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

Metabolic profiles and biomarkers of Auricularia cornea based on de-oiled camphor leaf substrate

This study investigates the metabolic responses of Auricularia cornea when cultured on de-oiled leaves of Cinnamomum longepaniculatum (DeCL), an underutilized waste product. The metabolic profiles of A. cornea cultured with four different quality ratios of DeCL substrate (0 %, 14 %, 28 % and 42 %) were analyzed by UHPLC-MS/MS-based metabolomics. A total of 516 metabolites were identified and classified into 78 categories, with phenols, alkaloids and flavonoids accounting for 26.7 % of the total. In addition, 32 metabolite biomarkers associated with eight major metabolic pathways were identified. This pioneering research provides valuable insights into the utilization of DeCL, and expands our knowledge of the metabolic dynamics underlying the growth of A. cornea on alternative substrates.

Identification and molecular docking of xanthine oxidase and α-glucosidase inhibitors in Opuntia ficus-indica fruit

Opuntia ficus-indica fruit (OFI) is rich in bioactive compounds, which can promote human health. In this work, the purified OFI extract was prepared from OFI and its bioactivities were investigated. Xanthine oxidase (XOD) and α-glucosidase (α-Glu) inhibitors of the purified OFI extract were screened and identified by bio-affinity ultrafiltration combined with UPLC-QTRAP-MS/MS technology. The inhibitory effect of these inhibitors on enzymes were verified, and the potential mechanism of action and binding sites of inhibitors with enzymes were revealed based on molecular docking. The results showed that the total phenolic content of the purified OFI extract was 355.03 mg GAE/g DW, which had excellent antioxidant activity. Additionally, the extract had a certain inhibitory effect on XOD (IC50 = 199.00 ± 0.14 µg/mL) and α-Glu (IC50 = 159.67 ± 0.01 µg/mL). Seven XOD inhibitors and eight α-Glu inhibitors were identified. Furthermore, XOD and α-Glu inhibition experiments in vitro confirmed that inhibitors such as chlorogenic acid, taxifolin, and naringenin had significant inhibitory effects on XOD and α-Glu. The molecular docking results indicated that inhibitors could bind to the corresponding enzymes and had strong binding force. These findings demonstrate that OFI contains potential substances for the treatment of hyperuricemia and hyperglycemia.

Metabolomics analysis reveals metabolite diversity of the rare cliff plant Oresitrophe rupifraga unge

Oresitrophe is monotypic, with the only species, Oresitrophe rupifraga Bunge, which is exclusive to China, having special growth and developmental traits due to its habitat. Furthermore, it has bright flowers and medicinal benefits. This study investigated the metabolites present in various tissues of Oresitrophe rupifraga Bunge. Using a widely targeted metabolomics approach, 1965 different metabolites were identified in Oresitrophe rupifraga Bunge. Based on principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA), the aboveground and underground metabolites of Oresitrophe rupifraga differed significantly. The comparison between bulblets and leaves revealed the differential expression of 461 metabolites, whereas the comparison between rhizomes and leaves showed the differential expression of 423 metabolites, and the comparison between bulblets and rhizomes showed the differential expression of 249 metabolites. The bulblets exhibited 49 metabolites that were higher and 412 metabolites that were lower than those of the leaves, whereas the rhizomes showed 123 upregulated and 300 downregulated metabolites. Bulblets showed an increase in 18 metabolites and a decrease in 231 metabolites compared to the rhizomes. Leaves contain more phenolic acids than the rhizomes and bulblets, whereas the rhizomes and bulblets contain more terpenoids than the leaves. KEGG pathway analysis showed an association between metabolites and metabolic pathways, as well as their effect on the progression and maturation of Oresitrophe rupifraga Bunge. The research findings can provide some insight into the growth and developmental traits of Oresitrophe rupifraga Bunge, thus providing a theoretical foundation for cultivating and utilising this plant.

Recent Advances in Polysaccharides from Chaenomeles speciosa (Sweet) Nakai.: Extraction, Purification, Structural Characteristics, Health Benefits, and Applications

This article systematically reviews the extraction and purification methods, structural characteristics, structure-activity relationship, and health benefits of C. speciosa polysaccharides, and their potential application in food, medicine, functional products, and feed, in order to provide a useful reference for future research. Chaenomeles speciosa (Sweet) Nakai. has attracted the attention of health consumers and medical researchers as a traditional Chinese medicine with edible, medicinal, and nutritional benefits. According to this study, C. speciosa polysaccharides have significant health benefits, such as anti-diaetic, anti-inflammatory and analgesic, anti-tumor, and immunomodulatory effects. Researchers determined the molecular weight, structural characteristics, and monosaccharide composition and ratio of C. speciosa polysaccharides by water extraction and alcohol precipitation. This study will lay a solid foundation for further optimization of the extraction process of C. speciosa polysaccharides and the development of their products. As an active ingredient with high value, C. speciosa polysaccharides are worthy of further study and full development. C. speciosa polysaccharides should be further explored in the future, to innovate their extraction methods, enrich their types and biological activities, and lay a solid foundation for further research and development of products containing polysaccharides that are beneficial to the human body.

Comparative pharmacognosy and secondary metabolite analysis of Balanophorae herbs from different sources

The Balanophorae are not only traditional Chinese herbal medicines but also functional foods with diverse sources. This study aimed to distinguish pharmacognostic characteristics and secondary metabolites among different species of Balanophorae. Eight species of Balanophorae herbs were harvested, including 21 batches with 209 samples. Ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry was used to analyze secondary metabolites of Balanophorae from 21 sources. Targeted metabolomic analysis was performed to compare differences among the groups. Rhopalocnemis phalloide and B. indica can be identified by their pharmacognostic characteristics. Then, 41 secondary metabolites were identified or characterized in the mixed extracts of the 209 samples, mainly phenolic acids, flavonoids, and their derivatives. The distribution of these secondary metabolites revealed apparent differences among different species. In addition, targeted metabolomic analysis suggested that the secondary metabolite profiles of seven species of Balanophorae showed noticeable differences, and differences were also observed among different growing regions. Finally, five important metabolic markers were screened to successfully distinguish B. laxiflora, B. harlandii, and B. polyandra, including three phenolic acids and two flavonoids. This is the first study to systematically compare both the morphology and secondary metabolites among different sources of Balanophorae, which could provide effective information for identifying diverse species.

Metabolomics for Clinical Biomarker Discovery and Therapeutic Target Identification

As links between genotype and phenotype, small-molecule metabolites are attractive biomarkers for disease diagnosis, prognosis, classification, drug screening and treatment, insight into understanding disease pathology and identifying potential targets. Metabolomics technology is crucial for discovering targets of small-molecule metabolites involved in disease phenotype. Mass spectrometry-based metabolomics has implemented in applications in various fields including target discovery, explanation of disease mechanisms and compound screening. It is used to analyze the physiological or pathological states of the organism by investigating the changes in endogenous small-molecule metabolites and associated metabolism from complex metabolic pathways in biological samples. The present review provides a critical update of high-throughput functional metabolomics techniques and diverse applications, and recommends the use of mass spectrometry-based metabolomics for discovering small-molecule metabolite signatures that provide valuable insights into metabolic targets. We also recommend using mass spectrometry-based metabolomics as a powerful tool for identifying and understanding metabolic patterns, metabolic targets and for efficacy evaluation of herbal medicine.

Widely Targeted Metabolomics Analysis Reveals Metabolites Important for Antioxidant Properties and Quality Traits in Different Fruit Parts of Aurantii Fructus Immatures

In traditional Chinese medicine, Aurantii Fructus Immatures (AFIs) have been utilized for more than 2000 years. The proportions of different fruit parts are crucial for evaluating AFI quality in China. However, the basis for this statement's substance is unclear. Differences in quality are intimately correlated with a plant's metabolite composition. On the basis of a widely targeted metabolome, this study intended to investigate the metabolite composition and evaluate the antioxidant capacity of the peel and pulp of an AFI. Metabolites were identified and quantified by UHPLC-QqQ-MS. To assess their antioxidant ability, DPPH and ABTS assays were carried out. There were 1327 chemical compounds identified by UHPLC-QqQ-MS. After screening the differential metabolites using a multivariate statistical analysis, it was found that there were 695 significant differences in the metabolites between the peel and the pulp. Among them, it was discovered that the content of active ingredients in the peel group was higher than that in the pulp group. Furthermore, the aqueous extracts from the peel showed stronger antioxidant capacities than those from the pulp. The metabolites and antioxidant capacities were significantly different between the peel and the pulp. This study of different fruit parts might provide a guide for AFI quality assessments.

Flower opening dynamics, pollen-ovule ratio, stigma receptivity and stigmatic pollen germination (in-vivo) in Chaenomeles speciosa (Sweet) Nakai

Although Chaenomeles is widely used in horticulture, traditional Chinese medicine and landscape greening, insufficient research has hindered its breeding and seed selection. This study investigated the floral phenology, floral organ characteristics, palynology, and breeding systems of Chaenomeles speciosa (Sweet) Nakai. The floral characteristics of C. speciosa were observed both visually and stereoscopically. The microstructures of the flower organs were observed using scanning electron microscopy. Pollen stainability was determined using triphenyl tetrazolium chloride staining. Stigma receptivity was determined using the benzidine-H2O2 method and the post-artificial pollination pollen germination method. The breeding system was assessed based on the outcrossing index and pollen-ovule ratio. The flowers of C. speciosa were bisexual with a flowering period from March to April. The flowering periods of single flowers ranged from 8 to 19 d, and those of single plants lasted 18-20 d. The anthers were cylindrical, with the base attached to the filament, and were split longitudinally to release pollen. The flower had five styles, with a connate base. The ovaries had five carpels and five compartments. The inverted ovules were arranged in two rows on the placental axis. The stigma of C. speciosa was dry and had many papillary protrusions. In the early flowering stage (1-2 d of flowering), the pollen exhibited high stainability (up to 84.24%), but all stainability was lost at 7 d of flowering. Storage at - 20 °C effectively delayed pollen inactivation. The stigma receptivity of C. speciosa lasted for approximately 7 days, and the breeding system was classified as outcrossing with partial self-compatibility.

An investigation into the effects of various processing methods on the characteristic compounds of highland barley using a widely targeted metabolomics approach

This study explored the influence of diverse processing methods (cooking (CO), extrusion puffing (EX), and steam explosion puffing (SE), stir-frying (SF) and fermentation (FE)) on highland barley (Qingke) chemical composition using UHPLC-MS/MS based widely targeted metabolomics. Overall, 827 metabolites were identified and categorized into 16 classes, encompassing secondary metabolites, amino acids, nucleotides, lipids, etc. There 43, 85, 131, 51 and 98 differential metabolites were respectively selected from five comparative groups (raw materials (RM) vs CO/EX/SE/SF/FE), mainly involved in amino acids, nucleotides, flavonoids, and alkaloids. Compared to other treated groups, FE group possessed the higher content of crude protein (15.12 g/100 g DW), and the relative levels of free amino acids (1.32 %), key polyphenols and arachidonic acid (0.01 %). EX group had the higher content of anthocyanins (4.22 mg/100 g DW), and the relative levels of free amino acids (2.02 %) and key polyphenols. SE group showed the higher relative levels of phenolic acids (0.14 %), flavonoids (0.20 %) and alkaloids (1.17 %), but the lowest free amino acids (0.75 %). Different processing methods all decreased Qingke's antioxidant capacity, with the iron reduction capacity (988.93 μmol/100 g DW) in SE group was the lowest. On the whole, FE and EX were alleged in improving Qingke's nutritional value. CO and SF were also suitable for Qingke processing since fewer differential metabolites were identified in CO vs RM and SF vs RM groups. Differential metabolites were connected to 14 metabolic pathways, with alanine, aspartate, and glutamate metabolism being central. This study contributed theoretical groundwork for the scientific processing and quality control of Qingke products.

Comprehensive quality evaluation of different types of Gardeniae Fructus (Zhizi) and Shuizhizi based on LC-MS/MS

Gardeniae Fructus (Zhizi) serves as both a medicinal and edible substance and finds widespread use in various industries. There are often two kinds of medicinal materials in the market: Zhizi and Shuizhizi. Typically, Zhizi with small, round fruit is used for medicinal purposes, while Shuizhizi, characterized by large, elongated fruit, is employed for dyeing. Market surveys have revealed a diverse range of Zhizi types, and modern research indicates that Shuizhizi contains rich chemical components and pharmacological activities. In this study, we collected 25 batches of Zhizi and Shuizhizi samples, categorizing them based on appearance into obovate and round fruits, with seven length grades (A-G). Using the ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QQQ-MS/MS) method, we simultaneously quantified 13 main chemical components in fruits of Gardenia species. In addition, we compared the weight percentage of the pericarp, flesh, and seeds parts of samples with different traits, and quantified 13 chemical components in different parts. Results indicated that, aside from a few instances of overlapping fruit size ranges, Shuizhizi generally exhibits larger and longer dimensions than Zhizi. The weight proportion of the Shuizhizi pericarp is often higher than that of the Zhizi pericarp. Quantitative results highlighted significant differences in the chemical component content between Zhizi and Shuizhizi, with Shuizhizi generally containing higher levels of iridoids. The PCA and OPLS-DA analysis distinctly divided Shuizhizi and Zhizi, among which three iridoids, two organic acids, and one flavonoid made significant contributions to their classification. Cluster heatmap analysis also demonstrated complete separation between Zhizi and Shuizhizi, with clear distinctions among Zhizi samples from different origins. The distribution of the 13 chemical components in different Zhizi and Shuizhizi parts remained consistent, with iridoids and pigments concentrated in the seeds and flesh, and two organic acids and one flavonoid enriched in the pericarp. In summary, this study contributes valuable insights for classifying Zhizi and offers guidance on the rational use of Shuizhizi and the different parts of Zhizi.

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 telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa

Chaenomeles speciosa (2n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.

De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers

As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of C. speciosa and closely related species. This work is the first to report the C. speciosa mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.

Integrated untargeted metabolome, full-length sequencing, and transcriptome analyses reveal insights into the fruit quality at different harvest times of Chaenomeles speciosa

Chaenomeles speciosa fruit is a homologous medicine and food plant with a long history of multiple uses. It could be harvested near maturity and last for a long time. However, the optimal harvest strategy of Chaenomeles speciosa for various uses is currently unavailable. Here, untargeted metabolome at different harvest times during maturation was investigated for the first time, and 896 metabolites, including sugars, organic acids, amino acids, and phenylpropanoids, were identified. Optimal harvesting methods were proposed for different purposes. During the early maturation stages (before 105 days after full bloom), Ch. speciosa fruit could be harvested as Chinesemedicine. Whereas as snacks and food, Ch. speciosa fruit might be harvested at late maturity (after 120 days after full bloom). In addition, the overall network was revealed by integrating full-length Iso-seq and transcriptomics (RNA-seq) to investigate the association between quality-associated metabolites and Chaenomeles speciosa fruit gene expression during maturation. A few putative genes were captured via screening, dissecting and correlation analysis with the quality-associated metabolites (including d-glucose, catechin, gallocatechin, and succinic acid). Overall, in addition to providing a harvesting strategy for food and medicine, we also investigated the metabolism and gene expression pattern of Chaenomeles speciosa fruit during maturation. This comprehensive data and analyses laid the foundation for further investigating potential regulatory mechanisms during harvest and provided a new possibility for its development and utilization.

Changes in the Primary Metabolites of ‘Fengtang’ Plums during Storage Detected by Widely Targeted Metabolomics

Plums are one of the most popular stone fruits worldwide owing to their high nutritional value. After harvest, plum fruit quality and flavor change during storage; however, little is known about the changes in metabolites during this period. A comprehensive comparison of primary metabolites in ‘Fengtang’ plum fruits during storage is performed using widely targeted primary metabolomics. A total of 272 primary metabolites were identified by means of ultra-performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS) in the plums at different storage periods. There was a significant increase in the relative amounts of twenty-eight lipids, twenty amino acids and their derivatives, thirteen organic acids, ten saccharides and alcohols, six nucleotides and their derivatives, and two vitamins. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differential metabolites revealed that glucosinolate biosynthesis, starch and sucrose metabolism, ascorbate and aldarate metabolism, lysine degradation, and other metabolic pathways were significantly enriched; therefore, changes in these metabolic pathways may be key to the quality and flavor change in ‘Fengtang’ plum fruits during storage. Our results provide a theoretical foundation and technical support to evaluate ‘Fengtang’ plum fruit quality.