Flavonoid Synthesis Pathway Research Articles

Drought stress-mediated alterations in secondary metabolites and biosynthetic gene expression in cumin plants: Insights from gene-specific and metabolite-level analyses

In this research, we investigated the impact of drought stress on secondary metabolite production in cumin plants and the associated transcriptional changes in biosynthetic genes. Drought stress induced a significant increase in the levels of beta-carotene, lycopene, terpenes, anthocyanin, phenolic compounds, flavonoids, and alkaloids, indicating an adaptive metabolic shift in response to adverse conditions. Concurrently, there was an upregulation in the expression of key biosynthetic genes, including Phenylalanine ammonia-lyase (PAL), 3-deoxy-7-phosphoheptulonate synthase (DAHP synthase), Deoxy xylose phosphate reductase (DXS), 3‑hydroxy-3-methylglutaryl-CoA reductase (HMGR), and Geranyl diphosphate synthase (GPPS), which corroborated the metabolite findings. Notably, while most secondary metabolites exhibited an increasing trend under drought stress, flavonoids displayed a disproportionate elevation, even as there was an overall decrease in phenolic compounds and other metabolites. This observation suggests the potential activation of alternative flavonoid synthesis pathways or the conversion of phenolic compounds to flavonoids during stress. Strong correlations were identified between the expression of biosynthetic genes and their respective metabolite concentrations, underscoring the central role of transcriptional regulation in secondary metabolite synthesis during drought stress. Collectively, our results provide a comprehensive understanding of the transcriptional and metabolic adaptations of cumin plants when exposed to drought stress. Such insights can be pivotal in designing drought-resilient crops, with significant implications for food security amidst escalating climatic challenges.

Metabolomic and transcriptomic analyses provide insights into the flavonoid biosynthesis in sea buckthorn (Hippophae rhamnoides L.)

Sea buckthorn is a plant with similarities to both food and medicine, possessing abundant flavonoids. However, the metabolic mechanism of flavonoid synthesis in sea buckthorn is unclear. Here, we performed transcriptomic and metabolomic analyses to explore the metabolic characteristics of flavonoids in different sea buckthorn tissues and their associated gene regulatory networks. A total of 441 metabolites were identified from sea buckthorn by metabolomics (UPLC-MS/MS), which includes 104 flavonoids with significant differences in the relative contents among tissues. Transcriptomic analysis identified 75 genes involved in the flavonoid biosynthesis pathway. The weighted gene correlation network analysis revealed that the MEdarkgreen module showed a significant correlation with flavonoid compounds and comprised ten genes related to flavonoid synthesis. Overexpression of HrMYB114 resulted in a significant increase in flavonoid content and expression of structural genes in the flavonoid synthesis pathway in transgenic hairy roots. This study provided a comprehensive analysis of metabolic and transcriptomic profiles, which helped to investigate the molecular mechanism of flavonoid biosynthesis.

Changes in antioxidant substances and antioxidant enzyme activities in raspberry fruits at different developmental stages

Raspberry is a small berry shrub with a relatively recent cultivation history in China, and its fruits have remarkable antioxidant activity. In this study, the raspberry cultivars 'Clode Summit', 'Heritage' and 'Bristol' were used as experimental materials to determine the color parameters, dry and fresh weights, ROS, MDA, ASA and GSH contents, activities of SOD, CAT and POD, and total antioxidant activity of fruits in different harvest periods. In addition, we analyzed the relative gene expression levels of SOD, CAT, POD and related transcription factors in the flavonoid synthesis pathway during fruit development. The results showed that the production rate of O2− and the content of MDA increased gradually, while the activities of CAT and POD decreased gradually. The growth and development of raspberry fruits activated the SOD enzyme system, but the change trend of SOD activity was different among different cultivars. Principal component analysis and correlation analysis showed that the antioxidant capacity of raspberry mainly came from ASA, GSH and anthocyanins. The content of ASA in green raspberry fruits was generally higher than that in red raspberry and black raspberry fruits. Black raspberry had the highest content of GSH and anthocyanin, as well as antioxidant activity. Correlation analysis showed that POD activity was significantly correlated with the expression level of RuPER17. The expression levels of RuPAL, RuFLS, RuMYB6, RuMYB306 and RuWRKY24 in the three raspberry fruits first increased and then decreased. The results provide a reference for further exploration of the mechanism of antioxidation and for regulating the biosynthesis of related enzymes in raspberry fruits.

Integrated Metabolome and Transcriptome during Fruit Development Reveal Metabolic Differences and Molecular Basis between Lycium barbarum and Lycium ruthenicum

Wolfberry (Lycium barbarum) is a traditional cash crop in China and is well-known worldwide for its outstanding nutritional and medicinal value. Lycium ruthenicum is a close relative of Lycium barbarum but differs significantly in size, color, flavor and nutritional composition. To date, the metabolic differences between the fruits of the two wolfberry varieties and the genetic basis behind them are unclear. Here, we compared metabolome and transcriptome data of two kinds of wolfberry fruits at five stages of development. Metabolome results show that amino acids, vitamins and flavonoids had the same accumulation pattern in various developmental stages of fruit but that Lycium ruthenicum accumulated more metabolites than Lycium barbarum during the same developmental stage, including L-glutamate, L-proline, L-serine, abscisic acid (ABA), sucrose, thiamine, naringenin and quercetin. Based on the metabolite and gene networks, many key genes that may be involved in the flavonoid synthesis pathway in wolfberry were identified, including PAL, C4H, 4CL, CHS, CHI, F3H, F3’H and FLS. The expression of these genes was significantly higher in Lycium ruthenicum than in Lycium barbarum, indicating that the difference in the expression of these genes was the main reason for the variation in flavonoid accumulation between Lycium barbarum and Lycium ruthenicum. Taken together, our results reveal the genetic basis of the difference in metabolomics between Lycium barbarum and Lycium ruthenicum and provide new insights into the flavonoid synthesis of wolfberry.

NtLTPI.38, a plasma membrane-localized protein, mediates lipid metabolism and salt tolerance in Nicotiana tabacum

Non-specific lipid transfer proteins (nsLTPs) typically have conserved structural resemblance, low sequence identity, and broad biological functions in plant growth and stress resistance. Here, a plasma membrane-localized nsLTP, NtLTPI.38, was identified in tobacco plants. Multi-omics integrated analysis revealed that NtLTPI.38 overexpression or knock out significantly changed glycerophospholipid and glycerolipid metabolism pathways. NtLTPI.38 overexpression remarkably increased phosphatidylcholine, phosphatidylethanolamine, triacylglycerol, and flavonoid levels, but decreased ceramides compared to wild type and mutant lines. Differentially expressed genes were associated with lipid metabolite and flavonoid synthesis. Many genes related to Ca2+ channels, abscisic acid (ABA) signal transduction, and ion transport pathways were upregulated in overexpressing plants. NtLTPI.38 overexpression in salt-stressed tobacco triggered a Ca2+ and K+ influx in leaves, increased the contents of chlorophyll, proline, flavonoids, and osmotic tolerance, and raised enzymatic antioxidant activities as well as the expression level of related genes. However, mutants accumulated more O2− and H2O2, exhibited ionic imbalance, gathered excess Na+, Cl−, and malondialdehyde, with more severe ion leakage. Therefore, NtLTPI.38 enhanced salt tolerance in tobacco by regulating lipid and flavonoid synthesis, antioxidant activity, ion homeostasis, and ABA signaling pathways.

Integrative transcriptome and metabolome analysis reveals the mechanism of exogenous melatonin alleviating drought stress in maize roots

Melatonin (MT) is essential for plant development and drought adaptation. However, the molecular and metabolic mechanisms underlying MT-induced drought tolerance in maize roots remain largely unclear. Herein, we investigated the effects of MT on drought tolerance in maize roots using integrated transcriptomic and metabolomic analyses, and identified MT-induced genes and metabolites associated with drought resistance. Compared with the untreated control plants, MT application alleviated the deleterious effects of drought on roots, by decreasing the malondialdehyde level and increasing the solute potential, eventually promoting root growth. Transcriptome and metabolome analysis demonstrated that MT significantly upregulates the expression of genes related to flavonoid biosynthesis (PAL, C4H, 4CL, HCT, CHS, CHI, F3′5′H, and DFR), activates drought-responsive transcription factors (ERFs, NACs, MYBs, and bHLHs), and regulates hormone signaling-related genes, especially ethylene response factors (ERF4, ERF81, and ERF110). Moreover, MT increased the accumulation of flavonoid metabolites, particularly apigenin, luteolin, and quercetin, under drought-stress conditions. These findings were further supported by quantitative real-time polymerase chain reaction analysis and total flavonoid measurements. Altogether, our findings suggest that MT promotes maize root growth during drought by regulating flavonoid synthesis pathways, transcription factors, and plant hormone signals. This study provides new insights into the complex mechanisms by which MT enhances crop resistance to drought damage.

Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry (Vaccinium spp.).

As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.

Transcriptome and metabolome analysis reveals the potential mechanism of tuber dynamic development in yam (Dioscorea polystachya Turcz.)

Yam (Dioscorea spp.) is a multispecies and multipurpose tuber crop. To clarify the mechanism of tuber development, we performed a time-course phenotypic, cytological, physiological, metabolomic, and transcriptomic analysis of yam tubers. The results showed that the tuber weight increased with the accumulation of starch, and sucrose metabolism was also active during tuber development. Meanwhile, abscisic acid (ABA) levels were positively correlated with tuber weight, while gibberellin (GA) was negatively. Metabonomic analysis showed that 400 metabolites accumulated during tuber development, which played an important role in the regulation of tuber growth and development, flavor and medicinal ingredients. A total of 743 differentially expressed genes (DEGs) were assigned to 21 KEGG pathways such as starch and sucrose metabolism, plant hormone signal transduction pathway and flavonoid pathway by comparative transcriptome. Comprehensive transcriptome and metabolome analysis revealed the DEGs and differentially accumulated metabolites (DAMs) of plant hormone signal transduction pathway, starch and sucrose metabolism, and flavonoid synthesis pathway. In conclusion, the DAMs and DEGs involved in plant hormone signal transduction pathway, starch and sucrose metabolism pathway and flavonoid metabolism pathway play an important role in the regulation of tuber development. This study provides theoretical basis and practical guidance in molecular breeding and quality improvement of yam.

Cloning and functional analysis of GhDFR1, a key gene of flavonoid synthesis pathway in naturally colored cotton.

The naturally colored brown cotton fiber is the most widely used environmentally friendly textile material, which primarily contains proanthocyanidins and their derivatives. Many structural genes in the flavonoid synthesis pathway are known to improve the genetic resources of naturally colored cotton. Among them, DFR is a crucial late enzyme to synthesis both anthocyanins and proanthocyanidins in the plant flavonoid pathway. The protein sequences of GhDFRs were analyzed using bioinformatic tools. The expression levels of GhDFRs in various tissues and organs of upland cotton Zongxu1 (ZX1), were analyzed by quantitative real-time PCR, and the expression pattern of GhDFR1 during fiber development of white cotton and brown cotton was analyzed further. The function of GhDFR1 in NCC ZX1 was preliminarily analyzed by virus induced gene silencing (VIGS) technology. Bioinformatic analysis revealed that GhDFRs sequences in upland cotton genome were extremely conserved. Furthermore, evolutionary tree analysis revealed that the functions of GhDFR1 and GhDFR2, and GhDFR3 and GhDFR4, presented different and shared some similarities. Our study showed GhDFR1 and GhDFR2 were specifically expressed in fibers, while GhDFR3 and GhDFR4 were specifically expressed in petals. GhDFR1 was exclusively expressed in brown cotton fiber at various stages of development and progressively increased with the growth of fiber, but the trend of expression in white cotton was quite the opposite. We silenced GhDFR1 expression in brown cotton fiber using VIGS technology, and observed the VIGS-interference plants. After reducing the expression level of GhDFR1, the period for significant GhDFR1 expression in the developing fibers changed, reducing the content of anthocyanins, and lightening the color of mature cotton fibers. GhDFR1 was preferentially expressed in brown cotton during fiber development. The timing of GhDFR1 expression for flavonoid synthesis altered, resulting in anthocyanin contents reduced and the fiber color of the GhDFR1i lines lightened. These findings showed the role of GhDFR1 in fiber coloration of NCC and provided a new candidate for NCC genetic improvement.

Screening β-glucosidase and α-rhamnosidase for biotransformation of naringin to naringenin by the one-pot enzymatic cascade

Naringenin is a kind of flavonoid with many kinds of pharmacological activities, and is also a key intermediate metabolite in the flavonoid synthesis pathway. In this study, three α-rhamnosidases from Thermotoga petrophia DSM 13995 (TpeRha), Alternaria sp. L1 (AsRha), and Aspergillus mulundensis (AmRha), and three β-glucosidases from T. thermarum DSM 5069 T (BGLI-Tt and BGLII-Tt), and A. niger NL-1 (BGL-NL) were cloned, expressed, and characterized. The Kcat/Km value of AmRha for naringin was 2.389 s−1mM−1 which was 796-fold and 26-fold of TpeRha and AsRha. The Kcat/Km value of BGL-NL for prunin was 0.946 s−1mM−1, which was about 4.4-fold and 4.6-fold of BGLI-Tt and BGLII-Tt. According to the catalytic efficiency, expression level, and reaction condition compatibility, AmRha was coupled with BGL-NL to construct a one-pot enzymatic cascade for preparing naringenin from naringin. The effects of the ratio and dosage of the enzyme, the naringin concentration, and reaction conditions on naringenin production were optimized. At a dosage of 200 U/L AmRha and 1000 U/L BGL-NL, a temperature of 50 °C and pH 5.0, 30 mM naringin was transformed into 29.3 mM naringenin for 24 h reaction with a corresponding molar conversion of 97.6%. Therefore, this study provides an efficient enzymatic cascade to meet the large-scale and low cost preparation of naringenin from naringin.

How does phosphorus influence Cd tolerance strategy in arbuscular mycorrhizal - Phragmites australis symbiotic system?

To clarify how phosphorus (P) influences arbuscular mycorrhizal fungi (AMF) interactions with host plants, we measured the effects of variation in environmental P levels and AMF colonization on photosynthesis, element absorption, ultrastructure, antioxidant capacity, and transcription mechanisms in Phragmites australis (P. australis) under cadmium (Cd) stress. AMF maintained photosynthetic stability, element balance, subcellular integrity and enhanced antioxidant capacity by upregulating antioxidant gene expression. Specifically, AMF overcame Cd-induced stomatal limitation, and mycorrhizal dependence peaked in the high Cd-moderate P treatment (156.08%). Antioxidants and compatible solutes responded to P-level changes: the primary driving forces of removing reactive oxygen species (ROS) and maintaining osmotic balance were superoxide dismutase, catalase, and sugars at limited P levels and total polyphenol, flavonoid, peroxidase, and proline at abundant P levels, we refer to this phenomenon as “functional link.” AMF and phosphorus enhanced Cd tolerance in P. australis, but the regulation of AMF was P-dependent. Phosphorus prevented increases in total glutathione content and AMF-induced GSH/GSSG ratio (reduced to oxidized glutathione ratio) by inhibiting the expression of assimilatory sulfate reduction and glutathione reductase genes. The AMF-induced flavonoid synthesis pathway was regulated by P, and AMF activated Cd-tolerance mechanisms by inducing P-dependent signaling.

Genome-Wide Analysis of Long Non-Coding RNAs Related to UV-B Radiation in the Antarctic Moss Pohlia nutans

Antarctic organisms are consistently suffering from multiple environmental pressures, especially the strong UV radiation caused by the loss of the ozone layer. The mosses and lichens dominate the vegetation of the Antarctic continent, which grow and propagate in these harsh environments. However, the molecular mechanisms and related regulatory networks of these Antarctic plants against UV-B radiation are largely unknown. Here, we used an integrated multi-omics approach to study the regulatory mechanism of long non-coding RNAs (lncRNAs) of an Antarctic moss (Pohlia nutans) in response to UV-B radiation. We identified a total of 5729 lncRNA sequences by transcriptome sequencing, including 1459 differentially expressed lncRNAs (DELs). Through functional annotation, we found that the target genes of DELs were significantly enriched in plant-pathogen interaction and the flavonoid synthesis pathway. In addition, a total of 451 metabolites were detected by metabonomic analysis, and 97 differentially change metabolites (DCMs) were found. Flavonoids account for 20% of the total significantly up-regulated metabolites. In addition, the comprehensive transcriptome and metabolome analyses revealed the co-expression pattern of DELs and DCMs of flavonoids. Our results provide insights into the regulatory network of lncRNA under UV-B radiation and the adaptation of Antarctic moss to the polar environments.

Identification of key genes involved in flavonoid and terpenoid biosynthesis and the pathway of triterpenoid biosynthesis in Passiflora edulis

Passion fruit (Passiflora edulis Sims) is a vine of the Passiflora genus in the Passifloraceae family. The extracted components include flavonoids and terpenoids, which have good anti-anxiety and anti-inflammatory effects in humans. In this study, we analyzed the transcriptomes of four tissues of the ‘Zixiang’ cultivar using RNA-Seq, which provided a dataset for functional gene mining. The de novo assembly of these reads generated 96 883 unigenes, among which 61 022 unigenes were annotated (62.99% yield). In addition to its edible value, another important application of passion fruit is its medicinal value. The flavonoids and terpenoids are mainly derivatives of luteolin, apigenin, cycloartane triterpenoid saponins and other active substances in leaf extracts. A series of candidate unigenes in the transcriptome data that are potentially involved in the flavonoid and terpenoid synthesis pathways were screened using homology-based BLAST and phylogenetic analysis. The results showed that the biosynthesis of triterpenoids in passion fruit comes from the branches of the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (MEP/DOXP) pathways, which is different from the MVA pathway that is used in other fruit trees. Most of the candidate genes were found to be highly expressed in the leaves and/or flowers. Quantitative real-time PCR (qRT-PCR) verification was carried out and confirmed the reliability of the RNA-Seq data. Further amplification and functional analysis of these putative unigenes will provide additional insight into the biosynthesis of flavonoids and terpenoids in passion fruit.

Metabolic profiling and transcriptome analysis provide insights into the accumulation of flavonoids in chayote fruit during storage.

Chayote (Sechium edulel) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and the corresponding regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, an integrated transcriptome and metabolite analysis of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, exogenous application of phenylalanine increased the total content of flavonoids and promoted some flavonoid biosynthesis-related gene expression in chayote fruits. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.

Transcriptome Analysis Reveals the Central Role of the Transcription Factor MYB in Regulating Anthocyanin Accumulation in Economic Grape Species (Vitis vinifera)

To cultivate different grape varieties according to market needs, it is necessary to study the regulation mechanism of color changes in different development stages of grapes. In this study, RNA-sequencing (RNA-Seq) technology was used to compare and analyze the transcriptome data of four grape varieties at the same development stage. Among the annotated differential genes, the anthocyanin synthesis pathway in the flavonoid pathway was mainly studied. Further RT-qPCR analysis of key enzyme genes, in the flavonoid synthesis pathway of the anthocyanin metabolism pathway, showed that the MYB transcription factor family had binding sites at the start of the four enzyme genes. The relative expression of the MYB transcription factor and enzyme gene in the transcriptome data was verified by reverse transcription polymerase chain reaction. Subcellular localization and gene function verification of the transcription factor MYB2 confirmed its regulatory role in anthocyanins.

Transcriptome and Metabolome Analysis Reveals Salt-Tolerance Pathways in the Leaves and Roots of ZM-4 (Malus zumi) in the Early Stages of Salt Stress.

The breeding of salt-tolerant rootstock relies heavily on the availability of salt-tolerant Malus germplasm resources. The first step in developing salt-tolerant resources is to learn their molecular and metabolic underpinnings. Hydroponic seedlings of both ZM-4 (salt-tolerant resource) and M9T337 (salt-sensitive rootstock) were treated with a solution of 75 mM salinity. ZM-4's fresh weight increased, then decreased, and then increased again after being treated with NaCl, whereas M9T337's fresh weight continued to decrease. The results of transcriptome and metabolome after 0 h (CK) and 24 h of NaCl treatment showed that the leaves of ZM-4 had a higher content of flavonoids (phloretinm, naringenin-7-O-glucoside, kaempferol-3-O-galactoside, epiafzelechin, etc.) and the genes (CHI, CYP, FLS, LAR, and ANR) related to the flavonoid synthesis pathway showed up-regulation, suggesting a high antioxidant capacity. In addition to the high polyphenol content (L-phenylalanine, 5-O-p-coumaroyl quinic acid) and the high related gene expression (4CLL9 and SAT), the roots of ZM-4 exhibited a high osmotic adjustment ability. Under normal growing conditions, the roots of ZM-4 contained a higher content of some amino acids (L-proline, tran-4-hydroxy-L-prolin, L-glutamine, etc.) and sugars (D-fructose 6-phosphate, D-glucose 6-phosphate, etc.), and the genes (GLT1, BAM7, INV1, etc.) related to these two pathways were highly expressed. Furthermore, some amino acids (S-(methyl) glutathione, N-methyl-trans-4-hydroxy-L-proline, etc.) and sugars (D-sucrose, maltotriose, etc.) increased and genes (ALD1, BCAT1, AMY1.1, etc.) related to the pathways showed up-regulation under salt stress. This research provided theoretical support for the application of breeding salt-tolerant rootstocks by elucidating the molecular and metabolic mechanisms of salt tolerance during the early stages of salt treatment for ZM-4.

Transcriptomic and physiological analysis reveal phytohormone and phenylpropanoid biosynthesis in root of Cynanchum auriculatum

Baishouwu (Cynanchum auriculatum), a medicinal and food dual-use plant, has been cultivated for centuries and is favored by consumers. C. auriculatum tuberous roots contain enormous amounts of flavonoids, lignin, and other nutrients. However, the developmental characteristics and phenylpropanoid metabolic mechanism in C. auriculatum have not been clarified. Here, the phenotypes of C. auriculatum tuberous roots at three stages of developmental were observed, compared with root forming stage (S1), there were significant morphological differences at root expanding stage (S2) and harvest stage (S3). Through next-generation sequencing (NGS) on Illumina HiSeq2500 platform, nine transcriptomic libraries were constructed for transcriptomic analysis. A total of 28,926 DEGs were identified during the development of C. auriculatum tuberous root, and many DEGs were enriched in GO terms/ KEGG pathways of ‘phytohormone signal transduction’ and ‘phenylpropanoid biosynthesis’. The analysis of phytohormone content and gene expression revealed that auxin and cytokinin acted in concert to regulate C. auriculatum tuberous root development, while the biosynthesis and signaling of ethylene were inhibited. Phloroglucinol staining results showed that lignified cells were mainly distributed in the central xylem at S1, followed by ring-like structure formation at S2, and finally formed the connecting rays between the xylem and the phloem at S3. Lignin content increased at S2 and then decreased at S3, and the expression of lignin synthesis genes also presented a similar trend. Total flavonoids content showed a gradually increasing trend, and the expression of flavonoid synthesis genes was also gradually up-regulated. The flavonoid synthesis pathway was enhanced by reducing the activity of key enzymes in lignin synthesis in C. auriculatum. This study provided a basis for the developmental mechanism of C. auriculatum and the further utilization of C. auriculatum tuberous roots.

Integrative analysis of transcriptome and metabolome revealed the mechanisms by which flavonoids and phytohormones regulated the adaptation of alfalfa roots to NaCl stress.

Salinity critically affects the growth and development of alfalfa (Medicago sativa), making it necessary to understand the molecular mechanism of alfalfa's adaptation to salt stress. In this study, alfalfa roots were subjected to salt stress and transcriptomics and metabolomics analyses were performed. The results showed that flavonoid synthesis, hormone synthesis, and transduction pathways may be involved in the alfalfa salt stress adaptation reaction, and that they are related. Combined analysis of differential genes and differential metabolites found that dihydroquercetin and beta-ring hydroxylase (LUT5), ABA responsive element binding factor 2 (ABF2), protein phosphatase PP2C (PP2C) and abscisic acid (ABA) receptor PYL2 (PYL), luteolinidin was significantly correlated with PP2C and phytochrome-interacting factor 4 (PIF4) and (+)-7-isomethyl jasmonate were significantly correlated with flavonol synthase (FLS) gene. (+)-7-isomethyl jasmonate and homoeriodictyol chalcone were significantly correlated with peroxidase (POD). POD was significantly up-regulated under NaCl stress for 6 and 24 h. Moreover, flavonoids, gibberellin (GA), jasmonic acid (JA) and ABA were suggested to play an important role in alfalfa's response to salt stress. Further, GA,ABA, and JA may be involved in the regulation of flavonoids to improve alfalfa's salt tolerance, and JA may be a key signal to promote the synthesis of flavonoids. This study revealed the possible molecular mechanism of alfalfa adaptation to salt stress, and identified a number of salt-tolerance candidate genes from the synthesis and signal transduction pathways of flavonoids and plant hormones, providing new insights into the regulatory network of alfalfa response to salt stress.

Integrated transcriptome and metabolome analysis reveals that flavonoids function in wheat resistance to powdery mildew.

Powdery mildew is a fungal disease devastating to wheat, causing significant quality and yield loss. Flavonoids are important secondary plant metabolites that confer resistance to biotic and abiotic stress. However, whether they play a role in powdery mildew resistance in wheat has yet to be explored. In the present study, we combined transcriptome and metabolome analyses to compare differentially expressed genes (DEGs) and differentially accumulated flavonoids identified in plants with and without powdery mildew inoculation. Transcriptome analysis identified 4,329 DEGs in susceptible wheat cv. Jimai229, and 8,493 in resistant cv. HHG46. The DEGs were functionally enriched using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, revealing the flavonoid synthesis pathway as the most significant in both cultivars. This was consistent with the upregulation of flavonoid synthesis pathway genes observed by quantitative PCR. Metabolome analysis indicated flavone and flavonol biosynthesis pathways as the most significantly enriched following powdery mildew inoculation. An accumulation of total flavonoids content was also found to be induced by powdery mildew infection. Exogenous flavonoids treatment of inoculated plants led to less severe infection, with fewer and smaller powdery mildew spots on the wheat leaves. This reduction is speculated to be regulated through malondialdehyde content and the activities of peroxidase and catalase. Our study provides a fundamental theory for further exploration of the potential of flavonoids as biological prevention and control agents against powdery mildew in wheat.

Relative quantification of phenolic compounds in exocarp-mesocarp and endocarp of sumac (Toxicodendron vernicifluum) combined with transcriptome analysis provides insights into glycosylation of flavonoids and biflavonoid biosynthesis

The pericarp of fruit can be differentiated into endocarp, mesocarp, and exocarp. To explore the differences in gene expression and metabolites in different tissues of the pericarp, the fruits of sumac (Toxicodendron vernicifluum) were separated into endocarp and mesocarp-exocarp. The metabolites and transcriptome of exocarp-mesocarp and endocarp of Toxicodendron vernicifluum were analyzed by HPLC–QTOF-MS/MS and RNA sequencing, respectively. A total of 52 phenolic compounds were identified, including 3 phenylpropane derivatives, 10 urushiol compounds and 39 flavonoids. The exocarp-mesocarp contained more urushiol compounds and flavonoid glycosides while the endocarp contained more biflavonoids, such as rhusflavone and dihydromorelloflavone. The characteristic component of endocarp was rhusflavone and the characteristic component of exocarp-mesocarp was urushiol (triene). Most of the genes involved in flavonoid synthesis pathway were upregulated in endocarp compared with exocarp-mesocarp and positively correlated with the content of flavonoids. The candidate genes related to the synthesis of components of flavonoid glycosides and biflavonoids were screened. Metabolomic and transcriptomic analyses provide new insights into the synthesis and distribution of flavonoid glycosides and biflavonoids in the fruits of Toxicodendron vernicifluum.