Integrated transcriptomic and metabolomic data reveal the flavonoid biosynthesis metabolic pathway in Perilla frutescens (L.) leaves

Combined transcriptome and widely targeted metabolome analysis reveals the potential mechanism of HupA biosynthesis and antioxidant activity in Huperzia serrata

Introduction

Huperzia serrata is a traditional Chinese herb that has gained much attention for its production of Huperzine A (HupA). HupA has shown promise on treating Alzheimer's disease (AD). However, the biosynthetic pathway and molecular mechanism of HupA in H. serrata are still not well understood.

Methods

Integrated transcriptome and metabolome analysis was performed to reveal the molecular mechanisms related to HupA biosynthesis and antioxidant activity in Huperzia serrata.

Results

HT (in vitro H. serrata thallus) exhibits higher antioxidant activity and lower cytotoxicity than WH (wild H. serrata). Through hierarchical clustering analysis and qRT-PCR verification, 7 important enzyme genes and 13 transcription factors (TFs) related to HupA biosynthesis were detected. Among them, the average |log2FC| value of CYP (Cytochrome P450) and CAO (Copper amine oxidase) was the largest. Metabolomic analysis identified 12 metabolites involved in the HupA biosynthesis and 29 metabolites related to antioxidant activity. KEGG co-enrichment analysis revealed that tropane, piperidine and pyridine alkaloid biosynthesis were involved in the HupA biosynthesis pathway. Furthermore, the phenylpropanoid, phenylalanine, and flavonoid biosynthesis pathway were found to regulate the antioxidant activity of H. serrata. The study also identified seven important genes related to the regulation of antioxidant activity, including PrAO (primary-amine oxidase). Based on the above joint analysis, the biosynthetic pathway of HupA and potential mechanisms of antioxidant in H. serrata was constructed.

Discussion

Through differential transcriptome and metabolome analysis, DEGs and DAMs involved in HupA biosynthesis and antioxidant-related were identified, and the potential metabolic pathway related to HupA biosynthesis and antioxidant in Huperzia serrata were constructed. This study would provide valuable insights into the HupA biosynthesis mechanism and the H. serrata thallus medicinal value.

Integrated Metabolomics and Transcriptomics Analysis of Flavonoid Biosynthesis Pathway in Polygonatum cyrtonema Hua

Flavonoids, a class of phenolic compounds, are one of the main functional components and have a wide range of molecular structures and biological activities in Polygonatum. A few of them, including homoisoflavonoids, chalcones, isoflavones, and flavones, were identified in Polygonatum and displayed a wide range of powerful biological activities, such as anti-cancer, anti-viral, and blood sugar regulation. However, few studies have systematically been published on the flavonoid biosynthesis pathway in Polygonatum cyrtonema Hua. Therefore, in the present study, a combined transcriptome and metabolome analysis was performed on the leaf, stem, rhizome, and root tissues of P. cyrtonema to uncover the synthesis pathway of flavonoids and to identify key regulatory genes. Flavonoid-targeted metabolomics detected a total of 65 active substances from four different tissues, among which 49 substances were first study to identify in Polygonatum, and 38 substances were flavonoids. A total of 19 differentially accumulated metabolites (DAMs) (five flavonols, three flavones, two dihydrochalcones, two flavanones, one flavanol, five phenylpropanoids, and one coumarin) were finally screened by KEGG enrichment analysis. Transcriptome analysis indicated that a total of 222 unigenes encoding 28 enzymes were annotated into three flavonoid biosynthesis pathways, which were "phenylpropanoid biosynthesis", "flavonoid biosynthesis", and "flavone and flavonol biosynthesis". The combined analysis of the metabolome and transcriptome revealed that 37 differentially expressed genes (DEGs) encoding 11 enzymes (C4H, PAL, 4CL, CHS, CHI, F3H, DFR, LAR, ANR, FNS, FLS) and 19 DAMs were more likely to be regulated in the flavonoid biosynthesis pathway. The expression of 11 DEGs was validated by qRT-PCR, resulting in good agreement with the RNA-Seq. Our studies provide a theoretical basis for further elucidating the flavonoid biosynthesis pathway in Polygonatum.

Antioxidant compounds and activities of Perilla frutescens var. crispa and its processed products

Perilla frutescens var. crispa 'Antisperill' has stronger anti-inflammatory effects than the original cultivar (red perilla), but studies on its bioactive compounds are limited. This study aimed to evaluate the antioxidant compounds and activity of red perilla and 'Antisperill', as well as their processed products using freeze drying (FD) and microwave-assisted low temperature vacuum drying (MVD). Red perilla had higher antioxidant compounds and activities than 'Antisperill'. MVD showed significantly greater antioxidant properties than FD among the processed products. Isoegomaketone, studied for its anti-obesity, antioxidant, anti-inflammatory, and anticancer properties, was only found in 'Antisperill' and its processed products, with the highest content in 'Antisperill' MVD samples. This study highlights that 'Antisperill' contains various antioxidants, and MVD is the optimal drying method to preserve and enhance its antioxidant content. As a result, 'Antisperill' could potentially serve as a natural antioxidant with both anti-inflammatory and antioxidant functions.

Genome-wide characterization and expression analysis of MADS-box transcription factor gene family in Perilla frutescens

MADS-box transcription factors are widely involved in the regulation of plant growth, developmental processes, and response to abiotic stresses. Perilla frutescens, a versatile plant, is not only used for food and medicine but also serves as an economical oil crop. However, the MADS-box transcription factor family in P. frutescens is still largely unexplored. In this study, a total of 93 PfMADS genes were identified in P. frutescens genome. These genes, including 37 Type I and 56 Type II members, were randomly distributed across 20 chromosomes and 2 scaffold regions. Type II PfMADS proteins were found to contain a greater number of motifs, indicating more complex structures and diverse functions. Expression analysis revealed that most PfMADS genes (more than 76 members) exhibited widely expression model in almost all tissues. The further analysis indicated that there was strong correlation between some MIKCC-type PfMADS genes and key genes involved in lipid synthesis and flavonoid metabolism, which implied that these PfMADS genes might play important regulatory role in the above two pathways. It was further verified that PfMADS47 can effectively mediate the regulation of lipid synthesis in Chlamydomonas reinhardtii transformants. Using cis-acting element analysis and qRT-PCR technology, the potential functions of six MIKCC-type PfMADS genes in response to abiotic stresses, especially cold and drought, were studied. Altogether, this study is the first genome-wide analysis of PfMADS. This result further supports functional and evolutionary studies of PfMADS gene family and serves as a benchmark for related P. frutescens breeding studies.

Anti-Inflammatory Activity of the Constituents from the Leaves of Perilla frutescens var. acuta

Perilla frutense var. acuta (Lamiaceae) has been used to treat indigestion, asthma, and allergies in traditional medicine. In this study, luteolin 7-O-diglucuronide (1), apigenin 7-O-diglucuronide (2), and rosmarinic acid (3) were isolated from the leaves of P. frutescens var. acuta through various chromatographic purification techniques. Several approaches were used to investigate the anti-inflammatory activity of the constituents (1-3) and their working mechanisms. In silico docking simulation demonstrated that 1-3 would work as a PPAR-α/δ/γ agonist, and in vitro PPAR-α/δ/γ transcriptional assay showed that the Perilla water extract (PWE) and 3 increased PPAR-α luciferase activity (1.71 and 1.61 times of the control (PPAR-α + PPRE, p < 0.001)). In the NF-κB luciferase assay, 1 suppressed NF-κB activity the most (56.83% at 5 µM; 74.96% at 10 µM; 79.86% at 50 µM). In addition, 1 and 2 inhibited the mRNA expression of NF-κB target genes, including Il6, Mcp1, and Tnfa, at 50 µM, and 3 suppressed the genes at the mRNA level in a dose-dependent manner. We report that 1 and 2 exert anti-inflammatory effects through NF-κB inhibition, and the PPAR-α/NF-κB signaling pathway is related to the anti-inflammatory activity of 3.

Study on Purification, Identification and Antioxidant of Flavonoids Extracted from Perilla leaves

The flavonoids from Perilla leaves were extracted using flash extraction assisted by ultrasonic extraction with ethanol. Subsequently, macroporous resin was employed for the isolation and purification of these flavonoids, followed by an investigation into their antioxidant activity. The process conditions for the extraction of flavonoids from Perilla leaves were designed and optimized using a one-way experiment combined with a response surface methodology. The optimal extraction conditions were determined as follows: the liquid-solid ratio was 20:1, ethanol volume fraction of 60%, ultrasound temperature of 60 °C, ultrasound time of 10 min and flash evaporation time of 60 s. The optimal extraction rate of flavonoids is 9.8 mg/g. In terms of separation and purification, a high-performance macroporous resin (HPD450 resin) with high purification efficiency was selected through static analysis and adsorption experiments. The optimal enrichment conditions were as follows: loading concentration of 0.06 mg/mL, optimal loading concentration of 20 mL, elution concentration of 70% and 76 mL, providing a reference for the further development and utilization of Perilla leaf flavonoids.

A comprehensive view of metabolic responses to CYP98 perturbation in ancestral plants

Cytochrome P450 monooxygenase 98 (CYP98) is a critical rate-limiting enzyme of the phenylpropanoid pathway. One of the end-product of the phenylpropanoid pathway is a lignin monomer, although the occurrence of lignin in bryophytes is controversial. Here we investigated the functions of PpCYP98 in Physcomitrium patens by transcriptome and metabolome analyses. We identified 5266 differentially expressed genes (DEGs) and 68 differentially abundant secondary metabolites between wild-type and ΔPpCYP98 gametophores. Of the identified metabolites, 23 phenolic acids were identified, with only one showing upregulation. Among the phenolic acids, 4-coumaroyl tartaric acid and chlorogenic acid showed significant decreases. Declines were also observed in coniferylaldehyde and coniferin, precursor substances and downstream products of the lignin monomer coniferyl alcohol, respectively. Thus, the pre-lignin synthesis pathway already exists in bryophytes, and PpCYP98 plays vital roles in this pathway. Besides, most flavonoids show significant reductions, including eriodyctiol, dihydroquecetin, and dihydromyricetin, whereas naringenin chalone and dihydrokaempferol were increased after PpCYP98 knockout. Therefore, the synthesis of flavonoids shares the core pathway with phenylpropanoids and mainly starts from caffeoyl-CoA, that is the compound of divergence between the two pathways in moss. PpCYP98 showed systemic effects on metabolisms, including carbohydrate, fatty acid, and hormonal signaling transductions, suggesting that PpCYP98 might indirectly regulate carbon influx allocation. Our results demonstrated roles of PpCYP98 were essential for the development of the early landing plant.

Investigation of the Relationship between Genetic and Breeding Characteristics of WBPH Behavior according to Resistant Materials in Rice

Rice accounts for most of the calories consumed by the world's population. However, the whitebacked planthopper (WBPH), Sogatella furcifera (Horvath), is an insect that can cause rice yield loss. WBPH sucks the stems of rice and negatively affects yield and grain quality. Therefore, numerous insecticides have been developed to control WBPH in rice fields. However, chemical pesticides cause serious problems such as environmental pollution and ecosystem disturbance. Here, we research the possibility of using previously reported rice extracts obtained using methanol, Chrysoeriol 7(C7) and Cochlioquinone-9 (cq-9), as potential insect repellents. WBPH was caged with C7 or cq-9 and monitored, and the WBPH behavior was recorded. The number of WBPHs approaching the periphery of the C7 and cq-9 was very low. In cages containing the C7 and cq-9, only 13 and 7 WBPHs out of 100, respectively, walked around the material. In addition, foliar spraying with C7 and cq-9 did not negatively affect the plant height. The expression level of genes related to resistance was maintained at a high level in the resistant lines when treated with WBPHs alone, but was at a similar level to those of the controls when treated with C7 or cq-9. Interfering with WBPH access did not adversely affect the plant phenotype. Recently, people's interest in the environment has increased, and the use of plant-derived materials is also increasing. There is a new trend towards using plant extracts as an environmentally friendly means of managing resistance to WBPH during the rice cultivation period, while also avoiding environmental pollution.

Monofloral Corn Poppy Bee-Collected Pollen-A Detailed Insight into Its Phytochemical Composition and Antioxidant Properties

The aim of this study was to compile a detailed phytochemical profile and assess the antioxidant properties of bee-collected pollen (PBP) obtained from corn poppy (Papaver rhoeas L.) plants. To achieve this, a lipid fraction was prepared for quantifying fatty acids using GC-FID. Extractable and alkaline-hydrolysable PBP fractions (obtained from a defatted sample) were used to determine the qualitative and quantitative profiles of phenolic compounds, phenylamides and alkaloids using UHPLC/Q-ToF-MS. Additionally, various spectrophotometric assays (TAC, FRP, CUPRAC, DPPH^⦁) were conducted to evaluate the antioxidant properties. Phenolic compounds were more present in the extractable fraction than in the alkaline-hydrolysable fraction. Luteolin was the predominant compound in the extractable fraction, followed by tricetin and various derivatives of kaempferol. This study presents one of the first reports on the quantification of tricetin aglycone outside the Myrtaceae plant family. The alkaline-hydrolysable fraction exhibited a different phenolic profile, with a significantly lower amount of phenolics. Kaempferol/derivatives, specific compounds like ferulic and 5-carboxyvanillic acids, and (epi)catechin 3-O-gallate were the predominant compounds in this fraction. Regarding phenylamides, the extractable fraction demonstrated a diverse range of these bioactive compounds, with a notable abundance of different spermine derivatives. In contrast, the hydrolysable fraction contained six spermine derivatives and one spermidine derivative. The examined fractions also revealed the presence of seventeen different alkaloids, belonging to the benzylisoquinoline, berberine and isoquinoline classes. The fatty-acid profile confirmed the prevalence of unsaturated fatty acids. Furthermore, both fractions exhibited significant antioxidant activity, with the extractable fraction showing particularly high activity. Among the assays conducted, the CUPRAC assay highlighted the exceptional ability of PBP's bioactive compounds to reduce cupric ions.

Integration of Volatilomics and Metabolomics Unveils Key Flavor-Related Biological Pathways in Different Carambola Cultivars

Carambola is a tropical fruit that is highly sought after by consumers due to its unique flavor, star shape, and nutritional value. Enhancing the flavor quality of this fruit can increase the consumer acceptance and market demand. However, flavor is an intrinsic characteristic of fruits. Its decoding requires in-depth knowledge based on recognizing key biological pathways relevant to flavor formation and development. In this study, the volatile and non-volatile metabolites contributing to the flavor variation of five carambola cultivars were investigated by a novel strategy combining GC-MS/O-based volatilomics with LC-MS-based metabolomics. Several significant flavor-related pathways, involving biosynthesis or metabolism of amino acids, terpenoids, fatty acids, sugar and organic acid, and flavonoids were identified based on the enrichment analysis of important volatile and non-volatile metabolites. The results indicated that there were metabolites in the flavor-related pathways being up- or downregulated, leading to the differences in flavor traits of different carambola cultivars. This study could provide a valuable reference for breeders and researchers of interest in the mechanisms underlying the regulation of flavor, which would ultimately lead to the creation of carambola cultivars with more attractive flavor profiles and pleasurable consuming experiences.

Histone Deacetylase GiSRT2 Negatively Regulates Flavonoid Biosynthesis in Glycyrrhiza inflata

Glycyrrhiza inflata Batalin is a medicinal licorice species that has been widely used by humans for centuries. Licochalcone A (LCA) is a characteristic flavonoid that accumulates in G. inflata roots with high economical value. However, the biosynthetic pathway and regulatory network of its accumulation remain largely unknown. Here we found that a histone deacetylase (HDAC) inhibitor nicotinamide (NIC) could enhance the accumulation of LCA and total flavonoids in G. inflata seedlings. GiSRT2, a NIC-targeted HDAC was functionally analyzed and its RNAi transgenic hairy roots accumulated much more LCA and total flavonoids than its OE lines and the controls, indicating a negative regulatory role of GiSRT2 in the accumulation of LCA and total flavonoids. Co-analysis of transcriptome and metabolome of RNAi-GiSRT2 lines revealed potential mechanisms in this process. An O-methyltransferase gene, GiLMT1 was up-regulated in RNAi-GiSRT2 lines and the encoded enzyme catalyzed an intermediate step in LCA biosynthesis pathway. Transgenic hairy roots of GiLMT1 proved that GiLMT1 is required for LCA accumulation. Together, this work highlights the critical role of GiSRT2 in the regulation of flavonoid biosynthesis and identifies GiLMT1 as a candidate gene for the biosynthesis of LCA with synthetic biology approaches.

Comparative transcriptome sequencing analysis to postulate the scheme of regulated leaf coloration in Perilla frutescens

Perilla as herb, ornamental, oil and edible plant is widely used in East Asia. Until now, the mechanism of regulated leaf coloration is still unclear. In this study, four different kinds of leaf colors were used to measure pigment contents and do transcriptome sequence to postulate the mechanism of leaf coloration. The measurements of chlorophyll, carotenoid, flavonoid, and anthocyanin showed that higher contents of all the aforementioned four pigments were in full purple leaf 'M357', and they may be determined front and back leaf color formation with purple. Meanwhile, the content of anthocyanin was controlled back leaf coloration. The chromatic aberration analysis and correlative analysis between different pigments and L*a*b* values analysis also suggested front and back leaf color change was correlated with the above four pigments. The genes involved in leaf coloration were identified through transcriptome sequence. The expression levels of chlorophyll synthesis and degradation related genes, carotenoid synthesis related genes and anthocyanin synthesis genes showed up-/down-regulated expression in different color leaves and were consistent of accumulation of these pigments. It was suggested that they were the candidate genes regulated perilla leaf color formation, and genes including F3'H, F3H, F3',5'H, DFR, and ANS are probably important for regulating both front and back leaf purple formation. Transcription factors involved in anthocyanin accumulation, and regulating leaf coloration were also identified. Finally, the probable scheme of regulated both full green and full purple leaf coloration and back leaf coloration was postulated.

The Amsterdam petunia germplasm collection: A tool in plant science

Petunia hybrida is a plant model system used by many researchers to investigate a broad range of biological questions. One of the reasons for the success of this organism as a lab model is the existence of numerous mutants, involved in a wide range of processes, and the ever-increasing size of this collection owing to a highly active and efficient transposon system. We report here on the origin of petunia-based research and describe the collection of petunia lines housed in the University of Amsterdam, where many of the existing genotypes are maintained.

Applications of Perilla frutescens Extracts in Clinical Practice

(1) Background: Perilla frutescens (L.) Britt. is an important pharmaceutical crop that remains a focus point for researchers worldwide due to its complex phytochemical constituents, medicinal effects, and nutraceutical properties. The literature data are based on animal and cell culture studies, so the clinical evidence for the therapeutic effects is poorly outlined. The aim of this review was to provide an updated and thorough understanding of Perilla frutescens applications in clinical practice using data derived from human studies, and to outline the potential directions and perspectives for further studies on this crop. (2) Methods: Medline, Embase, and Cochrane databases were used to find relevant studies. All interventional studies that evaluated the effect of Perilla frutescens in human subjects were assessed. (3) Results: The main perspectives that can be contoured from the presented literature evaluation are an important clinical effect of Perilla frutescens extracts on allergic rhinoconjuctivitis, especially in young populations, a potent hypolipemiant effect that, in conjunction with increased serum biological antioxidant potential, determines significant improvements in cognitive function and a wide variety of miscellaneous clinical effects that need further exploration. (4) Conclusions: Supplementary research is needed in order to demonstrate the therapeutic effects of Perilla frutescens in controlled clinical settings.

Genome-wide identification and expression pattern analysis of R2R3-MYB transcription factor gene family involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii

BACKGROUND

R2R3-MYB transcription factors regulate secondary metabolism, stress responses and development in various plants. Puerarin is a bioactive ingredient and most abundant secondary metabolite isolated from Pueraria lobata. The biosynthesis of puerarin proceeds via the phenylpropanoid pathway and isoflavonoids pathway, in which 9 key enzymes are involved. The expression of these structural genes is under control of specific PtR2R3-MYB genes in different plant tissues. However, how PtR2R3-MYB genes regulates structural genes in puerarin biosynthesis remains elusive. This study mined the PtR2R3-MYB genes involved in puerarin biosynthesis and response to hormone in Pueraria lobata var. thomsonii.

RESULTS

A total of 209 PtR2R3-MYB proteins were identified, in which classified into 34 subgroups based on the phylogenetic topology and the classification of the R2R3-MYB superfamily in Arabidopsis thaliana. Furtherly physical and chemical characteristics, gene structure, and conserved motif analysis were also used to further analyze PtR2R3-MYBs. Combining puerarin content and RNA-seq data, speculated on the regulated puerarin biosynthesis of PtR2R3-MYB genes and structural genes, thus 21 PtR2R3-MYB genes and 25 structural genes were selected for validation gene expression and further explore its response to MeJA and GSH treatment by using qRT-PCR analysis technique. Correlation analysis and cis-acting element analysis revealed that 6 PtR2R3-MYB genes (PtMYB039, PtMYB057, PtMYB080, PtMYB109, PtMYB115 and PtMYB138) and 7 structural genes (PtHID2, PtHID9, PtIFS3, PtUGT069, PtUGT188, PtUGT286 and PtUGT297) were directly or indirectly regulation of puerarin biosynthesis in ZG11. It is worth noting that after MeJA and GSH treatment for 12-24 h, the expression changes of most candidate genes were consistent with the correlation of puerarin biosynthesis, which also shows that MeJA and GSH have the potential to mediate puerarin biosynthesis by regulating gene expression in ZG11.

CONCLUSIONS

Overall, this study provides a comprehensive understanding of the PtR2R3-MYB and will paves the way to reveal the transcriptional regulation of puerarin biosynthesis and response to phytohormone of PtR2R3-MYB genes in Pueraria lobata var. thomsonii.

Mass Spectrometry-Based Untargeted Metabolomics Reveals the Importance of Glycosylated Flavones in Patterned Lentil Seed Coats

Lentil seed coats are rich in antioxidant polyphenols that are important for plant defense and have potential as valorized byproducts. Although biochemical differences among lentil seed coat colors have been previously studied, differences among seed coat patterns remain largely unexplored. This study used mass spectrometry-based untargeted metabolomics to investigate polyphenol differences among lentil seed coat patterns to search for biochemical pathways potentially responsible for seed coat pattern differences. Comparing patterned with non-patterned green lentil seed coats, 28 significantly upregulated metabolites were found in patterned seed coats; 19 of them were identified as flavones. Flavones were virtually absent in non-patterned seed coats, thereby strongly suggesting a blockage in their flavone biosynthetic pathway. Although the black pattern is not readily discernible on black seed coats, many of the same flavones found in green marbled seed coats were also found in black seed coats, indicating that black seed coats likely have a marbled pattern.

Integrative metabolome and transcriptome analyses reveals the black fruit coloring mechanism of Crataegus maximowiczii C. K. Schneid

Crataegus is an economically important plant due to its medicinal and health-promoting properties. Flavonoids are the main functional components of Crataegus fruit. Fruits of naturally pollinated Crataegus maximowiczii possess an extraordinary black skin and are rich in anthocyanins and other flavonoids. However, the composition of anthocyanins and the overall molecular mechanism of anthocyanin biosynthesis in C. maximowiczii fruits have not been fully elucidated. In this study, the metabolome and transcriptome of C. maximowiczii fruits with black and red skin were analyzed. The results revealed that the differential metabolites and genes were enriched in the anthocyanin biosynthesis pathways in C. maximowiczii fruits. In total, 52 differentially accumulated flavonoid metabolites, 12 differentially accumulated anthocyanins and 22 differentially expressed genes were identified. After weighted gene coexpression network analysis, two modules were found to be highly interrelated with the accumulation of anthocyanin components. The coexpression networks of these two modules were used to identify key candidate transcription factors associated with anthocyanin biosynthesis, such as MYB5, MYB113, bHLH60, ERF105, bZIP44, NAC082, and WRKY11. The results revealed that cyanidin-based anthocyanins were the main pigments responsible for the black coloration of C. maximowiczii fruits. Based on these differentially accumulated anthocyanins and key genes, genetic and metabolic regulatory networks of anthocyanin biosynthesis were also proposed. Overall, this study elucidates the molecular basis of the formation of black color in C. maximowiczii fruits, and provides an intensive study on anthocyanin biosynthesis in C. maximowiczii for comprehensive utilization.

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

Metabolomic profiling of developing perilla leaves reveals the best harvest time

Ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS) and gas chromatography-mass spectrometry (GC-MS) were applied to analyze metabolites in perilla leaves (PLs) during its developmental process. In total, 118 metabolites were identified, including volatile and non-volatile compounds, such as terpenoids, sugars, amino acids, organic acids, fatty acids, phenolic acids, flavonoids, and others. Principal component analysis (PCA) indicated great variations of metabolites during PLs development. Clustering analysis (CA) clarified the dynamic patterns of the metabolites. The heatmap of CA showed that most of the detected metabolites were significantly accumulated at stage 4 which is the pre anthesis period, and declined afterwards. The results of the present study provide a comprehensive overview of the metabolic dynamics of developing PLs which suggested that pre anthesis period is the best harvest time for PLs.

Integrated metabolomic and transcriptomic analyses reveal molecular response of anthocyanins biosynthesis in perilla to light intensity

The perilla anthocyanins have important medicinal and ornamental value, and their contents are significantly affected by light intensity. In view of their molecular mechanisms were not well understood, we integrated the metabolomic and transcriptomic analyses of the light-sensitive perilla variety under different light intensity. The perilla leave color were obviously affected under different treatments. Totally 140 flavonoid metabolites and 2461 genes showed steady change, among which 60 flavonoid metabolites were increased accumulation and 983 genes were upregulated expression under elevated light intensity treatment. Light treatment prominently affected the expression of genes involved in the main anthocyanin metabolites accumulation in perilla leaves. Using WGCNA analysis, we identified 4 key genes in anthocyanin biosynthesis pathway (CHI, DFR, and ANS) and 147 transcription factors (MYB, bHLH, bZIP, ERF, and NAC) involved in malonylshisonin biosynthesis. Among them, 6 MYBs and 4 bZIPs were predicted to play important roles in light regulation of malonylshisonin biosynthesis based on phylogenetic construction, correlation analysis, cis-acting element identification and qPCR verification. The identified key genes and regulatory factors will help us to understand the potential mechanism of photo-regulated anthocyanin accumulation in perilla.

Integrative Metabolome and Transcriptome Analysis Reveals the Regulatory Network of Flavonoid Biosynthesis in Response to MeJA in Camelliavietnamensis Huang

Flavonoids are secondary metabolites widely found in plants, which perform various biological activities, such as antiinflammation, antioxidation, antitumor, and so on. Camellia vietnamensis Huang, a species of oil-tea Camellia tree, is an important woody oil crop species widely planted on Hainan Island, which provides health benefits with its high antioxidant activity and abundant flavonoid content. However, very little is known about the overall molecular mechanism of flavonoid biosynthesis in C. vietnamensis Huang. In this study, methyl jasmonate (MeJA) is used as an inducer to change the content of secondary metabolites in C. vietnamensis. Then, the potential mechanisms of flavonoid biosynthesis in C. vietnamensis leaves in response to MeJA were analyzed by metabolomics and transcriptomics (RNA sequencing). The results showed that metabolome analysis detected 104 flavonoids and 74 fatty acyls which showed different expression patterns (increased or decreased expression). It was discovered by KEGG analysis that three differentially accumulated metabolites (cinnamaldehyde, kaempferol and quercitrin) were annotated in the phenylpropanoid biosynthesis (ko00940), flavonoid biosynthesis (ko00941), and flavone and flavonol biosynthesis (ko00944) pathways. In the transcriptome analysis, 35 different genes involved in the synthesis of flavonoids were identified by MapMan analysis. The key genes (PAL, 4CL, CCR, CHI, CHS, C4H, FLS) that might be involved in the formation of flavonoid were highly expressed after 2 h of MeJA treatment. This study provides new insights and data supporting the molecular mechanism underlying the metabolism and synthesis of flavonoids in C. vietnamensis under MeJA treatment.

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

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

SUPPLEMENTARY INFORMATION

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

Transcriptomic and metabolomic investigation of metabolic disruption in Vigna unguiculata L. triggered by acetamiprid and cyromazine

A variety of pesticides are often used in agricultural management to control target pests but may trigger disruptions in the metabolism of nontarget organisms, ultimately affecting crop quality. Acetamiprid (ACE) and cyromazine (CYR) are two frequently used insecticides on cowpea, so it is critical to understand whether these two insecticides cause metabolic disorders in cowpea quality changes and the mechanism by which they do so. Here, we used metabolomic and transcriptomic methods to explore the mechanisms of the effects of ACE, CYR, and their mixture (MIX) on cowpea. In this study, ACE, CYR and MIX had no significant effects on plant biomass or growth status but decreased the contents of starch, soluble protein, and total flavonoids. All treatments reduced the total flavonoid content, but MIX showed the largest reduction of 10.02%. Metabolomic and transcriptomic analyses revealed that ACE markedly affected amino acid metabolism, and CYR and MIX affected sugar metabolism and flavonoid synthesis pathways. ACE and CYR reduced the levels of alanine, glutamic acid, isoleucine and phenylalanine and the expression of amino acid-related genes in cowpea, while MIX significantly increased the levels of most amino acids. All pesticide treatments reduced saccharide levels and related genes, with the most pronounced reduction in the MIX treatment. Exposure to ACE decreased the content of naringenin chalcone and quercetin and increased the content of anthocyanins in cowpeas, while MIX caused a significant decrease in the contents of quercetin and anthocyanins. According to the current study, single and mixed pesticides had different effects on the active ingredients of cowpea, with MIX causing the most significant decrease in the metabolite content of cowpea. These results provide important insights from a molecular perspective on how neonicotinoids and triazine insecticides affect cowpea metabolism.

Integrative Analysis of Metabolome and Transcriptome Identifies Potential Genes Involved in the Flavonoid Biosynthesis in Entada phaseoloides Stem

Entada phaseoloides stem is known for its high medicinal benefits and ornamental value. Flavonoids are one of the main active constituents in E. phaseoloides stem. However, the regulatory mechanism of flavonoids accumulation in E. phaseoloides is lacking. Here, phytochemical compounds and transcripts from stems at different developmental stages in E. phaseoloides were investigated by metabolome and transcriptome analysis. The metabolite profiling of the oldest stem was obviously different from young and older stem tissues. A total of 198 flavonoids were detected, and flavones, flavonols, anthocyanins, isoflavones, and flavanones were the main subclasses. The metabolome data showed that the content of acacetin was significantly higher in the young stem and older stem than the oldest stem. Rutin and myricitrin showed significantly higher levels in the oldest stem. A total of 143 MYBs and 143 bHLHs were identified and classified in the RNA-seq data. Meanwhile, 34 flavonoid biosynthesis structural genes were identified. Based on the expression pattern of structural genes involved in flavonoid biosynthesis, it indicated that flavonol, anthocyanin, and proanthocyanin biosynthesis were first active during the development of E. phaseoloides stem, and the anthocyanin or proanthocyanin biosynthesis branch was dominant; the flavone biosynthesis branch was active at the late developmental stage of the stem. Through the correlation analysis of transcriptome and metabolome data, the potential candidate genes related to regulating flavonoid synthesis and transport were identified. Among them, the MYBs, bHLH, and TTG1 are coregulated biosynthesis of flavonols and structural genes, bHLH and transporter genes are coregulated biosynthesis of anthocyanins. In addition, the WDR gene TTG1-like (AN11) may regulate dihydrochalcones and flavonol biosynthesis in specific combinations with IIIb bHLH and R2R3-MYB proteins. Furthermore, the transport gene protein TRANSPARENT TESTA 12-like gene is positively regulated the accumulation of rutin, and the homolog of ABC transporter B family member gene is positively correlated with the content of flavone acacetin. This study offered candidate genes involved in flavonoid biosynthesis, information of flavonoid composition and characteristics of flavonoids accumulation, improved our understanding of the MYBs and bHLHs-related regulation networks of flavonoid biosynthesis in E. phaseoloides stem, and provided references for the metabolic engineering of flavonoid biosynthesis in E. phaseoloides stem.

Functional characterization of key polyketide synthases by integrated metabolome and transcriptome analysis on curcuminoid biosynthesis in Curcuma wenyujin

Leaf and tuber extracts of Curcuma wenyujin contain a mixture of curcuminoids. However, the curcuminoid constituents and their molecular mechanisms are poorly understood, and the relevant curcumin synthases remain unclear. In this study, we comprehensively compared the metabolite profiles of the leaf and tuber tissues of C. wenyujin. A total of 11 curcuminoid metabolites were identified and exhibited differentially changed contents in the leaf and tuber tissues. An integrated analysis of metabolomic and transcriptomic data revealed the proposed biosynthesis pathway of curcuminoid. Two candidate type Ⅲ polyketide synthases (PKSs) were identified in the metabolically engineering yeasts, indicating that CwPKS1 and CwPKS2 maintained substrate and product specificities. Especially, CwPKS1 is the first type Ⅲ PKS identified to synthesize hydrogenated derivatives of curcuminoid, dihydrocurcumin and tetrehydrocurcumin. Interestingly, the substitution of the glycine at position 219 with aspartic acid (G219D mutant) resulted in the complete inactivation of CwPKS1. Our results provide the first comparative metabolome analysis of C. wenyujin and functionally identified type Ⅲ PKSs, giving valuable information for curcuminoids biosynthesis.

The antioxidant activity, α-glucosidase and acetylcholinesterase inhibition activity, and chemical composition of Paeonia delavayi petal

Objectives

This study aimed to evaluate the functional activity and phytochemical compositions in the flower petals of Paeonia delavayi with different colors.

Materials and Methods

P. delavayi petal extracts were prepared by maceration in methanol, including purple petal extract (PPE), red petal extract (RPE) and yellow petal extract (YPE), and their antioxidant activity, α-glucosidase and acetylcholinesterase inhibition activities were evaluated. To correlate these measured activities to phytochemicals in the petals, UPLC-MS/MS-based metabolomics method was applied to profile the compositions in the petals of different colors. Finally, the KEGG metabolic pathways database was used to identify the related metabolic pathways that are responsible for the production of these polyphenolic phytochemicals in the petals.

Results

The results showed that PPE had the highest total phenolic content (TPC), total flavonoid content (TFC), and the strongest ABTS· + scavenging ability, ferric reducing antioxidant power, and acetylcholinesterase inhibition ability in all three samples, while YPE showed the strongest DPPH· scavenging activity and α-glucosidase inhibition ability. A total of 232 metabolites were detected in the metabolomic analysis, 198 of which were flavonoids, chalcones, flavonols, and anthocyanins. Correlation analysis indicated that Peonidin-3-O-arabinoside and cyanidin-3-O-arabinoside were the major contributors to their antioxidant activity. Principal component analysis showed a clear separation between these three petals. In addition, a total of 38, 98, and 96 differential metabolites were identified in PPE, RPE, and YPE, respectively. Pathway enrichment revealed 6 KEGG pathways displayed significant enrichment differences, of which the anthocyanin biosynthesis, flavone and flavonol biosynthesis were the most enriched signaling pathways. It revealed the potential reason for the differences in metabolic and functional levels between different colors of P. delavayi petals.

Conclusions

P. delavayi petals of different colors have different metabolite contents and functional activities, of which the anthocyanin, flavone, and flavonol metabolites are critical in its functional activities, suggesting the anthocyanin biosynthesis, flavone and flavonol biosynthesis pathways be the key pathways responsible for both the petal color and bioactive phytochemicals in P. delavayi flowers.

Integrated Metabolomic and Transcriptomic Analyses to Understand the Effects of Hydrogen Water on the Roots of Ficus hirta Vahl

Wuzhimaotao (Ficus hirta Vahl) is an important medicinal and edible plant in China. The extract from the roots of Ficus hirta Vahl contains phenylpropanoid compounds, such as coumarins and flavonoids, which are the main active components of this Chinese herbal medicine. In this study, we analyzed the transcriptomic and metabolomic data of the hydrogen-water-treated roots of Ficus hirta Vahl and a control group. The results showed that many genes and metabolites were regulated in the roots of Ficus hirta Vahl that were treated with hydrogen water. Compared with the control group, 173 genes were downregulated and 138 genes were upregulated in the hydrogen-rich water treatment group. Differential metabolite analysis through LC-MS showed that 168 and 109 metabolites had significant differences in positive and negative ion mode, respectively. In the upregulated metabolites, the main active components of Wuzhimaotao, such as the phenylpropane compounds naringin, bergaptol, hesperidin, and benzofuran, were found. Integrated transcriptomic and metabolomic data analysis showed that four and one of the most relevant pathways were over enriched in positive and negative ion mode, respectively. In the relationship between metabolites and DEGs, phenylpropanoid biosynthesis and metabolism play an important role. This indicates that phenylpropanoid biosynthesis and metabolism may be the main metabolic pathways regulated by hydrogen water. Our transcriptome analysis showed that most of the DEGs with |log2FC| ≥ 1 are transcription factor genes, and most of them are related to plant hormone signal transduction, stress resistance, and secondary metabolism, mainly phenylpropanoid biosynthesis and metabolism. This study provides important evidence and clues for revealing the botanical effect mechanism of hydrogen and a theoretical basis for the application of hydrogen agriculture in the cultivation of Chinese herbal medicine.

Integration of Transcriptome and Metabolome Provides New Insights to Flavonoids Biosynthesis in Dendrobium huoshanense

Dendrobium huoshanense is both a traditional herbal medicine and a plant of high ornamental and medicinal value. We used transcriptomics and metabolomics to investigate the effects of growth year on the secondary metabolites of D. huoshanense stems obtained from four different years of cultivation. In this study, a total of 428 differentially accumulated metabolites (DAMs) and 1802 differentially expressed genes (DEGs) were identified. The KEGG enrichment analysis of DEGs and DAMs revealed significant differences in "Flavonoid biosynthesis", "Phenylpropanoid biosynthesis" and "Flavone and flavonol biosynthesis". We summarize the biosynthesis pathway of flavonoids in D. huoshanense, providing new insights into the biosynthesis and regulation mechanisms of flavonoids in D. huoshanense. Additionally, we identified two candidate genes, FLS (LOC110107557) and F3'H (LOC110095936), which are highly involved in flavonoid biosynthesis pathway, by WGCNA analysis. The aim of this study is to investigate the effects of growth year on secondarily metabolites in the plant and provide a theoretical basis for determining a reasonable harvesting period for D. huoshanense.

Defense responses of arbuscular mycorrhizal fungus-colonized poplar seedlings against gypsy moth larvae: a multiomics study

Arbuscular mycorrhizal (AM) fungi may help protect plants against herbivores; however, their use for the pest control of woody plants requires further study. Here, we investigated the effect of Glomus mosseae colonization on the interactions between gypsy moth larvae and Populus alba × P. berolinensis seedlings and deciphered the regulatory mechanisms underlying the mycorrhizal-induced resistance in the leaves of mycorrhizal poplar using RNA-seq and nontargeted metabolomics. The resistance assay showed that AM fungus inoculation protected poplar seedlings against gypsy moth larvae, as evidenced by the decreased larval growth and reduced larval survival. A transcriptome analysis revealed that differentially expressed genes (DEGs) were involved in jasmonic acid biosynthesis (lipoxygenase, hydroperoxide dehydratase, and allene oxide cyclase) and signal transduction (jasmonate-ZIM domain and transcription factor MYC2) and identified the genes that were upregulated in mycorrhizal seedlings. Except for chalcone synthase and anthocyanidin synthase, which were downregulated in mycorrhizal seedlings, all DEGs related to flavonoid biosynthesis were upregulated, including 4-coumarate-CoA ligase, chalcone isomerase, flavanone 3-hydroxylase, flavonol synthase, and leucoanthocyanidin reductase. The metabolome analysis showed that several metabolites with insecticidal properties, including coumarin, stachydrine, artocarpin, norizalpinin, abietic acid, 6-formylumbelliferone, and vanillic acid, were significantly accumulated in the mycorrhizal seedlings. These findings suggest the potential of mycorrhiza-induced resistance for use in pest management of woody plants and demonstrate that the priming of JA-dependent responses in poplar seedlings contributes to mycorrhiza-induced resistance to insect pests.

Characterization of Flavonoids and Transcripts Involved in Their Biosynthesis in Different Organs of Cissus rotundifolia Lam

Cissus rotundifolia Lam. is used as a medicinal herb and vegetable. Flavonoids are the major components for the therapeutic effects. However, flavonoids constituents and expression profiles of related genes in C. rotundifolia organs are unknown. Colorimetric assay showed the highest flavonoid concentration in roots compared to the stem and leaf. Widely target-based metabolome analysis allowed tentative identification of 199 compounds in three organs. Flavonols and flavones were the dominant flavonoids subclasses. Among the metabolites, 171 were common in the three organs. Unique accumulation profile was observed in the root while the stem and leaf exhibited relatively similar patterns. In the root, six unique compounds (jaceosidin, licoagrochalcone D, 8-prenylkaempferol, hesperetin 7-O-(6″malonyl) glucoside, aureusidin, apigenin-4′-O-rhamnoside) that are used for medicinal purposes were detected. In total, 18,427 expressed genes were identified from transcriptome of the three organs covering about 60% of annotated genes in C. rotundifolia genome. Fourteen gene families, including 52 members involved in the main pathway of flavonoids biosynthesis, were identified. Their expression could be found in at least one organ. Most of the genes were highly expressed in roots compared to other organs, coinciding with the metabolites profile. The findings provide fundamental data for exploration of metabolites biosynthesis in C. rotundifolia and diversification of parts used for medicinal purposes.

A Combination Extract of Gardeniae Fructus and Perillae Folium Exerts Anti-Inflammatory Effects on LPS-Activated RAW 264.7 Mouse Macrophages via an ER Stress-Induced CHOP Pathway

The aim of this study is to investigate the effects of a combination extract of Gardeniae Fructus and Perillae Folium (GP) on inflammatory reactions in lipopolysaccharide (LPS)-activated mouse macrophages RAW 264.7 cells. Multiplex cytokine assay, Fluo-4 calcium assay, Flow cytometry assay for phospho-P38 MAPK, and quantitative PCR were carried out. GP significantly reduced LPS-induced productions of macrophage inflammatory protein (MIP)-1α and monokine induced by gamma interferon (MIG) and release of intracellular calcium in LPS-activated RAW 264.7 cells. GP also significantly inhibited P38 MAPK phosphorylation and mRNA levels of Chop, Camk2a, Stat1, Stat3, Jak2, Fas, Nos2, and Ptgs2 in LPS-activated RAW 264.7 cells. Taken together, this study represents that GP exerts anti-inflammatory effects on LPS-activated RAW 264.7 cells via ER stress-induced CHOP pathway.

Genome-Wide Investigation of Major Enzyme-Encoding Genes in the Flavonoid Metabolic Pathway in Tartary Buckwheat (Fagopyrum tataricum)

Key enzymes play a vital role in plant growth and development. However, the evolutionary relationships between genes encoding key enzymes in the metabolic pathway of Tartary buckwheat flavonoids are poorly understood. Based on the published Tartary buckwheat genome sequence and related Tartary buckwheat transcriptome data, 48 key enzyme-encoding genes involved in flavonoid metabolism were screened from the Tartary buckwheat genome in this study; the chromosome localization, gene structure and promoter elements of these enzyme-encoding gene were also investigated. Gene structure analysis revealed relatively conserved 5' exon sequences among the 48 genes, indicating that the structural diversity of key enzyme-encoding genes is low in Tartary buckwheat. Through promoter analysis, these key enzyme-encoding genes were found to contain a large number of light-response elements and hormone-response elements. In addition, some genes could bind MYB transcription factors, participating in the regulation of flavonoid biosynthesis. The transcription level of the 48 key enzyme-encoding gene varied greatly among tissues. In this study, we identified 48 key enzyme-encoding genes involved in flavonoid metabolic pathways, and elucidated the structure, evolution and tissue-specific expression patterns of these genes. These results lay a foundation for further understanding the functional characteristics and evolutionary relationships of key enzyme-encoding genes involved in the flavonoid metabolic pathway in Tartary buckwheat.