were upregulated in colored hulls, and cyanidin 3-O-malonylhexoside was abundant only in pink and purple grain hulls. Moreover, the candidate gene was mapped into a 1.38 Mb region on chromosome 4 through bulked segregant analysis based on deep sequencing (BSA-seq) and gene mapping approaches. These results increased our understanding of anthocyanin biosynthesis in rice grains, helping rice breeders to select new rice varieties with desirable grain traits.

Identification and analysis of major flavor compounds in radish taproots by widely targeted metabolomics

Radish (Raphanus sativus L.) is an important Brassicaceous vegetable crop that is cultivated worldwide. The taste of radish can be described as pungent, sweet, and crisp. At present, the metabolic characteristics leading to differences in radish taste remain unclear, due to the lack of large-scale detection and identification of radish metabolites. In this study, UPLC-MS/MS-based targeted metabolome analysis was performed on the taproots of eight radish landraces. We identified a total of 938 metabolites, and each landrace exhibited a specific metabolic profile, making it unique in flavor and quality. Our results show that taste differences among the taproots of different radish landraces can be explained by changes in composition and abundance of glucosinolates, polyphenols, carbohydrates, organic acids, amino acids, vitamins, and lipids. This study reveals the potential metabolic causes of variation in the taste and flavor of radish taproots.

Comparative Metabolomics study of flavonoids in the pericarp of different coloured bitter gourds (Momordica charantia L.)

Bitter gourd (Momordica charantia L.) is a member of Cucurbitaceae family and has long been used as a source of food and medicine for its rich bioactive components or secondary metabolites. However, there are relatively few large-scale detection, identification, and quantitative studies on flavonoids in the pericarp of bitter gourds of different colours. To determine the differences in the diversity and specificity of flavonoids in the pericarp of bitter gourd of different colours, the metabolic profiles in the pericarp of three coloured bitter gourd accessions, dark green (mo), pale green (lv), and white (bai), were analysed by ultra-performance liquid chromatography-tandem mass spectrometry. Priorly, it was confirmed that the different shades of green were caused by the content of chlorophyll. A total of 93 metabolites, including 90 flavonoids and three tannins, were detected in the current study. These 90 flavonoids included three isoflavones, nine dihydroflavones, seven flavanols, 34 flavonols, 26 flavonoids, four chalcones, five flavonoid carbonosides, and two dihydroflavonols. Compared to mo, both lv and bai had 21 and 25 different metabolites, respectively, while there were only nine different metabolites between lv and bai. The relative contents of vitexin and isovitexin increased with the deeper colour of the bitter gourd. Thus, the different metabolites in coloured bitter gourds are mainly involved in the biosynthesis of flavonols, flavonoid carbonosides, and flavonoids. This study enables identification of metabolic differences in the pericarp of bitter gourds of different colours. The results will be helpful for quality breeding of new bitter gourd varieties and shall provide a reference for their medical application.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01210-7.

A comparative metabolomics study of anthocyanins and taste components in Chinese bayberry (Morella rubra) with different flesh colors

The Chinese bayberry (Morella rubra Sieb. et Zucc.) is grown commercially in China and other Asian countries for its flavorful and appealing fruit. Here, two bayberry varieties differing in both color and flavor, namely, BDK ('Baidongkui') and DK ('Dongkui'), in China were compared. A total of 18 anthocyanins, three proanthocyanidins, and 229 primary metabolites were identified in the pulp of the two varieties; these were analyzed and compared using ultra-performance liquid chromatography-tandem mass spectrometry. The DK pulp showed higher concentrations of all 18 anthocyanins compared with BDK, apart from peonidin-3,5-O-diglucoside which was not detected in BDK and which was responsible for the formation of pink pulp in BDK. Principal component analysis and cluster analysis of the primary metabolites indicated that the two bayberry varieties had distinct metabolite profiles with approximately 37% (85/229) of the primary metabolome being significantly different. Of these, 62 metabolites were down-regulated and 23 metabolites were up-regulated in BDK relative to DK. Our results suggested that the flavor of the BDK fruit was different from DK, which could be explained by the reduced saccharide, organic acid, amino acid, and proanthocyanidin contents. These findings enhance our understanding of the metabolites responsible for color and taste differences in the Chinese bayberry.

Metabolic Profiling of White and Green Radish Cultivars (Raphanus sativus)

Radish (Raphanus sativus) is a Brassica vegetable important for human nutrition and health because it is rich in diverse metabolites. Although previous studies have evaluated various metabolites, few studies have comprehensively profiled the primary and secondary metabolites in the roots of white- and green-colored radishes. Thus, this study aimed to provide information about the contents of metabolites beneficial for human health in both cultivars and to investigate the relationships between the various metabolites detected. In particular, among the 55 metabolites detected in radish roots, the levels of most amino acids and phenolic acids, vital to nutrition and health, were higher in green radish roots, while slightly higher levels of glucosinolates were observed in white radish roots—information which can be used to develop an effective strategy to promote vegetable consumption. Furthermore, glutamic acid, as a metabolic precursor of amino acids and chlorophylls, was positively correlated with other amino acids (cysteine, tryptophan, asparagine, alanine, serine, phenylalanine, valine, isoleucine, proline, leucine, beta-alanine, lysine, and GABA), and chlorophylls (chlorophyll a and chlorophyll b) detected in radish roots and phenylalanine, a metabolic precursor of phenolic compounds, were positively correlated with kaempferol, 4-hydroxybenzoate, and catechin. In addition, strong positive correlations between carbohydrates (sucrose and glucose) and phenolics were observed in this study, indicating that sucrose and glucose function as energy sources for phenolic compounds.

Comparative Metabolomics Study of Chaenomeles speciosa (Sweet) Nakai from Different Geographical Regions

Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is not only a Chinese herbal medicine but also a functional food widely planted in China. Its fruits are used to treat many diseases or can be processed into food products. This study aims to find key metabolic components, distinguish the differences between geographical regions and find more medicinal and edible values of C. speciosa fruits. We used ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) and widely targeted metabolomics analysis to reveal key and differential metabolites. We identified 974 metabolites and screened 548 differential metabolites from 8 regions. We selected significantly high-content differential metabolites to visualize a regional biomarker map. Comparative analysis showed Yunnan had the highest content of total flavonoids, the highest amounts of compounds related to disease resistance and drug targets and the most significant difference from the other regions according to the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database, a unique platform for studying the systematic pharmacology of Chinese herbal medicine and capturing the relationship between drugs, targets and diseases. We used oral bioavailability (OB) ≥ 30% and drug likeness (DL) ≥ 0.18 as the selection criteria and found 101 key active metabolites, which suggests that C. speciosa fruits were rich in healthy metabolites. These results provide valuable information for the development of C. speciosa.

Profiling alkaloids in Aconitum pendulum N. Busch collected from different elevations of Qinghai province using widely targeted metabolomics

Aconitum pendulum N. Busch (Ranunculaceae) is rich in alkaloids with anti-inflammatory and analgesic activities. Many studies have focused on the identification or quantification of alkaloid components using low-throughput tests. However, the metabolic differences of plants from environmentally distinct regions remain unclear. The present study profiled alkaloid chemical compounds in the rhizomes of A. pendulum from different regions. A total of 80 chemical compounds were identified using a widely targeted ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) approach. Principal component, hierarchical clustering, and orthogonal partial least squares-discriminant analyses of the chemical compounds indicated that the plants from 6 regions clearly separated into distinct groups. A total of 19 compounds contributed the most to the metabolite differences between collection areas and were identified as potential metabolic markers. The anti-inflammatory activities of the A. pendulum extracts were also evaluated and the potential environmental effects on the regulation of metabolite composition and bioactivity were explored. These results improve our understanding of the variation in chemical composition of plants from different regions and will serve as a reference for evaluating the medicinal value of A. pendulum in different environments.

Metabolomics Analysis Reveals the Differences Between Bupleurum chinense DC. and Bupleurum scorzonerifolium Willd

Bupleurum chinense DC. and Bupleurum scorzonerifolium Willd. are two varieties of Bupleuri Radix in Chinese Pharmacopoeia 2020. The clinical efficacy of the two bupleurum species is different. The difference in clinical efficacy is closely related to the composition of plant metabolites. In order to analyze the difference in metabolites, we used liquid chromatography coupled with mass spectrometry (LC-MS) for untargeted metabolome and gas chromatography coupled with mass spectrometry (GC-MS) for widely targeted metabolome to detect the roots (R), stems (S), leaves (L), and flowers (F) of two varieties, and detected 1,818 metabolites in 25 classes. We performed a statistical analysis of metabolites. Differential metabolites were screened by fold-change and variable importance in the projection values of the OPLS-DA model, and significant differences were found among different groups. The content of active components (triterpenoid saponins) was found to be high in the BcR group than in the BsR group. Other pharmacological metabolites were significantly different. By Kyoto Encyclopedia of Genes and Genomes annotation and enrichment analysis, we found that differential metabolites of the aboveground parts mainly concentrated in monoterpenoid biosynthesis, while the differential metabolites of the root mainly concentrated in sesquiterpenoid and triterpenoid biosynthesis. Differences in metabolic networks may indirectly affect the metabolic profile of Bc and Bs, leading to differences in clinical efficacy. Our study provides a scientific basis for subsequent biosynthesis pathway and related bioactivity research, and provides a reference for developing non-medicinal parts and guiding the clinical application of Bupleuri Radix.

Water Mediated One-Pot, Stepwise Green Synthesis, Anti-Inflammatory and Analgesic Activities of (3-Amino-1-Phenyl-1H-Benzo[f]Chromen-2-yl) (1H-Indol-3-yl) Methanone Catalysed by L-Proline

AIM

The reactions were carried out by one pot three-component synthesis, 3-cyanoacetylindole (1) on reaction with aromatic aldehydes (2) and β-naphthol (3) in an aqueous medium in presence of L-proline as a catalyst under reflux for 30 min, resulted (3-amino-1-phenyl-1H-benzo[f]chromen-2-yl) (1H-indol-3-yl)methanone (4). The method has many advantages like short reaction times, good yields and simple workup procedure besides being green in nature. Pharmacological evaluation of title compounds was done for anti-inflammatory and analgesic activities. Anti-inflammatory activity was carried carrageenan-induced paw edema model in which indomethacin was used as standard and analgesic activity was evaluated by eddy's hot plate method using diclofenac as standard drug.

BACKGROUND

Benzopyrans or chromenes are an important class of heterocyclic compounds due to their broad spectrum of biological activity and a wide range of applications in medicinal chemistry. The chromene moiety is found in various natural products with interesting biological properties. Chromenes constitute the basic backbone of various types of polyphenols and are widely found in alkaloids, tocopherols, flavonoids and anthocyanins. Indoles are omnipresent in various bioactive compounds like alkaloids, agrochemicals and pharmaceuticals.

OBJECTIVE

To synthesize one-pot stepwise Green synthesis, anti-inflammatory and analgesic activities of 3-amino-1-phenyl-1H-benzo[f]chromen-2-yl) (1H-indol-3-yl)methanones Methods: The acute anti-inflammatory effect was evaluated by carrageenan-induced mice paw edema (Ma Rachchh et al., 2011). Edema was induced by injecting carrageenan (1% w/v, 0.1 ml) in the right hind paw of mice. The test compounds 1-12, indomethacin (10 mg/kg) and the vehicle were administered orally one hour before injection of carrageenan. Paw volume was measured with digital plethysmometer at 0, 30, 60, 90, 120 min after injection. Percentage increase =A-B/ A *100 Results: Carrageenan Induced paw edema model was used for Anti-inflammatory activity in which animals treated with standard (indomethacin) and test compounds showed a significant decrease in the paw edema. Analgesic activity was estimated by using Eddy's hot plate method; animals were treated with standard (diclofenac) and test compounds showed a significant increase in the reaction time.

CONCLUSION

A green, One-pot, step-wise and three-component synthesis of 3-amino-1-phenyl-1H-benzo[f]chromen-2-yl) (1H-indol-3-yl) methanone was achieved by using water as a solvent, L-proline as catalyst under reflux conditions. The reactions were carried out in eco-friendly conditions with shorter reaction times, easier workup and high yields. Anti-inflammatory activity was evaluated by carrageenan-induced paw edema model where significant anti-inflammatory activity is shown by all the test compounds (4a-l) when compared to standard drug. Analgesic activity was studied by Eddy's Hot plate method and Test compounds 4e, 4f, 4h, 4i, 4j, 4k, 4l showed significant activities when compared to the reference drug.

Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis

Numerous plant secondary metabolites have remarkable impacts on both food supplements and pharmaceuticals for human health improvement. However, higher plants can only generate small amounts of these chemicals with specific temporal and spatial arrangements, which are unable to satisfy the expanding market demands. Cyanobacteria can directly utilize CO₂, light energy, and inorganic nutrients to synthesize versatile plant-specific photosynthetic intermediates and organic compounds in large-scale photobioreactors with outstanding economic merit. Thus, they have been rapidly developed as a "green" chassis for the synthesis of bioproducts. Flavonoids, chemical compounds based on aromatic amino acids, are considered to be indispensable components in a variety of nutraceutical, pharmaceutical, and cosmetic applications. In contrast to heterotrophic metabolic engineering pioneers, such as yeast and Escherichia coli, information about the biosynthesis flavonoids and their derivatives is less comprehensive than that of their photosynthetic counterparts. Here, we review both benefits and challenges to promote cyanobacterial cell factories for flavonoid biosynthesis. With increasing concerns about global environmental issues and food security, we are confident that energy self-supporting cyanobacteria will attract increasing attention for the generation of different kinds of bioproducts. We hope that the work presented here will serve as an index and encourage more scientists to join in the relevant research area.