A comparative UHPLC-QqQ-MS-based metabolomics approach for evaluating Chinese and North American wild rice

Untargeted metabolomics and physiological phenotypic analyses reveal the defense strategies of nitrite by Lactiplantibacillus plantarum PK25

A comprehensive understanding of the defense strategies against nitrite by Lactiplantibacillus plantarum remains unknown. Herein, the effects of nitrite degradation process on metabolic profiling of L. plantarum PK25 were investigated by metabolomics and phenomenological measurement. A total of 633 metabolites were significantly different at 6, 12, and 24 incubation hours. Specifically, citrulline and lysine reduction facilitated strain survival by limiting cell growth. A significant reduction of unsaturated fatty acids was observed, which could induce reduced cell membrane fluidity to prevent nitrite entry. The accumulation of thymine and cytosine might be resulted from accelerated RNA expression to accelerate the repair of cells. Dopamine and ergothioneine could serve as antioxidants to prevent bacteria from oxidative stress. Furthermore, cell filamentation production, increased hydrophobicity, and altered antioxidant enzyme activity were favorable alterations made by strain. Our study demonstrated the metabolite profile alteration of L. plantarum during nitrite degradation, which provided a theoretical basis for targeting strain function.

LC-MS-based serum metabolomics analysis and potential biomarkers for oxaliplatin induced neurotoxicity in colorectal cancer

Oxapliplatin-induced peripheral neuropathy (OIPN) is a significant adverse effect encountered in patients with colorectal cancer undergoing oxaliplatin therapy. However, the pathogenesis of OIPN remains unclear. This study aimed to identify potential diagnostic biomarkers for OIPN and discover the metabolic pathways associated with the disease. Serum samples were collected from 218 subjects, including patients with OIPN and control (CONT). The metabolite profiles were analyzed using nontargeted liquid chromatography-mass spectrometry (LC-MS) serum metabolomics method. Subsequently, differentially altered metabolites were identified and evaluated through multivariate statistical analyses. In this study, patients with OIPN and CONT were distinguished by ten significant metabolites. The levels of racemethionine, O-acetylcarnitine, stearolic acid, aminoadipic acid, iminoarginine, galactaric acid, and all-trans-retinoic acid were increased, whereas the levels of 3-methyl-L-tyrosine, 5-aminopentanoic acid, and erythritol compared were found to be diminished in patients with OIPN when compared to the CONT. Through receiver operating characteristic (ROC) curve analysis, racemethionine, stearolic acid, 5-aminopentanoic acid, erythritol, aminoadipic acid, and all-trans-retinoic acid were pinpointed as promising biomarkers for OIPN. Significantly altered pathways included amino acids (arginine biosynthesis, beta-alanine metabolism, arginine and proline metabolism, alanine, aspartate and glutamate metabolism, lysine degradation, and phenylalanine, tyrosine and tryptophan biosynthesis), lipid (linoleic acid metabolism and the biosynthesis of unsaturated fatty acids), and energy metabolism. This study, by identifying serum biomarkers and dissecting metabolic pathways, offers a groundbreaking perspective on the susceptibility mechanisms underlying OIPN. It stands as an invaluable resource for the adjunctive diagnosis of OIPN, with the potential to diminish the incidence of adverse reactions and to enhance the objectivity and reliability of clinical diagnoses of OIPN.

De novo assembly of a near-complete genome of aquatic vegetable Zizania latifolia in the Yangtze River Basin

The cultivated Zizania latifolia, an aquatic vegetable prevalent in the Yangtze River Basin, represents a unique plant-fungus complex whose domestication is associated with host-parasite co-evolution. In this study, we present a high-quality, chromosome-scale genome assembly of cultivated Z. latifolia. We employed PacBio long-read sequencing and Hi-C technology to generate ~578.42 Mb genome assembly, which contains 47.59% repeat sequences with a contig N50 of ~33.75 Mb. The contigs were successfully clustered into 17 chromosomal-sized scaffolds with a GC content of 43.26%, showing 98.39% completeness in BUSCO analysis. In total, we predicted 39,934 protein-coding genes, 88.79% of which could be functionally annotated. This genome assembly provides a valuable resource for unraveling Z. latifolia's domestication process, and advances our understanding of the evolutionary history and agricultural potential of Z. latifolia.

Overexpression of ZlMYB1 and ZlMYB2 increases flavonoid contents and antioxidant capacity and enhances the inhibition of α-glucosidase and tyrosinase activity in rice seeds

Anthocyanins are natural flavonoids with a high antioxidant power and many associated health benefits, but most rice produce little amounts of these compounds. In this study, 141 MYB transcription factors in 15 chromosomes, including the nucleus-localised ZlMYB1 (Zla03G003370) and ZlMYB2 (Zla15G015220), were discovered in Zizania latifolia. Overexpression of ZlMYB1 or ZlMYB2 in rice seeds induced black pericarps, and flavonoid content, antioxidant capacity, and α-glucosidase and tyrosinase inhibition effects significantly increased compared to those in the control seeds. ZlMYB1 and ZlMYB2 overexpression induced the upregulation of 764 and 279 genes, respectively, and the upregulation of 162 and 157 flavonoids, respectively, linked to a black pericarp phenotype. The expression of flavonoid 3'-hydroxylase and UDP-glycose flavonoid glycosyltransferase, as well as the activities of these enzymes, increased significantly in response to ZlMYB1 or ZlMYB2 overexpression. This study systematically confirmed that the overexpression of ZlMYB1 and ZlMYB2 promotes flavonoid biosynthesis (especially of anthocyanins) in rice.

Widely Targeted Metabolomics Reveal the Distribution of Metabolites in Shatian Pomelo Fruit

Using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) technology in multiple reaction monitoring mode, a widely targeted metabolomics approach was employed to identify metabolites in five tissues (exocarp, endocarp, segment membrane, pulp, and seeds) of the Shatian pomelo fruit. The differences in metabolite composition and abundance among different tissues were analyzed using multivariate statistical analysis methods. The results showed that a total of 1722 metabolites were identified from the five tissues of the Shatian pomelo, including 413 flavonoids and 277 amino acids and their derivatives. Flavonoid metabolites accumulate the most abundantly in the exocarp and seeds, while amino acids and their derivatives are primarily accumulated in the exocarp and pulp. A total of 649 key differential metabolites were screened, including flavonoids, amino acids, and their derivatives, indicating the presence of tissue-specific accumulation of metabolites in the Shatian pomelo. This study systematically investigated the metabolite distribution in different tissue parts of the Shatian pomelo, and validated the feasibility of widely targeted metabolomics technology in pomelo quality analysis. It provided a theoretical reference for metabolic research on the Shatian pomelo and other citrus fruits, and offered a theoretical basis for the efficient utilization of pomelo resources.

The Effect of Reduced Nitrogen Fertilizer Application on japonica Rice Based on Volatile Metabolomics Analysis

Nitrogen is critical for rice yield and quality, but its overuse can be detrimental to efficiency and the environment. To identify changes in the quality of rice in response to the reduced application of nitrogen fertilizer, we carried out a comprehensive metabolomics study of SuiJing 18 using volatile metabolomics methods. Our results showed that SuiJing 18 had a total of 358 volatile metabolites, mainly lipids (16.25%), terpenoids (15.41%), heterocyclic compounds (15.13%), and hydrocarbons (13.45%). SuiJing 18 underwent significant changes in response to the reduced application of nitrogen fertilizer. Key sweet volatile compounds such as 4-methyl-benzeneacetaldehyde, hexyl acetate, and 2-methylnaphthalene were present at significantly higher levels when nitrogen fertilizer was applied at a rate of 68 kg of pure nitrogen per hectare, and their flavor characteristics also differed significantly from the compounds resulting from the other two treatments. Focusing on 16 differential volatile metabolites, we further investigated their effects on flavor and quality, thus laying the foundation for a greater understanding of the biomarkers associated with changes in rice quality. This study contributes to a better understanding of the mechanisms underlying changes in rice quality after reduced nitrogen fertilizer application.

Characterisation of aroma compounds, sensory characteristics, and bioactive components of a new type of huangjiu fermented with Chinese wild rice (Zizania latifolia)

Chinese wild rice (CWR) is a nutritious and healthy whole grain, worth developing. To develop and use its value, a new type of huangjiu was brewed with CWR, and the flavour characteristics, sensory quality, functional and bioactive components were evaluated. CWR (67 flavour substances) and glutinous rice (GR)-CWR huangjiu (62 flavour substances) had a better flavour than GR huangjiu (54 flavour substances), and the overall style of GR-CWR huangjiu was more skewed towards GR. The fruity, honey, caramel-like, herb and smoky aroma attributes of CWR huangjiu were higher than those of GR huangjiu (P < 0.05), while only the alcoholic was weaker (P < 0.05) due to the lower alcohol content. The huangjiu brewed using CWR had a better taste than that brewed using only GR. Furthermore, CWR huangjiu had the highest content of total dietary fiber (732.0 ± 15.2 mg/100 g), followed by GR-CWR (307.0 ± 8.5 mg/100 g), and GR (127.0 ± 2.3 mg/100 g). CWR huangjiu also had the highest total phenolic compounds (3.32 ± 0.05 mg/100 g/%vol) and total saponins (2.46 ± 0.03 mg/100 g/%vol) contents, followed by GR-CWR and GR. This study provides guidance for exploring further possibilities for CWR in the future.

Widely targeted metabolomic and KEGG analyses of natural deep eutectic solvent-based saponins extraction from Camellia oleifera Abel.: Effects on composition

Camellia saponins are important by-products of Camellia Oleifer Abel. processing. In this study, an eco-friendly method based on natural deep eutectic solvents (NaDESs, proline and glycerol at a molar ratio of 2:5) was established to extract saponins from C.oleifera cakes. The content of saponin (702.22 ± 1.28 mg/g) obtained using NaDES was higher than those extracted using water or methanol. UPLC-Q-TOF MS analysis of chemical structure showed that the difference in the extraction technique alter individual saponins. A widely targeted metabolomic approach and KEGG metabolic pathway analysis showed that the upregulated metabolites in the NaDES-based extract mainly included flavonoids, alkaloids, and phenolic acids; and they were involved in arginine and proline metabolism, metabolic pathways, phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, and flavonoid biosynthesis. The present study proposes a selective substitute for use in the extraction of camellia saponins with composition analysis.

Metabolomics applications for plant-based foods origin tracing, cultivars identification and processing: Feasibility and future aspects

Metabolomics, the systematic study of metabolites, is dedicated to a comprehensive analysis of all aspects of plant-based food research and plays a pivotal role in the nutritional composition and quality control of plant-based foods. The diverse chemical compositions of plant-based foods lead to variations in sensory characteristics and nutritional value. This review explores the application of the metabolomics method to plant-based food origin tracing, cultivar identification, and processing methods. It also addresses the challenges encountered and outlines future directions. Typically, when combined with other omics or techniques, synergistic and complementary information is uncovered, enhancing the classification and prediction capabilities of models. Future research should aim to evaluate all factors affecting food quality comprehensively, and this necessitates advanced research into influence mechanisms, metabolic pathways, and gene expression.

Decoding the Effects of High Hydrostatic Pressure and High-Temperature Short-Time Sterilization on the Volatile Aroma Profile of Red Raspberry Juice

The loss of distinctive aromas due to sterilization significantly hinders efforts to enhance the sensory quality of fruit and vegetable juices. This study aimed to elucidate the impacts of high-hydrostatic pressure (HHP) and high-temperature short-time (HTST) sterilization methods on the loss of C6 aldehyde aroma-active compounds in red raspberry juice. External standard quantification and quantitative descriptive analysis (QDA) revealed a notable decline in the levels of hexanal and (Z)-3-hexenal following the HHP and HTST treatments (p < 0.05), resulting in a marked attenuation of the grassy aroma characteristic of red raspberry juice. Furthermore, a comprehensive examination of the precursors, pivotal enzymes, intermediates, and downstream aromas within the fatty acid metabolism pathway in different raspberry juice samples indicated that the C6 aldehydes loss induced by HHP and HTST sterilizations was primarily ascribed to the competitive inhibition of β-oxidation and the hindered enzymatic oxidation of fatty acids. These insights suggest that modifying sterilization protocols and enhancing enzymatic stability may help preserve the aroma integrity of raspberry juice. Our findings offer practical guidance for optimizing juice processing techniques to maintain flavor.

Nontargeted metabolomics and enzyme inhibitory and antioxidant activities for chemical and biological characterization of jujube (Ziziphus jujuba) extracts

The chemical and biologically active characterization of jujube samples (fruits, cores, and leaves) were carried out by the integrated nontargeted metabolomics and bioassay. Firstly, collision cross-section values of active compounds in jujubes were determined by ultrahigh-performance liquid chromatography coupled with ion mobility quadrupole time-of-flight mass spectrometry. Then, a multidimensional statistical analysis that contained principal component analysis, partial least squares-discriminant analysis and hierarchical clustering analysis was employed to effectively cluster different tissues and types of jujubes, making identification more scientific. Furthermore, angiotensin-converting enzyme (ACE) and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) were used to evaluate the quality of jujubes from a double activity dimension. The analytical results obtained by using ACE and DPPH to evaluate the quality of jujube were different from multivariate statistics, providing a reference for the application of jujube. Therefore, integrating chemical and biological perspectives to evaluate the quality of jujube provided a more comprehensive evaluation and effective reference for clinical needs.

Turning weeds into feed: Ensiling Calotropis gigantea (Giant milkweed) reduces its toxicity and enhances its palatability for dairy cows

Calotropis gigantea (Giant milkweed, GM) has the potential to be utilized as a new feed additive for ruminants, however, the presence of unpalatable or toxic compounds decreases animal feed intake. This study aimed to valorize GM as a potential new feed resource through the chemical and microbial biotransformation of toxic compounds that will henceforth, make the plant palatable for cows. After GM's ensiling using fermentative bacteria, the plant was sampled for UHPLC-MS/MS to analyse the metabolomic changes. Illumina Miseq of the 16 S rRNA fragment genes and ITS1 were used to describe the microbial composition and structure colonizing GM silage and contributing to the biodegradation of toxic compounds. Microbial functions were predicted from metataxonomic data and KEGG pathways analysis. Eight Holstein dairy cows assigned in a cross-over design were supplemented with GM and GM silage to evaluate palatability and effects on milk yield and milk protein. Cows were fed their typical diet prior to the experiment (positive control). After ensiling, 23 flavonoids, 47 amino acids and derivatives increased, while the other 14 flavonoids, 9 amino acids and derivatives decreased, indicating active metabolism during the GM ensiling process. Lactobacillus buchneri, Bacteroides ovatus, and Megasphaera elsdenii were specific to ensiled GM and correlated to functional plant metabolites, while Sphingomonas paucimobilis and Staphylococcus saprophyticus were specific to non-ensiled GM and correlated to the toxic metabolite 5-hydroxymethylfurfural."Xenobiotics biodegradation and metabolism", "cancer overview" and "neurodegenerative disease" were the highly expressed microbial KEGG pathways in non-ensiled GM. Non-ensiled GM is unpalatable for cows and drastically reduces the animal's feed intake, whereas ensiled GM does not reduce feed intake, milk yield and milk protein. This study provides essential information for sustainable animal production by valorizing GM as a new feed additive.

Effects of inoculation and dry matter content on microbiome dynamics and metabolome profiling of sorghum silage

Sorghum forage was ensiled for 90 days at two dry matter (DM) contents (27 vs. 39%) without or with Lactiplantibacillus plantarum inoculation. On day 90 of fermentation, silages were sampled to assess the microbial community dynamics and metabolome profile. L. plantarum inoculation improved silage quality, as shown by a lower pH and greater acetic acid concentration. Loss of DM remained unaffected by L. plantarum inoculation but was greater in low- vs. high-DM sorghum silages (14.4 vs. 6.62%). The microbiome analysis revealed that Pseudomonas congelans represented the dominant species of the epiphytic microbiota in both low- and high-DM sorghum forage before ensiling. However, L. buchneri represented the dominant species at the end of ensiling. Ensiling fermentation resulted in distinct metabolic changes in silages with varying DM content. In low-DM silages, ensiling fermentation led to the accumulation of 24 metabolites and a reduction in the relative concentration of 13 metabolites. In high-DM silages, ensiling fermentation resulted in an increase in the relative concentration of 26 metabolites but a decrease in the concentration of 8 metabolites. Compared to non-inoculated silages, L. plantarum inoculation resulted in an increased concentration of 3 metabolites and a reduced concentration of 5 metabolites in low-DM silages. Similarly, in high-DM silages, there was an elevation in the relative concentration of 3 metabolites, while a decrease in 7 other metabolites. Ten metabolites with bio-functional activity were identified, including chrysoeriol, isorhamnetin, petunidin 3-glucoside, apigenin, caffeic acid, gallic acid, p-coumaric acid, trans-cinnamic acid, herniarin, and 3,4-dihydroxy-trans-cinnamate. This study presents a comprehensive analysis of microbiome and metabolome profiling of sorghum forage during ensiling as a function of DM content and L. plantarum inoculation, with a particular emphasis on identifying metabolites that may possess bio-functional properties. KEY POINTS: • DM loss was not different by L. plantarum but higher in low- vs. high-DM silage. • L. buchneri dominated ensiling, regardless of DM level. • 10 metabolites with bio-functional activity were identified.

UPLC-ESI-MS/MS-Based Analysis of Various Edible Rosa Fruits Concerning Secondary Metabolites and Evaluation of Their Antioxidant Activities

The genus Rosa is globally popular with well-established applications since it has a high edible and medicinal value. However, relatively limited research has been conducted on the composition and quality of wild Rosa fruits. The present study aimed to compare the properties and chemical components of five wild edible Rosa fruits, Rosa roxburghii, Rosa sterilis, Rosa laevigata, Rosa davurica, and Rosa sericea. The UPLC-ESI-MS/MS approach identified the key metabolites among the five Rosa fruits as flavonoids, phenolic acids, and organic acids. The main differential metabolites among the five fruits are flavonoids (22.29-45.13%), phenolic acids (17-22.27%), and terpenoids (7.7-24%), respectively. In total, 125 compounds served as potential markers for the five Rosa species. Differential metabolic pathways of five Rosa fruits were analyzed using the KEGG approach. Rosa laevigata fruits showed the highest total polysaccharide (TPS) content of 64.48 g/100 g. All the five Rosa extracts effectively decreased the levels of malondialdehyde while increasing the activities of superoxide dismutase and glutathione peroxidase in the H2O2-induced HaCaT cell model, demonstrating high potential for antioxidant development. Our findings suggest that the five studied Rosa fruits exhibit biological activity and edible value worth further exploration.

Integrated analysis of multiple metabolome and transcriptome revealed the accumulation of flavonoids and associated molecular regulation mechanisms in Rubus chingii Hu at different developmental stages

The traditional Chinese herb Rubus chingii Hu (R. chingii) is widely used in clinical practice due to its beneficial effects. Flavonoids are the important class of pharmacological substances in R. chingii, however, the molecular mechanism underlying the differences in active flavonoid contents in R. chingii at different developmental stages remain poorly understood. In this experiment, we selected four developmental stages (GG, GY, YR, RR) of R. chingii as the research material. We studied the untargeted and targeted metabolic profiles of flavonoids in different periods of R. chingii, combining full-length and comparative transcriptome analyses. Functional analyses were conducted on genes implicated in flavonoid differences. GG and RR displayed relatively higher and lower contents of flavonols, flavones, flavanols, flavanones, and isoflavonoid, respectively. RNA-seq analyses showed structural genes such as RcPAL, RcC4H, Rc4CL, RcCHS, RcCHI, RcF3H, RcF3'H, and RcFLS in flavonoid biosynthesis pathway were upregulated in GG, which were essential for the accumulation flavanones, flavones, and flavonols (effective components). qRT-PCR analyses investigated that six structural genes RcCHI, RcF3H, 2 RcCHS, and 2 Rc4CL, two TFs RcMYB308 and RcMYB123 had a consistent expression pattern with which in transcriptome. Also, an interaction network showed that the RcMYB308 could positively regulate Ka3R, Qu, Qu3G, AS, Hy, Ti through RcF3H. Furthermore, Subcellular localization analysis revealed that RcMYB308 was localization to the nucleus. In tobacco, RcMYB308 was overexpressed, resulting in higher flavonoids, RcF3H, RcF3'H, RcCHI, and RcFLS. RcMYB308 upregulated RcF3H in dual-luciferase assays. These results provide new insights for further understanding the molecular mechanism regulating flavonol biosynthesis in R. chingii fruit, and also provide a potential MYB regulator for molecular breeding of R. chingii.

GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination

Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, L-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of L-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.

Insights into the metabolite profiles of Rubus chingii Hu at different developmental stages of fruit

The fruits of Rubus chingii Hu have high medicinal and nutritional values. However, the metabolite profiles of R. chingii, especially the alterations during different development stages of fruit, have not been comprehensively analyzed, hindering the effective utilization of the unique species. In this study, we comprehensively analyzed the metabolites of R. chingii fruit at four developmental stages using systematic untargeted and targeted liquid chromatography-mass spectrometry metabolomics analysis and identified 682 metabolites. Significant changes were observed in metabolite accumulation and composition in fruits during the different developmental stages. The contents of the index components, kaempferol-3-O-rutinoside and ellagic acid, were the highest in immature fruit. The analysis identified 64 differentially expressed flavonoids and 39 differentially expressed phenolic acids; the accumulation of most of these differentially expressed metabolites decreased with the developmental stages of fruit from immaturity to maturity. These results confirmed that the developmental stages of fruit are a critical factor in determining its secondary metabolite compositions. This study elucidated the metabolic profile of R. chingii fruit at different stages of development to understand the dynamic changes in metabolites.

Analysis of Metabolites and Metabolic Pathways of Three Chinese Jujube Cultivar

Most studies on metabolites in jujube fruits focus on specific types of metabolites, but there are only a few comprehensive reports on the metabolites in jujube fruits. In order to understand the variance of metabolites in fruits of different jujube varieties. The objective of this study was to explore the metabolic components of jujube fruit by comparing three cultivars, namely Linyi LiZao (LZ), Jiaocheng SuantianZao (STZ), and Xianxian Muzao (MZ). The metabolites present in the fruits of these three cultivars were evaluated and compared. The results revealed the detection of 1059 metabolites across the three jujube varieties, with each cultivar exhibiting distinct metabolic characteristics. Notably, MZ exhibited a higher abundance of six metabolite classes, namely amino acids and derivatives, flavonoids, lipids, organic acids, phenolic acids, and terpenoids, compared to LZ. Conversely, LZ exhibited higher concentrations of alkaloids, lignans, coumarins, nucleotides, and their derivatives compared to the other two cultivars. In terms of STZ, its content of amino acids and derivatives, lignans and coumarins, organic acids, and phenolic acids was largely similar to that of LZ. However, the content of alkaloids, nucleotides, and their derivatives, and terpenoids was significantly higher in STZ compared to LZ. Additionally, STZ exhibited lower levels of flavonoids and lipids compared to LZ. Moreover, MZ was found to be less nutritionally rich than STZ, except for lignans and coumarins, as it displayed lower levels of all the metabolites. KEGG pathway enrichment analysis revealed six significantly different metabolic pathways (p < 0.05) between LZ and MZ, including arginine and proline metabolism, sphingolipid metabolism, flavonoid biosynthesis, glutathione metabolism, glycerophospholipid metabolism, and cysteine and methionine metabolism. The metabolites in STZ and MZ exhibited three significantly different pathways (p < 0.05), primarily associated with flavonoid biosynthesis, arginine and proline metabolism, and sphingolipid metabolism. The significantly differential metabolites between LZ and STZ were observed in the phenylpropionic acid biosynthesis pathway and the ubiquinone and other terpenoid-quinone biosynthesis pathways. LZ showed a closer relationship with STZ than with MZ. STZ and LZ exhibited higher medicinal values, while LZ had lower acidity and MZ displayed better antioxidant activity. This study presents the first thorough analysis of metabolites in LZ, STZ, and MZ cultivars, which can serve as a theoretical basis for quality analysis, functional research, and classification processing of jujube fruit.

Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris

Wild rice (Zizania spp.), an aquatic grass belonging to the subfamily Gramineae, has a high economic value. Zizania provides food (such as grains and vegetables), a habitat for wild animals, and paper-making pulps, possesses certain medicinal values, and helps control water eutrophication. Zizania is an ideal resource for expanding and enriching a rice breeding gene bank to naturally preserve valuable characteristics lost during domestication. With the Z. latifolia and Z. palustris genomes completely sequenced, fundamental achievements have been made toward understanding the origin and domestication, as well as the genetic basis of important agronomic traits of this genus, substantially accelerating the domestication of this wild plant. The present review summarizes the research results on the edible history, economic value, domestication, breeding, omics research, and important genes of Z. latifolia and Z. palustris over the past decades. These findings broaden the collective understanding of Zizania domestication and breeding, furthering human domestication, improvement, and long-term sustainability of wild plant cultivation.

Rice Phytoalexins: Half a Century of Amazing Discoveries; Part I: Distribution, Biosynthesis, Chemical Synthesis, and Biological Activities

Cultivated rice is a staple food for more than half of the world's population, providing approximately 20% of the world's food energy needs. A broad spectrum of pathogenic microorganisms causes rice diseases leading to huge yield losses worldwide. Wild and cultivated rice species are known to possess a wide variety of antimicrobial secondary metabolites, known as phytoalexins, which are part of their active defense mechanisms. These compounds are biosynthesized transiently by rice in response to pathogens and certain abiotic stresses. Rice phytoalexins have been intensively studied for over half a century, both for their biological role and their potential application in agronomic and pharmaceutical fields. In recent decades, the growing interest of the research community, combined with advances in chemical, biological, and biomolecular investigation methods, has led to a notable acceleration in the growth of knowledge on rice phytoalexins. This review provides an overview of the knowledge gained in recent decades on the diversity, distribution, biosynthesis, chemical synthesis, and bioactivity of rice phytoalexins, with particular attention to the most recent advances in this research field.

Metabolic Profiling of Oryza sativa L. Triggered by Chilling Stress Using Ultraperformance Liquid Chromatography Coupled with Quadrupole/Time-of-Flight Mass Spectrometry (UPLC-QTOF-MS) with Transcriptome Analysis

Low temperature, a major abiotic stress, often causes molecular changes in crops, which leads to metabolic disturbances and probably affects crop yield. In this study, chilling stress induced distinct metabolic profiles associated with transcriptome regulation, exhibiting great metabolic differences between Qiutianxiaoting (japonica) and 93-11 (indica). In total, 41 and 58 differential metabolites were screened and identified in Qiutianxiaoting and 93-11, respectively. Five key metabolites were screened in response to chilling stress, which were involved or related to different metabolic pathways. Moreover, starch and sucrose metabolism, aminoacyl-tRNA biosynthesis, and phenylpropanoid biosynthesis were significantly enriched in Qiutianxiaoting to maintain cellular homeostasis. Aminoacyl-tRNA biosynthesis and antioxidation metabolism were significantly enriched in 93-11, but disorders of the metabolome and transcriptome occurred at recovery stage. The results could provide some useful information for in-depth understanding of cold-resistant mechanisms, as well as reference for the selection and breeding of rice varieties.

Phytochemical analysis of Ziziphus jujube leaf at different foliar ages based on widely targeted metabolomics

Based on metabolomics, the metabolites of Jujube leaves LS1 (one bud and two leaves), LS2 (one bud and three leaves), and LS3 (one bud and four leaves) were taken and examined by ultra-high performance liquid chromatography-mass spectrometry technique. There were 22 substance categories that were identified. Principal component analysis was also utilized to distinguish the metabolomics at the three different foliar ages, and the results suggested that the samples at different foliar ages were clearly separated, demonstrating that the metabolites in the three foliar ages were significantly different. Through the screening of differential metabolites and hierarchical clustering analysis, our results suggested that the composition and the content distribution of the differential metabolites at three different foliar ages were significantly different. In the LS1, delphinidin, N-hydroxy tryptamine, serotonin, methylquercetin O-hexoside, tricin 7-O-hexoside, and eriodictyol C-hexoside were identified as the distinctive compounds. In the LS2, N-caffeoyl agmatine, lysoPC 18:3 (2n isomer), N-(4′-O-glycosyl)-p-coumaroyl-agmatine, dihydromyricetin, and hydroxy-methoxycinnamate were identified as the distinctive compounds. Similarly, the 3-O-p-coumaroyl-quinic acid, O-feruloyl 4-hydroxylcoumarin, isorhamnetin 3-O-neohesperidoside, cyanidin 3-O-galactoside, quercetin O-acetylhexoside, and DIMBOA glucoside were identified as the distinctive compounds in LS3. These characteristic compounds could provide a strong theoretical basis for rapid identification of jujube leaves at different foliar ages.

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.

Sensory and metabolite migration from tilapia skin to soup during the boiling process: fast and then slow

This study mainly studied sensory and metabolite migration from the skin to the soup in the boiling process of tilapia skin using content analysis, electronic nose technique, electronic tongue technique, and metabolomics technique based on ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry and gas chromatography-time-of-flight-mass spectrometry. The content changes, flavor changes, taste changes, metabolite numbers and differential metabolite numbers for both tilapia skin and soup mainly occurred in the initial 30 min. Moreover, the initial 10 min was the key period for the metabolite changes in the boiling process. Further, the differential metabolites in these three periods (0–10, 10–30, and 30–60 min) were identified to show the metabolites migration process. Six (adenine, gingerol, terephthalic acid, vanillin, pentanenitrile, and 2-pyrrolidinonede) and seven (butyramide, lysope(0:0/20:4(5z,8z,11z,14z)), lysope(22:6(4z,7z,10z,13z,16z,19z)/0:0), linoleic acid, N-acetylneuraminic acid, L-threose, and benzoin) chemicals were screened out in the differential metabolites of tilapia skin and soup, respectively, with Variable Importance in the Projection of >1 and p value of <0.05. This work would be beneficial to understand the sensory and metabolite migration in the preparation process of fish soup and provided a metabolomic analysis route to analyze metabolites migration in food.

Transcriptional regulation mechanism of flavonoids biosynthesis gene during fruit development in astragalus membranaceus

Astragalus membranaceus, as an important medicinal plant, are an excellent source of flavonoids. Flavonoid compounds in A. membranaceus have been widely used in medicine and supplement, but known of the molecular mechanism of flavonoid biosynthesis is still very few. Here, we analyzed the association between flavonoid content and gene expression pattern during six different fruit developmental stages. Sixteen gene expression trends were significantly identified, involving 8,218 genes. The gene expression trend in profile 0 was positively correlated with flavonoid content, while the gene expression trend in profile 79 was negatively correlated with flavonoid content at six developmental stages. The expression level of genes involved in the general phenylpropane pathway was higher than that of genes involved in the flavonoid biosynthesis pathway. A total of 37 genes involved in flavonoid synthesis were identified in A. membranaceus. The expression pattern of flavonoid-related genes was highly correlated with flavonoid content. Our study deepened the understanding of the flavonoid synthesis mechanism and provided useful resources for future studies on the high flavonoid molecular breeding of A. membranaceus.

Comprehensive metabolomics analysis of key taste components in different varieties of table grapes

Grapes are one of the world's largest fruit crops, which are rich in nutrients and taste. Summer Black, Gui Fei, Kyoho Grape, Giant Rose, Shine Muscat, and Rosario Bianco are the six most popular table grapes in Wuxi city, Jiangsu province. Owing to the lack of comprehensive investigations of metabolites in table grapes, the metabolic causes of differences in their taste are unknown. In this study, metabolites of six table grapes were profiled using ultra-high-performance liquid chromatography-Q-Exactive Orbitrap tandem mass spectrometry combined with a multivariate analysis. Orthogonal partial least squares discriminant analysis clearly discriminated among the metabolites of these varieties. Metabolic pathway analysis revealed that carbohydrate and amino acid metabolisms was highly conserved among these varieties. Our results suggest that the taste differences in the six table grape varieties can be explained by variations in composition and abundance of carbohydrates, organic acids, amino acids, and polyphenols. This study provides comprehensive insights into the underlying metabolic causes of taste variation in table grapes. This article is protected by copyright. All rights reserved.

Metabolic changes in cucumber leaves are enhanced by blue light but differentially affected by UV interactions with light signalling pathways in the visible spectrum

Ultraviolet radiation (UV, 280-400 nm) as an environmental signal triggers metabolic acclimatory responses. However, how different light qualities affect UV acclimation during growth is poorly understood. Here, cucumber plants (Cucumis sativus) were grown under blue, green, red, or white light in combination with UV. Their effects on leaf metabolites were determined using untargeted metabolomics. Blue and white growth light triggered increased levels of compounds related to primary and secondary metabolism, including amino acids, phenolics, hormones, and compounds related to sugar metabolism and the TCA cycle. In contrast, supplementary UV in a blue or white light background decreased leaf content of amino acids, phenolics, sugars, and TCA-related compounds, without affecting abscisic acid, auxin, zeatin, or jasmonic acid levels. However, in plants grown under green light, UV induced increased levels of phenolics, hormones (auxin, zeatin, dihydrozeatin-7-N-dihydrozeatin, jasmonic acid), amino acids, sugars, and TCA cycle-related compounds. Plants grown under red light with UV mainly showed decreased sugar content. These findings highlight the importance of the blue light component for metabolite accumulation. Also, data on interactions of UV with green light on the one hand, and blue or white light on the other, further contributes to our understanding of light quality regulation of plant metabolism.

Plant flavonoids: Classification, distribution, biosynthesis, and antioxidant activity

Flavonoids are a group of natural polyphenol substances abundant in vegetables, fruits, grains, and tea. As plant secondary metabolites, flavonoids play essential roles in many biological processes and responses to environmental factors in plants. Flavonoids are common in human diets and have antioxidant effects as well as other bioactivities (e.g., antimicrobial and anti-inflammatory properties), which reduce the risk of disease. Flavonoid bioactivity depends on structural substitution patterns in their C6-C3-C6 rings. However, reviews of plant flavonoid distribution and biosynthesis, as well as the health benefits of its bioactivity, remain scarce. Therefore, in the present review, we systematically summarize recent progress in the research of plant flavonoids, focusing on their biosynthesis (pathway and transcription factors) and bioactive mechanisms based on epidemic evidence, in vitro and in vivo research, and bioavailability in the human body. We also discuss future opportunities in flavonoid research, including biotechnology, therapeutic phytoproducts, and dietary flavonoids.

Metabolomic Analysis Reveals Insights into Deterioration of Rice Quality during Storage

To determine the changes in the quality of rice during storage, this study investigated the comprehensive metabolomic profiles of Nanjing 9108 (typical japonica rice) and Jianzhen 2 (typical indica rice) varieties in China, using metabolomics. A total of 13 categories of 593 metabolites including lipids (134 species), phenolic acids (78 species), flavonoids (70 species), alkaloids (67 species), organic acids (64 species), amino acids and derivatives (64 species), saccharides and alcohols (44 species), nucleotides and derivatives (37 species), vitamins (14 species), lignans and coumarins (9 species), tannins (2 species), terpenoids (2 species), and others (8 species) were identified in both varieties. The result showed significant changes in 204 metabolites in Nanjing 9108, while only 26 were altered in Jianzhen 2 during storage. These metabolites involved 46 metabolic pathways. The TCA cycle, linoleic, and α-linolenic acid metabolic pathways were unique in Nanjing 9108. Finally, the results of quantitative mass spectrometry of 11 metabolites provided insight into biomarkers associated with quality deterioration of rice. This study provides insights into the mechanism of deterioration in the quality of rice during storage.

UPLC-QQQ-MS/MS-based widely targeted metabolomic analysis reveals the effect of solid-state fermentation with Eurotium cristatum on the dynamic changes in the metabolite profile of dark tea

Eurotium cristatum is the predominant fungus and key contributor to the characteristics of post-fermented Fu brick tea (FBT) during manufacturing. In this study, the influence of solid-state fermentation (SSF) with E. cristatum on the chemical profile dynamic changes of dark tea was investigated. Results indicated that total phenolics, flavonoids, theaflavins, thearubigins, and galloyl catechins consistently decreased, degalloyl catechins and gallic acid increased in the initial stage of fermentation and decreased after long-term fermentation, and theabrownins continually increased. UPLC-QQQ-MS/MS-based widely targeted metabolomic analysis revealed that the metabolites of dark tea processed by SSF with E. cristatum were drastically different from the raw material. A total of 574 differential metabolites covering 11 subclasses were detected in the whole SSF of dark tea, and the most drastic changes occurred in the middle stage. Phenolic acids and flavonoids were the two major classes of differential metabolites. A series of reactions such as degradation, glycosylation, deglycosylation, methylation, and oxidative polymerization occurred during SSF. Overall, SSF with E. cristatum greatly influenced the metabolites of dark tea, which provided valuable insights that E. cristatum is critical in forming the chemical constituents of FBT.

Comparative Analysis of Fruit Metabolome Using Widely Targeted Metabolomics Reveals Nutritional Characteristics of Different Rosa roxburghii Genotypes

The fruits of Rosa roxburghii (R. roxburghii) Tratt., which are rich in bioactive compounds, provide numerous health benefits, yet the overall metabolism of R. roxburghii fruits and the metabolic profiles among different genotypes of R. roxburghii fruits are not fully understood. In the research, we used ultra-performance liquid chromatography/tandem mass spectrometry analysis to identify and quantify metabolites including phenolic acids, amino acids, and organic acids in six R. roxburghii genotypes; a total of 723 metabolites were identified. Comparative analysis showed some different characteristic metabolites in each genotype. Moreover, flavonoids, triterpenoids, and phenolic acids were significantly correlated with the antioxidant capacity of the fruit extract. Our results suggest that R. roxburghii fruits have rich bioactive metabolites beneficial to human health and that Rr-7 and Rr-f have more potential to be used as medicinal material or functional food than other genotypes. This research provides helpful information for developing new functional foods of R. roxburghii genotypes.

Comparative metabolomics study of Tartary (Fagopyrum tataricum (L.) Gaertn) and common (Fagopyrum esculentum Moench) buckwheat seeds

Tartary buckwheat has higher health-promoting value than common buckwheat. However, the related metabolites information except flavonoids is largely deficient. Here, we compared the seed metabolomes of the two species using a UHPLC-QqQ-MS-based metabolomics approach. In total, 722 metabolites were obtained, of which 84 and 78 were identified as the key active ingredients of Traditional Chinese Medicines and the active pharmaceutical ingredients for six major diseases-resistance, respectively. Comparative analysis showed there were obviously difference in metabolic profiles between the two buckwheat species, and further found 61 flavonoids and 94 non-flavonoids metabolites displayed significantly higher contents (≥2 fold) in Tartary buckwheat than in common buckwheat. Our results suggest that Tartary and common buckwheat seeds are rich in metabolites beneficial to human health, and non-flavonoids metabolites also contributed to Tartary buckwheat's higher health-promoting value than common buckwheat. This study provides valuable information for the development of new functional foods of Tartary buckwheat.

Analyses of key gene networks controlling carotenoid metabolism in Xiangfen 1 banana

BACKGROUND

Banana fruits are rich in various high-value metabolites and play a key role in the human diet. Of these components, carotenoids have attracted considerable attention due to their physiological role and human health care functions. However, the accumulation patterns of carotenoids and genome-wide analysis of gene expression during banana fruit development have not been comprehensively evaluated.

RESULTS

In the present study, an integrative analysis of metabolites and transcriptome profiles in banana fruit with three different development stages was performed. A total of 11 carotenoid compounds were identified, and most of these compounds showed markedly higher abundances in mature green and/or mature fruit than in young fruit. Results were linked to the high expression of carotenoid synthesis and regulatory genes in the middle and late stages of fruit development. Co-expression network analysis revealed that 79 differentially expressed transcription factor genes may be responsible for the regulation of LCYB (lycopene β-cyclase), a key enzyme catalyzing the biosynthesis of α- and β-carotene.

CONCLUSIONS

Collectively, the study provided new insights into the understanding of dynamic changes in carotenoid content and gene expression level during banana fruit development.

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

Chinese wild rice (Zizania latifolia; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 38,852 genes, with 52.89% of the genome comprising repetitive sequences. Phylogenetic analyses revealed close relation of Z. latifolia to Leersia perrieri and Oryza species, with a divergence time of 19.7-31.0 million years. Collinearity and transcriptome analyses revealed candidate genes related to seed shattering, providing basic information on abscission layer formation and degradation in Z. latifolia. Moreover, two genomic blocks in the Z. latifolia genome showed good synteny with the rice phytocassane biosynthetic gene cluster. The updated genome will support future studies on the genetic improvement of Chinese wild rice and comparative analyses between Z. latifolia and other plants.

Polyploidization Increases the Lipid Content and Improves the Nutritional Quality of Rice

Plant polyploidization is frequently associated with changes in nutrient contents. However, the possible contribution of metabolites to this change has not been investigated by characterizing the metabolite contents of diploid and tetraploid forms of rice (Oryza sativa L.). We compared the metabolites of a group of diploid-tetraploid japonica brown rice and a group of diploid-tetraploid indica brown rice based on liquid chromatography-tandem mass spectrometry. In total, 401 metabolites were identified; of these, between the two diploid-tetraploid groups, 180 showed opposite expression trends, but 221 showed the same trends (147 higher abundance vs. 74 lower abundance). Hierarchical cluster analysis of differential metabolites between diploid and tetraploid species showed a clear grouping pattern, in which the expression abundance of lipids, amino acids and derivatives, and phenolic acids increased in tetraploids. Further analysis revealed that the lipids in tetraploid rice increased significantly, especially unsaturated fatty acids and phospholipids. This study provides further basis for understanding the changes in rice nutritional quality following polyploidization and may serve as a new theoretical reference for breeding eutrophic or functional rice varieties via polyploidization.

A Comparative Metabolomic Analysis Reveals Difference Manufacture Suitability in "Yinghong 9" and "Huangyu" Teas (Camellia sinensis)

"Yinghong 9" is a widely cultivated large-leaf variety in South China, and the black tea made from it has a high aroma and strong sweet flavor. "Huangyu" is a light-sensitive tea variety with yellow leaves. It was cultivated from the bud-mutation of "Yinghong 9" and has a very low level of chlorophyll during young shoot development. Due to chlorophyll being involved in carbon fixation and assimilation, the changes in photosynthesis might potentially affect the accumulation of flavor metabolites, as well as the quality of "Huangyu" tea. Although "Huangyu" has a golden yellow color and high amino acid content, the mechanism underlying the formation of leaf color and drinking value remains unclear. The widely targeted metabolomics and GC-MS analysis were performed to reveal the differences of key metabolites in fresh and fermented leaves between "Yinghong 9" and "Huangyu." The results showed that tea polyphenols, total chlorophyll, and carotenoids were more abundant in "Yinghong 9." Targeted metabolomics analysis indicated that kaempferol-3-glycoside was more abundant in "Yinghong 9," while "Huangyu" had a higher ratio of kaempferol-3-glucoside to kaempferol-3-galactoside. Compared with "Yinghong 9" fresh leaves, the contents of zeaxanthin and zeaxanthin palmitate were significantly higher in "Huangyu." The contents of α-farnesene, β-cyclocitral, nerolidol, and trans-geranylacetone, which were from carotenoid degradation and involved in flowery-fruity-like flavor in "Huangyu" fermented leaves, were higher than those of "Yinghong 9." Our results indicated that "Huangyu" was suitable for manufacturing non-fermented tea because of its yellow leaf and flowery-fruity-like compounds from carotenoid degradation.

Nontargeted metabolomic and multigene expression analyses reveal the mechanism of oil biosynthesis in sea buckthorn berry pulp rich in palmitoleic acid

Sea buckthorn berry pulp (SBP) oil is abundant in palmitoleic acid (C16:1). However, metabolic mechanisms of oil biosynthesis in SBP (non-seed tissues) are not clear. Thus, comparative nontargeted metabolomic analysis of the four developmental stages of berry pulp in two lines, Za56 and TF2-36, was performed. The results revealed that glycerol-3-phosphate (G3P) was critical for high oil accumulation in the mid-early developmental stages. In particular, the metabolism of phosphatidylcholine (PC) (16:0/16:0), PC (16:0/16:1), and PC (16:1/16:1) was also significantly altered. Sufficient supply of G3P and 16:1-CoA, coupled with upregulated expression of the glycerol-3-phosphate dehydrogenase (GPD1) and delta-9 desaturase (Δ9D) genes, were associated with high oil content enriched in C16:1 in SBP. Our results provide a scientific basis for the development of metabolic engineering strategies to increase the oil content in SBP with a high level of C16:1.

UPLC-Q-TOF-MS based metabolomics study of hawthorn leaves in different geographical regions

The quality evaluation of hawthorn leaves in different geographical regions derived from the dried leaves of Crataegus pinnatifida Bge. Var. Major N.E.Br. or Crataegus pinnatifida Bge., a common blood-activating and stasis-eliminating traditional Chinese medicine, has hardly been reported. In this study, the chemical comparison of 40 batches of hawthorn leaf samples collected from Hebei, Liaoning, Shandong and Shanxi Provinces was performed using an ultra-high performance liquid chromatography with electrospray ionization-tandem mass spectrometry-based metabolic profile and pattern recognition analysis approach. A total of 233 compounds were determined. Among them, 40 compounds were selected as potential metabolites responsible for the differential clustering, and the differential metabolite-based evaluation model was applied to well distinguish the origin of seven batches of hawthorn leaves sold on the market. Further analysis of the KEGG pathway showed that five core metabolites containing flavonoids and lignins were mainly involved in flavonoid biosynthesis, flavone and flavonol biosynthesis, and stilbenoid, diarylheptanoid and gingerol biosynthesis. Taking the content of flavonoids, core markers, as the evaluation basis, it was found that the quality of hawthorn leaves in Hebei and Liaoning was better. The study provides a reference for the rational utilization of hawthorn leaves, and highlights that the metabolomics-driven analysis method is more suitable for the quality evaluation of traditional Chinese medicine.

Metabolomics combined with physiology and transcriptomics reveals how Citrus grandis leaves cope with copper-toxicity

Limited data are available on metabolic responses of plants to copper (Cu)-toxicity. Firstly, we investigated Cu-toxic effects on metabolomics, the levels of free amino acids, NH₄⁺-N, NO₃^--N, total nitrogen, total soluble proteins, total phenolics, lignin, reduced glutathione (GSH) and malondialdehyde, and the activities of nitrogen-assimilatory enzymes in 'Shatian' pummelo (Citrus grandis) leaves. Then, a conjoint analysis of metabolomics, physiology and transcriptomics was performed. Herein, 59 upregulated [30 primary metabolites (PMs) and 29 secondary metabolites (SMs)] and 52 downregulated (31 PMs and 21 SMs) metabolites were identified in Cu-toxic leaves. The toxicity of Cu to leaves was related to the Cu-induced accumulation of NH₄⁺ and decrease of nitrogen assimilation. Metabolomics combined with physiology and transcriptomics revealed some adaptive responses of C. grandis leaves to Cu-toxicity, including (a) enhancing tryptophan metabolism and the levels of some amino acids and derivatives (tryptophan, phenylalanine, 5-hydroxy-l-tryptophan, 5-oxoproline and GSH); (b) increasing the accumulation of carbohydrates and alcohols and upregulating tricarboxylic acid cycle and the levels of some organic acids and derivatives (chlorogenic acid, quinic acid, d-tartaric acid and gallic acid o-hexoside); (c) reducing phospholipid (lysophosphatidylcholine and lysophosphatidylethanolamine) levels, increasing non-phosphate containing lipid [monoacylglycerol ester (acyl 18:2) isomer 1] levels, and inducing low-phosphate-responsive gene expression; and (d) triggering the biosynthesis of some chelators (total phenolics, lignin, l-trytamine, indole, eriodictyol C-hexoside, quercetin 5-O-malonylhexosyl-hexoside, N-caffeoyl agmatine, N'-p-coumaroyl agmatine, hydroxy-methoxycinnamate and protocatechuic acid o-glucoside) and vitamins and derivatives (nicotinic acid-hexoside, B₁ and methyl nicotinate). Cu-induced upregulation of many antioxidants could not protect Cu-toxic leaves from oxidative damage. To conclude, our findings corroborated the hypothesis that extensive reprogramming of metabolites was carried out in Cu-toxic C. grandis leaves in order to cope with Cu-toxicity.

Comparison of nutritional compositions of foxtail millet from the different cultivation regions by UPLC-Q-Orbitrap HRMS based metabolomics approach

Foxtail millet (Setaria italica (L.) P. Beauv) is cultivated throughout most parts of Shanxi province. Although quite a number of reports have been conducted on the bioactivities of foxtail millet, little information was available on the metabolite differences of the foxtail millet seeds from different cultivation regions. In this study, a systematic study on the metabolite composition of the foxtail millet seed from Shanxi province was conducted by ultra-high performance liquid chromatography combined with electrospray ionization quadrupole/orbitrap high-resolution mass spectrometry, and 158 compounds were characterized through analysis of mass fragmentation patterns and comparison with the data in the databases and literatures. Then the metabolomic analysis, in combination with heatmap and hierarchical clustering analysis revealed the significant differences between the foxtail millet from northern and southern Shanxi province, which was ascribed to 20 differential metabolites. Then metabolic pathway analysis was performed based on these differential metabolites, and three metabolic pathways were selected as the key contributors. The results showed that foxtail millet from different cultivation regions showed obvious metabolite differences, which was probably related to environmental factors. In addition, the findings also provide an important reference for further research on the functional food development from foxtail millet. PRACTICAL APPLICATIONS: Foxtail millet (Setaria italica (L.) P. Beauv) as a staple food among the majority of people, is rich in bioactive nutrients, including free fatty acids, triglycerides, cellulose, protein, vitamins, and polyphenol, et al. The metabolite composition of the foxtail millet seed was investigated systematically and the results showed that the climate conditions can directly affect the metabolite composition of foxtail millets, and provided important reference for the further research on the resource utilization and functional food development from foxtail millet.

Quality chemical analysis of crush-tear-curl (CTC) black tea from different geographical regions based on UHPLC-Orbitrap-MS

Crush-tear-curl (CTC) black tea is a popular beverage, owing to its unique taste characteristics and health benefits. However, differences in the taste quality and chemical profiles of CTC black tea from different geographical regions remain unclear. In this study, 28 CTC black tea samples were collected from six geographical regions and analyzed using electronic tongue and ultrahigh performance liquid chromatography-Orbitrap-mass spectroscopy. The e-tongue analysis indicated that each region's CTC black tea has its own relatively prominent taste characteristics: Sri Lanka (more umami and astringent), North India (more umami), China (more sweetness and astringent), South India (moderate umami and sweetness), and Kenya (moderate umami and astringent). Based on multivariate statistical analysis, 78 metabolites were tentatively identified and used as potential markers for CTC black tea of different origins, mainly including amino acids, flavone/flavonol glycosides, and pigments. Different metabolites, which contributed to the taste characteristics of CTC black tea, were clarified by partial least squares regression correlation analysis. Our findings may serve as useful references for future studies on origin traceability and quality characteristic determination of CTC black teas. PRACTICAL APPLICATION: This study provides useful references for future studies on the origin traceability and taste characteristic determination of CTC black teas from different geographical regions.

Candidate genes involved in the biosynthesis of lignan in Schisandra chinensis fruit based on transcriptome and metabolomes analysis

Schisandra chinensis Turcz. (Baill.) is a plant species with fruits that have been well known in Far Eastern medicine for a long time. It has traditionally been used as a stimulating and fortifying agent in cases of physical exhaustion and to inhibit fatigue. The major bioactive compounds found in S. chinensis are lignans with a dibenzocyclooctadiene skeleton, but little is known about their biosynthesis in plants. S. chinensis is the ideal medicinal plant for studying the biosynthesis of lignans, especially the dibenzocyclooctadiene skeleton. Genomic information for this important herbal plant is unavailable. To better understand the lignan biosynthesis pathway, we generated transcriptome sequences from the fruit during ripening and performed de novo sequence assembly, yielding 136 843 unique transcripts with N50 of 1778 bp. Putative functions could be assigned to 41 824 transcripts (51.57%) based on BLAST searches against annotation databases including GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). Furthermore, 22 candidate cytochrome P450 genes and 15 candidate dirigent proteins genes that were most likely involved in the lignan biosynthesis pathway were discovered based on transcriptome sequencing of S. chinensis. The genomic data obtained from S. chinensis, especially the identification of putative genes involved in the lignan biosynthesis pathway, will facilitate our understanding of lignan biosynthesis at the molecular level. The lignan metabolite profiles were analyzed by metabolomes, the accumulation patterns of 30 metabolites involved in the lignan pathway were studied. Co-expression network of lignan contents and transcriptional changes showed 355 strong correlations (correlation coefficient, R² > 0.9) between 21 compounds and 153 transcripts. Furthermore, the comprehensive analysis and characterization of the genes involved in lignan pathways and the metabolite profiles of lignans are expected to provide better insight regarding the diversity of the chemical composition, synthetic characteristics, and regulatory mechanisms of this medical herb.

Dynamics of Bacterial and Fungal Communities and Metabolites During Aerobic Exposure in Whole-Plant Corn Silages With Two Different Moisture Levels

The study was aimed to investigate the effect of moisture content on microbial communities, metabolites, fermentation quality, and aerobic stability during aerobic exposure in whole-plant corn silages preserved long time to improve the quality and aerobic stability of the silage during feed-out. Corn plants with two different moisture levels (high-moisture content, 680 g/kg; low-moisture content, 620 g/kg) were harvested at one-third and two-thirds milk-line stages, respectively, ensiled in laboratory-scale silos, and then sampled at 350 day after ensiling and at 2 and 5 day after opening to investigate bacterial and fungal communities, metabolites, and aerobic stability. High-moisture content increased aerobic stability and pH and decreased lactic acid and microbial counts in silages (P < 0.05). During aerobic exposure, the low-moisture silages had higher pH and lactic acid bacterial count and lower lactic acid than the high-moisture silages (P < 0.05); Acinetobacter sp. was the most main bacterial species in the silages; Candida glabrata and unclassified Candida had an increasing abundance and negatively correlation with aerobic stability of high-moisture silages (P < 0.05), while C. glabrata, Candida xylopsoci, unclassified Saccharomycetaceae, and unclassified Saccharomycetales negative correlated with aerobic stability of low-moisture silages (P < 0.05) with a rising Saccharomycetaceae; the silages had a reducing concentration of total metabolites (P < 0.05). Moreover, the high-moisture silages contained greater total metabolites, saturated fatty acids (palmitic and stearic acid), essential fatty acids (linoleic acid), essential amino acids (phenylalanine), and non-essential amino acids (alanine, beta-alanine, and asparagine) than the low-moisture silages at 5 day of opening (P < 0.05). Thus, the high-moisture content improved the aerobic stability. Acinetobacter sp. and Candida sp. dominated the bacterial and fungal communities, respectively; Candida sp. resulted in the aerobic deterioration in high-moisture silages, while the combined activities of Candida sp. and Saccharomycetaceae sp. caused the aerobic deterioration in low-moisture silages. The greater aerobic stability contributed to preserve the palmitic acid, stearic acid, linoleic acid, phenylalanine, alanine, beta-alanine, and asparagine during aerobic exposure.

Spatial distribution analysis of phospholipids in rice by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry imaging

Phospholipids are one of the main nutrients in rice, which have a positive effect on cancer, coronary heart disease and inflammation. However, phospholipids will become small molecular volatile substances during the aging process of rice, resulting in change the flavor of rice. Therefore, mapping the concentration and the spatial distribution of phospholipids in rice are of tremendous significance in its function research. In this work, we established a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) imaging method for the spatial distribution analysis of phospholipids in rice. A total of 12 phospholipid compounds were found in the range of m/z 500-1000 through a series of conditions optimization. According to the results, lysophosphatidylcholine (LPC) species spread throughout the rice tissue sections and phosphatidylcholine (PC) species distributed in the bran and embryo (particularly in the scutellum). We also compared the signal intensities of phospholipids in different parts of white rice and brown rice by region of interest (ROI) analysis, which showed the relative content of PC species was higher in the embryo and gradually decreased until disappeared with the increase of processing degree during the processing of brown rice to white rice. The PC species on the surface of rice could be used as an important indicator to identify the processing degree of rice. Our work not only establish a MALDI-TOF-MS imaging method for spatial distribution analysis of rice, but also provide the necessary reference for ensuring food security, improving the eating quality of rice and the health benefits of consumers.