Metabolomics Integrated with Transcriptomics Reveals Redirection of the Phenylpropanoids Metabolic Flux in Ginkgo biloba

Citric acid treatment inhibits fading of sorghum (Sorghum bicolor) by modulating the accumulation of flavonoids

Sorghum seeds can discolor during storage. Treatment of seeds with citric acid improves sensory quality and antioxidant activity. This study compared the differences in phenotypic and antioxidant activity between citric acid-treated and water-treated sorghum seeds. The study used transcriptomics and metabolomics approaches to investigate the regulatory mechanisms. The ∆a, ∆b and ∆l values of citric acid-treated sorghum seeds significantly increased after 6 months of storage. The SOD, POD and CAT enzyme activities of the citric acid-treated group were 1.94, 1.91 and 2.45 times higher than those of the control, respectively. The joint transcriptome and metabolome analysis showed that the citric acid-induced changes were mainly focused on the flavonoid biosynthetic pathway. Citric acid treatment up-regulated CHS, ANR, MYB and bHLH genes and promoted flavonoid accumulation. In conclusion, citric acid treatment promotes flavonoid accumulation, delays sorghum seed discoloration, and enhances antioxidant activity and storage life.

Saline-alkali stress affects the accumulation of proanthocyanidins and sesquiterpenoids via the MYB5-ANR/TPS31 cascades in the rose petals

Rose (Rosa rugosa) petals are rich in diverse secondary metabolites, which have important physiological functions as well as great economic values. Currently, it remains unclear how saline and/or alkaline stress(es) influence the accumulation of secondary metabolites in rose. In this study, we analyzed the transcriptome and metabolite profiles of rose petals under aline-alkali stress and uncovered the induction mechanism underlying major metabolites. Dramatic changes were observed in the expression of 1363 genes and the abundances of 196 metabolites in petals in response to saline-alkali stress. These differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) are mainly associated with flavonoid and terpenoid metabolism and the reconstruction of cell walls. Of them, TERPENE SYNTHASE 31 (TPS31) overexpression in tobacco leaves driven by its own promoter resulted in significant alterations in the levels of diverse terpenoids, which were differentially influenced by saline-alkali stress. An integrated analysis of metabolomic and transcriptomic data revealed a high correlation between the abundances of flavonoids/terpenoids and the expression of the transcription factor MYB5. MYB5 may orchestrate the biosynthesis of sesquiterpenoids and proanthocyanidins through direct regulation of TPS31 and ANR expression under aline-alkali stress. Our finding facilitates improving the bioactive substance accumulation of rose petals by metabolic engineering.

Metabolomic and transcriptomic analyses reveal the mechanism of polysaccharide and secondary metabolite biosynthesis in Bletilla striata tubers in response to shading

Polysaccharides and various secondary metabolites are the major bioactive ingredients in Bletilla striata tubers and their biosynthesis and accumulation are influenced by light intensity. However, the mechanisms underlying shading effects remain largely unknown. In the present study, we used a combined analysis of the physiology, metabolome, and transcriptome to investigate the physiological activities and bioactive component accumulation of B. striata under different shading treatments (S0, S50, S70, and S90). The dry weight of shoots and tubers, net photosynthetic rate, and polysaccharide content were highest in S50 and lowest in S90. The content of precursors (sucrose, Glucose-6P, and Mannose-6P) for polysaccharide synthesis significantly increased in S50. However, the expression levels of genes involved in starch biosynthesis decreased in S50. Several structural genes involved in secondary metabolism, including cinnamic acid 4-hydroxylase (C4H), chalcone synthase (CHS), and 1-Deoxy-D-xylulose-5-phosphate synthase (DXS), showed decreased expression in S50. However, the shading effect on the biosynthesis of secondary metabolites (phenylpropanoids, flavonoids, and terpenoids) was inconsistent. Our study provides the molecular mechanisms underlying the effects of shading on the biosynthesis of polysaccharides and secondary metabolites in B. striata and offers a theoretical basis for the artificial cultivation and industrial production of bioactive ingredients.

Using widely targeted metabolomics profiling to explore differences in constituents of three Bletilla species

Bletilla striata has been used in traditional Chinese medicine for thousands of years to treat a variety of health diseases. Currently, metabolic causes of differences in medicinal values are unknown, due to the lack of a large-scale and comprehensive investigation of metabolites in Bletilla species. In order to gain a better understanding of the major chemical constituents responsible for the medicinal value, this study aimed to explore the metabolomic differences among three Bletilla species (Bletilla striata: Bs, Bletilla ochracea: Bo and Bletilla formosana: Bf). There were 258 different metabolites between 'Bo' and 'Bf', the contents of 109 metabolites had higher abundance, while 149 metabolites showed less accumulation. There were 165 different metabolites between the 'Bs' and 'Bf', content of 72 metabolites was increased and content of 93 metabolites was decreased. There were 239 different metabolites between the 'Bs' and 'Bo', content of 145 metabolites was increased and content of 94 metabolites was decreased. In the Bo_vs_Bf, Bs_vs_Bf and Bs_vs_Bo groups, the major differential categories were flavonoids, phenolic acids, organic acids and alkaloids. Moreover, the differential metabolites were clustered into clear and distinct profiles via K-means analysis. In addition, the major differential categories were flavonoids, phenolic acids, organic acids and alkaloids. The 'Flavonoid biosynthesis' (ko00941) and 'Phenylalanine metabolism' (ko00360) pathways were significantly enriched in Bo_vs_Bf, Bs_vs_Bf and Bs_vs_Bo comparisons. These results clarify the metabolomics in different Bletilla species, as well as providing basis for the phamaceutical value of novel species of Bletilla.

Multi-omics explores the potential regulatory role of acetylation modification in flavonoid biosynthesis of Ginkgo biloba

Flavonoids are crucial medicinal active ingredients in Ginkgo biloba L. However, the effect of protein post-translational modifications on flavonoid biosynthesis remains poorly explored. Lysine acetylation, a reversible post-translational modification, plays a crucial role in metabolic regulation. This study aims to investigate the potential role of acetylation in G. biloba flavonoid biosynthesis. Through comprehensive analysis of transcriptomes, metabolomes, proteomes and acetylated proteins in different tissues, a total of 11,788 lysine acetylation sites were identified on 4324 acetylated proteins, including 89 acetylation sites on 23 proteins. Additionally, 128 types of differentially accumulated flavonoids were identified among tissues, and a dataset of differentially expressed genes related to the flavonoid biosynthesis pathway was constructed. Twelve (CHI, C3H1, ANR, DFR, CCoAOMT1, F3H1, F3H2, CCoAOMT2, C3H2, HCT, F3'5'H and FG2) acetylated proteins that might be involved in flavonoid biosynthesis were identified. Specifically, we found that the modification levels of CCoAOMT1 and F3'5'H sites correlated with the catalytic production of homoeriodictyol and dihydromyricetin, respectively. Inhibitors of lysine deacetylase (trichostatin A) impacted total flavonoid content in different tissues and increased flavonoid levels in G. biloba roots. Treatment with trichostatin A revealed that expression levels of GbF3'5'H and GbCCoAOMT1 in stems and leaves aligned with total flavonoid content variations, while in roots, expression levels of GbC3H2 and GbFG2 corresponded to total flavonoid content changes. Collectively, these findings reveal for the first time the important role of acetylation in flavonoid biosynthesis.

Integrated transcriptome and metabolome analysis reveals the regulation of phlorizin synthesis in Lithocarpus polystachyus under nitrogen fertilization

BACKGROUND

Nitrogen (N) is essential for plant growth and development. In Lithocarpus polystachyus Rehd., a species known for its medicinal and food value, phlorizin is the major bioactive compound with pharmacological activity. Research has revealed a positive correlation between plant nitrogen (N) content and phlorizin synthesis in this species. However, no study has analyzed the effect of N fertilization on phlorizin content and elucidated the molecular mechanisms underlying phlorizin synthesis in L. polystachyus.

RESULTS

A comparison of the L. polystachyus plants grown without (0 mg/plant) and with N fertilization (25, 75, 125, 175, 225, and 275 mg/plant) revealed that 75 mg N/plant fertilization resulted in the greatest seedling height, ground diameter, crown width, and total phlorizin content. Subsequent analysis of the leaves using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) detected 150 metabolites, including 42 flavonoids, that were differentially accumulated between the plants grown without and with 75 mg/plant N fertilization. Transcriptomic analysis of the L. polystachyus plants via RNA sequencing revealed 162 genes involved in flavonoid biosynthesis, among which 53 significantly differed between the N-treated and untreated plants. Fertilization (75 mg N/plant) specifically upregulated the expression of the genes phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), and phlorizin synthase (PGT1) but downregulated the expression of trans-cinnamate 4-monooxygenase (C4H), shikimate O-hydroxycinnamoyltransferase (HCT), and chalcone isomerase (CHI), which are related to phlorizin synthesis. Finally, an integrated analysis of the transcriptome and metabolome revealed that the increase in phlorizin after N fertilization was consistent with the upregulation of phlorizin biosynthetic genes. Quantitative real-time PCR (qRT‒PCR) was used to validate the RNA sequencing data. Thus, our results indicated that N fertilization increased phlorizin metabolism in L. polystachyus by regulating the expression levels of the PAL, PGT1, 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase (C3'H), C4H, and HCT genes.

CONCLUSIONS

Our results demonstrated that the addition of 75 mg/plant N to L. polystachyus significantly promoted the accumulation of flavonoids, including phlorizin, and the expression of flavonoid synthesis-related genes. Under these conditions, the genes PAL, 4CL, and PGT1 were positively correlated with phlorizin accumulation, while C4H, CHI, and HCT were negatively correlated with phlorizin accumulation. Therefore, we speculate that PAL, 4CL, and PGT1 participate in the phlorizin pathway under an optimal N environment, regulating phlorizin biosynthesis. These findings provide a basis for improving plant bioactive constituents and serve as a reference for further pharmacological studies.

Widely targeted metabolomics reveals differences in metabolites of Paeonia lactiflora cultivars

INTRODUCTION

Paeonia lactiflora contains diverse active constituents and exhibits various pharmacological activities. However, only partial identification of biologically active substances from P. lactiflora has been achieved using low-throughput techniques. Here, the roots of P. lactiflora, namely, Fenyunu (CK), Dafugui (DFG), and Red Charm (HSML), were studied. The primary and secondary metabolites were investigated using ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESIMS/MS).

METHODS

The chemical compounds and categories were detected using broadly targeted UPLC-MS/MS. Principal component analysis (PCA), orthogonal partial least-squares discriminant analysis (OPLS-DA), and hierarchical clustering analysis (HCA) were carried out for metabolites of different varieties of P. lactiflora.

RESULTS

A total of 1237 compounds were detected and classified into 11 categories. HCA, PCA, and OPLS-DA of these metabolites indicated that each variety of P. lactiflora was clearly separated from the other groups. Differential accumulated metabolite analysis revealed that the three P. lactiflora varieties contained 116 differentially activated metabolites (DAMs) involved in flavonoid, flavone, and flavonol metabolism. KEGG pathway analysis revealed that, in 65 pathways, 336 differentially abundant metabolites (DMs) were enriched in the CK and DFG groups; moreover, the type and content of terpenoids were greater in the CK group than in the DFG group. The CK and HSML groups contained 457 DMs enriched in 61 pathways; the type and amount of flavonoids, terpenoids, and tannins were greater in the CK group than in the HSML group. The DFG and HSML groups contained 497 DMs enriched in 65 pathways; terpenoids and alkaloids were more abundant in the HSML variety than in the DFG variety.

CONCLUSIONS

A total of 1237 compounds were detected, and the results revealed significant differences among the three P. lactiflora varieties. Among the three P. lactiflora varieties, phenolic acids and flavonoids composed the largest and most diverse category of metabolites, and their contents varied greatly. Therefore, CK is suitable for medicinal plant varieties, and DFG and HSML are suitable for ornamental plant varieties. Twelve proanthocyanidin metabolites likely determined the differences in color among the three varieties.

Integrated metabolomic and transcriptomic analyses revealed metabolite variations and regulatory networks in Cinnamomum cassia Presl from four growth years

To understand the mechanism of the dynamic accumulation of active ingredients in Cinnamomum cassia Presl, metabolomic and transcriptomic analyses of 5~8 years old C. cassia were performed. A total of 72 phenylpropanoids, 146 flavonoids, and 130 terpenoids showed marked changes. Most phenylpropanoids and flavonoids showed markedly higher abundances in 6-year-old C. cassia than in others, which was related to the higher expression of genes that synthesize and regulate phenylpropanoids and flavonoid. We identified transcription factors (TFs) and genes involved in phenylpropanoids and flavonoids synthesis and regulation through co-expression network analyses. Furthermore, most of the terpenoids in 5-year-old C. cassia showed markedly higher abundances than in others, which was due to the differentially expressed genes upstream of the terpenoids pathway. The results of our study provide new insights into the synthesis and accumulation of phenylpropanoid, flavonoids and terpenoids in C. cassia at four growth stages.

Cucumber abscisic acid 8'-hydroxylase Csyf2 regulates yellow flesh by modulating carotenoid biosynthesis

Cucumber (Cucumis sativus L.) flesh is typically colorless or pale green. Flesh with yellow or orange pigment, determined mainly by carotenoid content and composition, is mostly found in semi-wild Xishuangbanna cucumber, which has a very narrow genetic background. Here, we identified a spontaneous cucumber mutant with yellow flesh (yf-343), which accumulated more β-cryptoxanthin and less lutein than regular cultivated European glasshouse-type cucumbers. Genetic analysis revealed that the yellow flesh phenotype was controlled by a single recessive gene. Through fine mapping and gene sequencing, we identified the candidate gene C. sativus yellow flesh 2 (Csyf2), encoding an abscisic acid (ABA) 8'-hydroxylase. Overexpression and RNAi-silencing of Csyf2 in cucumber hairy roots produced lower and higher ABA contents than in non-transgenic controls, respectively. Further, RNA-seq analysis suggested that genes related to ABA signal transduction were differentially expressed in fruit flesh between yf-343 and its wild type, BY, with white flesh. The carotenoid biosynthesis pathway was specifically enriched in fruit flesh at 30 days after pollination when yf-343 fruit flesh turns yellow. Our findings highlight a promising target for gene editing to increase carotenoid content, expanding our genetic resources for pigmented cucumber flesh breeding for improving the nutritional quality of cucumber.

Metabolome and Transcriptome Analysis of Sulfur-Induced Kiwifruit Stem Laccase Gene Involved in Syringyl Lignin Synthesis against Bacterial Canker

Kiwifruit canker is caused by Pseudomonas syringae pv. actinidiae and is one of the most destructive diseases of kiwifruit worldwide. Sulfur can improve the deposit of lignin in kiwifruit stems and induce disease resistance, but the action mechanism at the molecular level remains unclear. This omics-based study revealed that sulfur-induced S lignin synthesis contributes to disease resistance. Histological staining verified sulfur-enhanced total lignin deposition in kiwifruit stems. High-performance liquid chromatography and confocal Raman microscopy showed that sulfur-activated S lignin was mainly deposited in the cell corner. Metabolome and transcriptome analysis revealed that the levels of phenylpropanoid pathway S lignin precursors sinapic acid and sinapyl alcohol were significantly increased and 16 laccase genes were upregulated. Sulfur-induced resistance defense promoted elevated laccase activity by activating the laccase genes, participating in sinapic acid and sinapyl alcohol substance synthesis, and ultimately polymerizing S lignin at cell corner against kiwifruit canker disease.

SA-responsive transcription factor GbMYB36 promotes flavonol accumulation in Ginkgo biloba

Flavonoids are abundant secondary metabolites in Ginkgo biloba and have a wide range of medicinal values. Salicylic acid (SA) can induce flavonoid accumulation in plants, but the detailed regulatory mechanism remains unclear. Here, we established the optimal media for ginkgo callus induction and subculture, and found that exogenous SA greatly increased the content of flavonol, including quercetin, kaempferol, isorhamnetin. Transcriptome changes in SA-treated calli showed that most structural genes involved in flavonoid biosynthesis were upregulated. Particularly, overexpression of GbF3'H in ginkgo calli significantly increased the content of flavonol, suggesting the vital role of GbF3'H in flavonoid biosynthesis. We further identified that a R2R3-MYB, GbMYB36, were significantly upregulated in SA treated calli. Transient overexpression and a LUC assay indicate that GbMYB36 act as an activator, and improve flavonoid biosynthesis through regulating the expression of GbF3'H. Our findings provide insight into the molecular basis of SA-induced flavonoid biosynthesis in ginkgo.

Transcriptome-based analysis of the effects of compound microbial agents on gene expression in wheat roots and leaves under salt stress

Introduction

Salt stress inhibits the beneficial effects of most plant growth-promoting rhizobacteria. The synergistic relationship between beneficial rhizosphere microorganisms and plants helps achieve more stable growth-promoting effects. This study aimed 1) to elucidate changes in gene expression profiles in the roots and leaves of wheat after inoculation with compound microbial agents and 2) to determine the mechanisms by which plant growth-promoting rhizobacteria mediate plant responses to microorganisms.

Methods

Following inoculation with compound bacteria, transcriptome characteristics of gene expression profiles of wheat, roots, and leaves at the flowering stage were investigated using Illumina high-throughput sequencing technology. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the genes that were significantly differentially expressed.

Results

The expression of 231 genes in the roots of bacterial preparations (BIO) -inoculated wheat changed significantly (including 35 upregulated and 196 downregulated genes) compared with that of non-inoculated wheat. The expression of 16,321 genes in leaves changed significantly, including 9651 upregulated genes and 6670 downregulated genes. The differentially expressed genes were involved in the metabolism of carbohydrates, amino acids, and secondary compounds as well as signal transduction pathways. The ethylene receptor 1 gene in wheat leaves was significantly downregulated, and genes related to ethylene-responsive transcription factor were significantly upregulated. GO enrichment analysis showed that metabolic and cellular processes were the main functions affected in the roots and leaves. The main molecular functions altered were binding and catalytic activities, among which the cellular oxidant detoxification enrichment rate was highly expressed in the roots. The expression of peroxisome size regulation was the highest in the leaves. KEGG enrichment analysis showed that linoleic acid metabolism expression was highest in the roots, and the expression of photosynthesis-antenna proteins was the highest in leaves. After inoculation with a complex biosynthesis agent, the phenylalanine ammonia lyase (PAL) gene of the phenylpropanoid biosynthesis pathway was upregulated in wheat leaf cells while 4CL, CCR, and CYP73A were downregulated. Additionally, CYP98A and REF1 genes involved in the flavonoid biosynthesis pathway were upregulated, while F5H, HCT, CCR, E2.1.1.104, and TOGT1-related genes were downregulated.

Discussion

Differentially expressed genes may play key roles in improving salt tolerance in wheat. Compound microbial inoculants promoted the growth of wheat under salt stress and improved disease resistance by regulating the expression of metabolism-related genes in wheat roots and leaves and activating immune pathway-related genes.

De novo transcriptome assembly and metabolomic analysis of three tissue types in Cinnamomum cassia

Objective

The barks, leaves, and branches of Cinnamomum cassia have been historically used as a traditional Chinese medicine, spice, and food preservative, in which phenylpropanoids are responsible compounds. However phenylpropanoid biosynthesis pathways are not clear in C. cassia. We elucidated the pathways by descriptive analyses of differentially expressed genes related to phenylpropanoid biosynthesis as well as to identify various phenylpropanoid metabolites.

Methods

Chemical analysis, metabolome sequencing, and transcriptome sequencing were performed to investigate the molecular mechanisms underlying the difference of active components content in the barks, branches and leaves of C. cassia.

Results

Metabolomic analysis revealed that small amounts of flavonoids, coumarine, and cinnamaldehyde accumulated in both leaves and branches. Transcriptome analysis showed that genes associated with phenylpropanoid and flavonoid biosynthesis were downregulated in the leaves and branches relative to the barks. The observed differences in essential oil content among the three tissues may be attributable to the differential expression of genes involved in the phenylpropanoid and flavonoid metabolic pathways.

Conclusion

This study identified the key genes in the phenylpropanoid pathway controling the flavonoid, coumarine, and cinnamaldehyde contents in the barks, branches and leaves by comparing the transcriptome and metabolome. These findings may be valuable in assessing phenylpropanoid and flavonoid metabolites and identifying specific candidate genes that are related to the synthesis of phenylpropanoids and flavonoids in C. cassia.

Identifying the Anti-MERS-CoV and Anti-HcoV-229E Potential Drugs from the Ginkgo biloba Leaves Extract and Its Eco-Friendly Synthesis of Silver Nanoparticles

The present study aimed to estimate the antiviral activities of Ginkgo biloba (GB) leaves extract and eco-friendly free silver nanoparticles (Ag NPs) against the MERS-CoV (Middle East respiratory syndrome-coronavirus) and HCoV-229E (human coronavirus 229E), as well as isolation and identification of phytochemicals from GB. Different solvents and high-performance liquid chromatography (HPLC) were used to extract and identify flavonoids and phenolic compounds from GB leaves. The green, silver nanoparticle synthesis was synthesized from GB leaves aqueous extract and investigated for their possible effects as anti-coronaviruses MERS-CoV and HCoV-229E using MTT assay protocol. To verify the synthesis of Ag NPs, several techniques were employed, including X-ray diffraction (XRD), scan, transmission electron microscopy, FT-IR, and UV-visible spectroscopy. The highest contents of flavonoids and phenolic compounds were recorded for acetone, methanol, and ethanol as mixtures with water, in addition to pure water. HPLC flavonoids were detected as apegenin, luteolin, myricetin, and catechin, while HPLC phenolic compounds were pyrogallol, caffeic acid, gallic acid, and ellagic acid. In addition, our results revealed that Ag NPs were produced through the shift from yellow to dark brown. TEM examination of Ag NPs revealed spherical nanoparticles with mean sizes ranging from 5.46 to 19.40 nm and an average particle diameter of 11.81 nm. A UV-visible spectrophotometric investigation revealed an absorption peak at λ max of 441.56 nm. MTT protocol signified the use of GB leaves extract as an anti-coronavirus to be best from Ag NPs because GB extract had moderate anti-MERS-CoV with SI = 8.94, while had promising anti-HCov-229E, with an SI of 21.71. On the other hand, Ag NPs had a mild anti-MERS-CoV with SI = 4.23, and a moderate anti-HCoV-229E, with an SI of 7.51.

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

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

Widely targeted metabolomics analysis of different parts of kudzu

Pueraria lobata is a traditional medicinal and edible plant. Its root is often used as a nutritional supplement, but its stems and leaves are often discarded. In this study, the types and contents of compounds in roots, stems and leaves of kudzu were studied by ultra-high-performance liquid chromatography electrospray ionization tandem mass spectrometry. A total of 446 metabolites were identified, which were mainly divided into eight categories; 40 unique compounds were detected in roots. Multivariate statistical analysis showed that there were significant differences in the contents of metabolites in the roots, stems and leaves of kudzu, and the most significant differences were found in the roots and stems. Most flavonoids and terpenoids accumulated in roots, while alkaloids, flavonoid glycosides, lignans and coumarins accumulated in stems and leaves. In addition, isoflavones accumulated least in stems and most in roots. These results improved our understanding of the accumulation of metabolites in kudzu and provided a reference for the full study of the medicinal value of different parts of kudzu.

Metabolomics and Transcriptomics Provide Insights into Lipid Biosynthesis in the Embryos of Walnut (Juglans regia L.)

Walnut (Juglans regia L.) is an important woody oilseed tree species due to its commercial value. However, the regulation mechanism of walnut oil accumulation is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. In order to explore the metabolic mechanism that regulates the synthesis of walnut oil, we used transcriptome sequencing technology and metabolome technology to comprehensively analyze the key genes and metabolites involved in oil synthesis of the walnut embryo at 60, 90, and 120 days after pollination (DAP). The results showed that the oil and protein contents increased gradually during fruit development, comprising 69.61% and 18.32% of the fruit, respectively, during ripening. Conversely, the contents of soluble sugar and starch decreased gradually during fruit development, comprising 2.14% and 0.84%, respectively, during ripening. Transcriptome sequencing generated 40,631 unigenes across 9 cDNA libraries. We identified 51 and 25 candidate unigenes related to the biosynthesis of fatty acid and the biosynthesis of triacylglycerol (TAG), respectively. The expression levels of the genes encoding Acetyl-CoA carboxylase (ACCase), long-chain acyl-CoA synthetases (LACS), 3-oxoacyl-ACP synthase II (KASII), and glycerol-3-phosphate acyl transfer (GPAT) were upregulated at 60 DAP relative to the levels at 90 and 120 DAP, while the stearoyl-ACP-desaturase (SAD) and fatty acid desaturase 2 (FAD2) genes were highly abundantly expressed during all walnut developmental periods. We found that ABSCISIC ACID INSENSEITIVE3 (ABI3), WRINKLEDl (WRI1), LEAFY COTYLEDON1 (LEC1), and FUSCA3 (FUS3) may be key transcription factors involved in lipid synthesis. Additionally, the metabolomics analysis detected 706 metabolites derived from 18 samples, among which, 4 are implicated in the TAG synthesis, 2 in the glycolysis pathway, and 5 in the tricarboxylic acid cycle (TCA cycle) pathway. The combined analysis of the related genes and metabolites in TAG synthesis showed that phospholipid:diacylglycerol acyltransferase (PDAT) genes were highly abundantly expressed across walnut fruit developmental periods, and their downstream metabolite TAG gradually accumulated with the progression of fruit development. The FAD2 gene showed consistently higher expression during fruit development, and its downstream metabolites 18:2-PC and 18:3-PC gradually accumulated. The ACCase, LACS, SAD, FAD2, and PDAT genes may be crucial genes required for walnut oil synthesis. Our data will enrich public databases and provide new insights into functional genes related to lipid metabolism in walnut.

Pseudotargeted metabolomics revealed the adaptive mechanism of Draba oreades Schrenk at high altitude

Strong ultraviolet radiation and low temperature environment on Gangshika Mountain, located in the eastern part of the Qilian Mountains in Qinghai Province, can force plants to produce some special secondary metabolites for resisting severe environmental stress. However, the adaptive mechanism of Draba oreades Schrenk at high altitude are still unclear. In the current study, Draba oreades Schrenk from the Gangshika Mountain at altitudes of 3800 m, 4000 m and 4200 m were collected for comprehensive metabolic evaluation using pseudotargeted metabolomics method. Through KEGG pathway enrichment analysis, we found that phenylpropanoid biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis and phenylalanine metabolism related to the biosynthesis of flavonoids were up-regulated in the high-altitude group, which may enhance the environmental adaptability to strong ultraviolet intensity and low temperature stress in high altitude areas. By TopFc20 distribution diagram, the content of flavonoids gradually increased with the elevation of altitude, mainly including apigenin, luteolin, quercetin, hesperidin, kaempferol and their derivatives. Based on the random forest model, 10 important metabolites were identified as potential biomarkers. L-phenylalanine, L-histidine, naringenin-7-O-Rutinoside-4'-O-glucoside and apigenin related to the flavonoids biosynthesis and plant disease resistance were increased with the elevation of altitude. This study provided important insights for the adaptive mechanism of Draba oreades Schrenk at high altitude by pseudotargeted metabolomics.

Selenium Application Enhances the Accumulation of Flavones and Anthocyanins in Bread Wheat (Triticum aestivum L.) Grains

Selenium (Se) biofortification in wheat reduces the risk of Se deficiency in humans. Se biofortification increases the concentration of Se and anthocyanins in wheat grains. However, it is unknown whether Se biofortification can enhance flavonoids other than anthocyanins and the mechanism underlying flavonoid accumulation in wheat grains. Here, foliar application of selenite solution in wheat was conducted 10 days after flowering. Metabolite profiling and transcriptome sequencing were performed in Se-treated grains. A significant increase in the total contents of Se, anthocyanins, and flavonoids was observed in Se-treated mature grains. Twenty-seven significantly increased flavonoids were identified in Se-treated immature grains. The significant accumulation of flavones (tricin, tricin derivatives, and chrysoeriol derivatives) was detected, and six anthocyanins, dihydroquercetin (the precursor for anthocyanin biosynthesis) and catechins were also increased. Integrated analysis of metabolites and transcriptome revealed that Se application enhanced the biosynthesis of flavones, dihydroquercetin, anthocyanins, and catechins by increasing the expression levels of seven key structural genes in flavonoid biosynthesis (two TaF3Hs, two TaDFRs, one TaF3'5'H, one TaOMT, and one TaANR). Our findings shed new light on the molecular mechanism underlying the enhancement in flavonoid accumulation by Se supplementation and pave the way for further enhancing the nutritional value of wheat grains.

Conduction of a chemical structure-guided metabolic phenotype analysis method targeting phenylpropane pathway via LC-MS: Ginkgo biloba and soybean as examples

The phenylpropane pathway (PPP) is one of the most extensively investigated metabolic routes. This pathway biosynthesizes many important active ingredients such as phenylpropanoids and flavonoids that affect the flavor, taste and nutrients of food. How to elucidate the metabolic phenotype of PPP is fundamental in food research and development. In this study, we designed a structural periodical table filled with 103 metabolites produced from PPP. All of them especially the 62 structural isomers were qualified and quantified with high resolution and sensitivity via multiple reaction mode in liquid chromatography tandem triple quadrupole mass spectrometry. Ginkgo biloba and soybean were used as samples for the practical application of this method: The delicate spatial-temporal metabolic balance of PPP from ginkgo biloba has been first elucidated; It is first confirmed that the salt and draught stresses could redirect the biosynthesis trend of PPP to produce more isoflavones in soybean leaves.

Genetic mapping, transcriptomic sequencing and metabolic profiling indicated a glutathione S-transferase is responsible for the red-spot-petals in Gossypium arboreum

A GST for red-spot-petals in Gossypium arboreum was identified as the candidate under the scope of multi-omics approaches. Colored petal spots are correlated with insect pollination efficiency in Gossypium species. However, molecular mechanisms concerning the formation of red spots on Gossypium arboreum flowers remain elusive. In the current study, the Shixiya1-R (SxyR, with red spots) × Shixiya1-W (SxyW, without red spots) segregating population was utilized to determine that the red-spot-petal phenotype was levered by a single dominant locus. This phenotype was expectedly related to the anthocyanin metabolites, wherein the cyanidin and delphinidin derivatives constituted the major partition. Subsequently, this dominant locus was narrowed to a 3.27 Mb range on chromosome 7 by genomic resequencing from the two parents and the two segregated progeny bulks that have spotted petals or not. Furthermore, differential expressed genes generated from the two bulks at either of three sequential flower developmental stages that spanning the spot formation were intersected with the annotated ones that allocated to the 3.27 Mb interval, which returned eight genes. A glutathione S-transferase-coding gene (Gar07G08900) out of the eight was the only one that exhibited simultaneously differential expression among all three developmental stages, and it was therefore considered to be the probable candidate. Finally, functional validation upon this candidate was achieved by the appearance of scattered petal spots with inhibited expression of Gar07G08900. In conclusion, the current report identified a key gene for the red spotted petal in G. arboreum under the scope of multi-omics approaches, such efforts and embedded molecular resources would benefit future applications underlying the flower color trait in cotton.

Metabolome and Transcriptome Analysis Reveals the Transcriptional Regulatory Mechanism of Triterpenoid Saponin Biosynthesis in Soapberry (Sapindus mukorossi Gaertn.)

Soapberry (Sapindus mukorossi Gaertn.) pericarps are rich in valuable bioactive triterpenoid saponins. However, the saponin content dynamics and the molecular regulatory network of saponin biosynthesis in soapberry pericarps remain largely unclear. Here, we performed combined metabolite profiling and transcriptome analysis to identify saponin accumulation kinetic patterns, investigate gene networks, and characterize key candidate genes and transcription factors (TFs) involved in saponin biosynthesis in soapberry pericarps. A total of 54 saponins were tentatively identified, including 25 that were differentially accumulated. Furthermore, 49 genes putatively involved in sapogenin backbone biosynthesis and some candidate genes assumed to be responsible for the backbone modification, including 41 cytochrome P450s and 45 glycosyltransferases, were identified. Saponin-specific clusters/modules were identified by Mfuzz clustering and weighted gene coexpression network analysis, and one TF-gene regulatory network underlying saponin biosynthesis was proposed. The results of yeast one-hybrid assay and electrophoretic mobility shift assay suggested that SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in the triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in the soapberry pericarp. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of saponin biosynthesis, enriching the gene resources, and guiding further research on triterpenoid saponin accumulation in soapberry pericarps.

Metabolomic and Transcriptomic Profiling Uncover the Underlying Mechanism of Color Differentiation in Scutellaria baicalensis Georgi. Flowers

Scutellaria baicalensis Georgi. (Chinese skullcap or Huang-qin) is an extremely crucial medicinal plant in the Labiate family, and the color of its flowers naturally appears purple. However, during the long-term cultivation of S. baicalensis, very few plants of S. baicalensis also present white and purple-red flower colors under the same ecological conditions. However, the complex metabolic and transcriptional networks underlying color formation in white, purple-red, and purple flowers of S. baicalensis remain largely unclarified. To gain an insight into this issue, we conducted transcriptome and metabolomic profiling to elucidate the anthocyanin synthesis metabolic pathway in the flowers of S. baicalensis, and to identify the differentially expressed candidate genes potentially involved in the biosynthesis of anthocyanins. The results showed that 15 anthocyanins were identified, among which cyanidin 3-rutinoside and delphin chloride were the primary anthocyanins, and accumulation was significantly related to the flower color changes of S. baicalensis. Furthermore, the down-regulation of SbDFR (Sb02g31040) reduced the anthocyanin levels in the flowers of S. baicalensis. The differential expression of the Sb3GT (Sb07g04780 and Sb01g72290) gene in purple and purple-red flowers affected anthocyanin accumulation, suggesting that anthocyanin levels were closely associated with the expression of SbDFR and Sb3GT, which play important roles in regulating the anthocyanin biosynthesis process of S. baicalensis flowers. Transcriptomic analysis revealed that transcription factors WRKY, bHLH, and NAC were also highly correlated with anthocyanin accumulation, especially for NAC35, which positively regulated SbDFR (Sb02g31040) gene expression and modulated anthocyanin biosynthesis in flower color variation of S. baicalensis. Overall, this study presents the first experimental evidence for the metabolomic and transcriptomic profiles of S. baicalensis in response to flower coloration, which provides a foundation for dynamic metabolic engineering and plant breeding, and to understand floral evolution in S. baicalensis plants.

Metabolomics Combined with Transcriptomics Analysis Revealed the Amino Acids, Phenolic Acids, and Flavonol Derivatives Biosynthesis Network in Developing Rosa roxburghii Fruit

Rosa roxburghii Tratt. is a specific fruit with high nutritional value and antioxidative activities. However, the key metabolites and their biosynthesis are still unknown. Herein, a main cultivated variety, ‘Guinong 5’ (Rr5), was chosen to analyze the metabolomics of the three developmental stages of R. roxburghii fruit by liquid chromatography–tandem mass spectrometry (LC-MS/MS). A total of 533 metabolites were identified, of which 339 were significantly altered. Total phenols, flavonoids, and amino acids were significantly correlated to at least one in vitro antioxidant activity. The conjoint Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis of metabolome and transcriptome was focused on amino acid, phenylpropanoid, and flavonoid biosynthesis pathways. The amino acid, phenolic acid, and flavonol biosynthesis networks were constructed with 32 structural genes, 48 RrMYBs, and 23 metabolites. Of these, six RrMYBs correlated to 9–15 metabolites in the network were selected to detect the gene expression in six different R. roxburghii genotypes fruits. Subsequently, 21 key metabolites were identified in the in vitro antioxidant activities in the fruits at various developmental stages or in fruits of different R. roxburghii genotypes. We found that four key RrMYBs were related to the significantly varied amino acids, phenolic acids, and flavonol derivatives in the network during fruit development and the key metabolites in the in vitro antioxidative activities in the fruits of six R. roxburghii genotypes. This finding provided novel insights into the flavonoid, polyphenol, and amino acid synthesis in R. roxburghii.

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.

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.

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.

Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

BACKGROUND

Bletilla striata is one of the important species belonging to the Bletilla genus of Orchidaceae. Since its extracts have an astringent effect on human tissues, B. striata is widely used for hemostasis and healing. Recently, some other beneficial effects have also been uncovered, such as antioxidation, antiinflammation, antifibrotic, and immunomodulatory activities. As a key step towards a thorough understanding on the medicinal ingredient production in B. striata, deciphering the regulatory codes of the metabolic pathways becomes a major task.

RESULTS

In this study, three organs (roots, tubers and leaves) of B. striata were analyzed by integrating transcriptome sequencing and untargeted metabolic profiling data. Five different metabolic pathways, involved in polysaccharide, sterol, flavonoid, terpenoid and alkaloid biosynthesis, were investigated respectively. For each pathway, the expression patterns of the enzyme-coding genes and the accumulation levels of the metabolic intermediates were presented in an organ-specific way. Furthermore, the relationships between enzyme activities and the levels of the related metabolites were partially inferred. Within the biosynthetic pathways of polysaccharides and flavonoids, long-range phytochemical transportation was proposed for certain metabolic intermediates and/or the enzymes.

CONCLUSIONS

The data presented by this work could strengthen the molecular basis for further studies on breeding and medicinal uses of B. striata.

Integrative analysis of transcriptomic and metabolomic profiles reveal the complex molecular regulatory network of meat quality in Enshi black pigs

Improving meat quality is a crucial purpose of commercial production and breeding systems. In this study, multiomics techniques were used to investigate the molecular mechanisms that impact the excessive diversity of meat quality in Enshi black pigs. The results suggest that 120 differentially expressed genes (DEGs) and 171 significantly changed metabolites (SCMs) contribute to the content of intramuscular fat (IMF) through the processes of fat accumulation and regulation of lipolysis. A total of 141 DEGs and 47 SCMs may regulate meat color through the processes of nicotinate and nicotinamide metabolism. Herein, we found some candidate genes associated with IMF and meat color. We also presented a series of metabolites that are potentially available biological indicators to measure meat quality. This research provides further insight into the detection of intramuscular fat accumulation and meat color variation and provides a reference for molecular mechanisms in the regulation of IMF and meat color.

Third-generation sequencing and metabolome analysis reveal candidate genes and metabolites with altered levels in albino jackfruit seedlings

BACKGROUND

Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual model plants, little is known about albino trees. Jackfruit (Artocarpus heterophyllus) is an important tropical fruit tree species. To gain insight into the mechanisms underlying the differential growth and development between albino jackfruit mutants and green seedlings, we analyzed root, stem, and leaf tissues by combining PacBio single-molecule real-time (SMRT) sequencing, high-throughput RNA-sequencing (RNA-seq), and metabolomic analysis.

RESULTS

We identified 8,202 differentially expressed genes (DEGs), including 225 genes encoding transcription factors (TFs), from 82,572 full-length transcripts. We also identified 298 significantly changed metabolites (SCMs) in albino A. heterophyllus seedlings from a set of 692 metabolites in A. heterophyllus seedlings. Pathway analysis revealed that these DEGs were highly enriched in metabolic pathways such as 'photosynthesis', 'carbon fixation in photosynthetic organisms', 'glycolysis/gluconeogenesis', and 'TCA cycle'. Analysis of the metabolites revealed 76 SCMs associated with metabolic pathways in the albino mutants, including L-aspartic acid, citric acid, succinic acid, and fumaric acid. We selected 225 differentially expressed TF genes, 333 differentially expressed metabolic pathway genes, and 76 SCMs to construct two correlation networks. Analysis of the TF-DEG network suggested that basic helix-loop-helix (bHLH) and MYB-related TFs regulate the expression of genes involved in carbon fixation and energy metabolism to affect light responses or photomorphogenesis and normal growth. Further analysis of the DEG-SCM correlation network and the photosynthetic carbon fixation pathway suggested that NAD-ME2 (encoding a malic enzyme) and L-aspartic acid jointly inhibit carbon fixation in the albino mutants, resulting in reduced photosynthetic efficiency and inhibited plant growth.

CONCLUSIONS

Our preliminarily screening identified candidate genes and metabolites specifically affected in albino A. heterophyllus seedlings, laying the foundation for further study of the regulatory mechanism of carbon fixation during photosynthesis and energy metabolism. In addition, our findings elucidate the way genes and metabolites respond in albino trees.

Integrated Transcriptome and Metabolome Analysis Revealed That Flavonoid Biosynthesis May Dominate the Resistance of Zanthoxylum bungeanum against Stem Canker

Stem canker of Zanthoxylum bungeanum is a devastating disease that seriously affects the plantation and industrial development of Z. bungeanum due to a lack of effective control measures. The objective of this study was to screen out resistant Z. bungeanum varieties and further explore their resistance mechanisms against stem canker. Results showed that the most resistant and susceptible varieties were, respectively, Doujiao (DJ) and Fengxian Dahongpao (FD). Combining transcriptomic and metabolomic analyses, we found that the genes and metabolites associated with the phenylpropanoid metabolism, especially flavonoid biosynthesis, were highly significantly enriched in DJ following pathogen infection compared with that in FD, which indicated that the flavonoid metabolism may positively dominate the resistance of Z. bungeanum. This finding was further confirmed by quantitative real-time polymerase chain reaction analysis, through which higher expression levels of core genes involved in flavonoid metabolism in resistant variety were observed. Moreover, by analyzing the differences in the flavonoid content in the stems of resistant and susceptible varieties and the antifungal activities of flavonoids extracted from Z. bungeanum stems, the conclusion that flavonoid metabolism positively regulates the resistance of Z. bungeanum was further supported. Our results not only aid in better understanding the resistance mechanisms of Z. bungeanum against stem canker but also promote the breeding and utilization of resistant varieties.

Transcriptomic and metabolomic analyses provide insights into the biosynthesis of chlorogenic acids in Lonicera macranthoides Hand.-Mazz

Lonicera macranthoides Hand.-Mazz (L. macranthoides) is a medicinal herb that is widely distributed in South China. The developmental stage and corolla dehiscence of the flower are the important factors affecting the quality of medicinal ingredients. However, neither the regulatory mechanism controlling chlorogenic acids biosynthesis in L. macranthoides nor the molecular basis of effect of corolla dehiscence on the quality of medicinal materials is fully understood. In this study, metabolomics and transcriptomics were used to analyze the metabolic and transcriptional differences of two different cultivars closed bud type (Bt), and flowering type (Ft), as well as the effect of jasmonic acid methyl ester (MeJA) on chlorogenic acids (CGAs) biosynthesis. In total, large number of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were filtered among three lines of samples. Gene metabolite correlation analyses revealed a ‘core set’ of 30 genes and 54 genes that were strongly correlated with CGAs biosynthesis and regulating the flowering, respectively. Quantitative real-time polymerase chain reaction results proved the alterations in the expression levels of genes encoding the pathways involved in CGAs biosynthesis. The ion abundances of CGAs were most significantly increased, while some of the CGAs derived and Caffeoyl-CoA-derived substances showed the most largely reduced abundances in the closed bud type (Bt) compared to the flowering type (Ft). MeJA may leads to the activation of downstream genes in CGAs biosynthesis pathway. Overall, there were significant differences in the transcriptional and metabolic levels of CGAs biosynthesis pathway in flower buds of different flowering cultivars. The redirection of metabolic flux may contribute to increased accumulation of CGAs. However, whether MeJA and flowering have direct effects on the accumulation of CGAs needs further studied. These researches effectively expanded the functional genomic library and provide new insights into CGAs biosynthesis in L. macranthoides.

Multiomics Analysis Reveals New Insights into the Apple Fruit Quality Decline under High Nitrogen Conditions

Excessive application of nitrogen (N) fertilizer is common in Chinese apple production. High N reduced the contents of soluble sugar and total flavonoids by 16.05 and 19.01%, respectively, resulting in poor fruit quality. Moreover, high N increased the total N and decreased the total C and C/N ratio of apple fruits. On the basis of the transcriptomic, proteomic, and metabolomic analyses, the global network was revealed. High N inhibited the accumulation of carbohydrates (sucrose, glucose, and trehalose) and flavonoids (rhamnetin-3-O-rutinoside, rutin, and trihydroxyisoflavone-7-O-galactoside) in fruits, and more C skeletons were used to synthesize amino acids and their derivatives (especially low C/N ratio, e.g., arginine) to be transferred to N metabolism. This study revealed new insights into the decline in soluble sugar and flavonoids caused by high N, and hub genes (MD07G1172700, MD05G1222800, MD16G1227200, MD01G1174400, and MD02G1207200) and hub proteins (PFK, gapN, and HK) were obtained.

Integrating transcriptome and metabolome analyses of the response to cold stress in pumpkin (Cucurbita maxima)

Cucurbita maxima belong to the genus Cucurbita and are of nutritional and economic importance. Physiological activity, transcriptome, and metabolome analyses of leaf samples from the C. maxima inbreding line IL7 treated at 5 °C and 25 °C were performed. Cold stress resulted in a significant increase in the malondialdehyde content, relative electrical conductivity, soluble protein, sugar content, and catalase activity. A total of 5,553 differentially expressed genes were identified, of which 2,871 were up-regulated and 2,682 down-regulated. In addition, the transcription of differentially expressed genes in the plant hormone signal transduction pathway and transcription factor families of AP2/ERF, bHLH, WRKY, MYB, and HSF was activated. Moreover, 114 differentially expressed metabolites were identified by gas chromatography time-of-flight mass spectrometry, particularly through the analysis of carboxylic acids and derivatives, and organooxygen compounds. The demonstration of a series of potential metabolites and corresponding genes highlighted a comprehensive regulatory mechanism. These findings will provide novel insights into the molecular mechanisms associated with the response to cold stress in C. maxima.

Early sex determination of Ginkgo biloba based on the differences in the electrocatalytic performance of extracted peroxidase

Ginkgo biloba is a dioecious plant. Male ginkgoes are mainly used in landscaping, while females are mainly used for fruit production. However, sex identification of ginkgo is a difficult task, especially at the seedling stage. In this work, we present for the first time the use of electrochemical techniques for the identification of ginkgo sex based on the differences in peroxides within male and female ginkgos. Graphene was used to concentrate peroxides in ginkgo extract, thereby improving electrochemical signal sensitivity. The electrochemical reduction of hydrogen peroxide catalyzed by peroxidase was used as a prob for sex determination in ginkgo. This electrochemical identification technique can be used not only for the analysis of adult ginkgo, but also successfully for the analysis of tissue culture seedlings and live seedlings. This electrochemical sensor has excellent discrimination ability due to the difference in peroxidase content in the leaves and petiole of ginkgo of different sexes. This electrochemical sensor allows for a rapid identification of the sex of ginkgo and has a very strong potential for field analysis.

Joint Transcriptomic and Metabolic Analysis of Flavonoids in Cyclocarya paliurus Leaves

Flavonoids are a class of commonly occurring natural compounds in the plant kingdom with various biological activities. This study compares the content of flavonoids in Cyclocarya paliurus at different developmental stages to better inform the selection of the optimal picking period. Thus, we analyzed the transcriptome and metabolome of C. paliurus at different developmental stages. The transcriptome analysis revealed 44 genes involved in the biosynthesis of flavonoids in C. paliurus, with 10 differentially expressed genes across the four different developmental stages. The metabolites were separated and identified by a combination of chromatography and mass spectrometry, followed by multi-reaction monitoring mode analysis of triple quadrupole mass spectrometry for complete metabolite quantification. In the flavonoid synthesis pathway, a total of 137 differential flavonoids were detected. The joint transcriptome and metabolome analysis showed that the expression trends in differential metabolites and genes were significantly related. Four MYB transcription factors and two bHLH transcription factors that are closely related to flavonoid biosynthesis were identified. The regulation network of flavonoid biosynthesis in C. paliurus was thus established, providing guidance for follow-up research.

Widely targeted metabolic analysis revealed the changed pigmentation and bioactive compounds in the ripening Berchemia floribunda (Wall.) Brongn. fruit

Berchemia plants were important materials for Chinese traditional medicines due to their special secondary metabolites. Unlike the root, stem and leaf tissues, Berchemia floribunda (Wall.) Brongn. fruit was lacked of systematic metabolic investigation. Biochemical analysis found that the total flavonoid and total phenolic content of Berchemia fruit pulp showed a peak value at red ripe stage, and then decreased, but the total anthocyanin content sharply increased along with the coloration. By widely targeted metabolomic analysis, 644 metabolites were identified and categorized into 23 groups mainly including flavonoid, organic acids, amino acids, lipids, phenylpropanoid, nucleotides, alkaloids, carbohydrates, alcohols, anthocyanins & proanthocyanidins, vitamins, terpenes, polyphenols, phenolamides, quinones, indole derivatives, and sterides. Among them, 111 metabolites and 123 metabolites respectively showed up- and down-regulation from break stage to full mature. KEGG enrichment analysis indicated that active secondary metabolism such as biosynthesis of phenylpropanoids, flavonoid, and alkaloids happened during Berchemia fruit ripening. More importantly, Cyanidin-3-O-galactoside and other 3 cyanidins were found to be the predominant pigments in mature Berchemia fruit and increased cyanidins and pelargonidins but decreased anthocyanins might be contributed to the purple pigmentation of Berchemia fruit. Interestingly, 29 pharmaceutical compounds previously reported in other Berchemia tissues were also detected in ripening Berchemia fruit pulp: 8 flavonoid, 2 quinones & sucrose showed up-regulated accumulation while 6 polyphenols, 5 flavonoid, 3 phenylpropanoid, 2 organic acids, 1 quinones and β-sitosterol showed down-regulated accumulation In conclusion, our first comprehensive metabolic fingerprint will promote the further study of B. floribunda fruit and its medical and food application.

Widely Targeted Metabolomics Analysis of Different Parts of Salsola collina Pall

Salsola collina Pall has a long history of being used as a traditional medicine to treat hypertension, headache, insomnia, constipation and vertigo. However, only a few biologically active substances have been identified from S. collina. Here, the shoots and roots of S. collina, namely L-Sc and R-Sc, were studied. The primary and secondary metabolites were investigated using ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS). A total of 637 putative metabolites were identified and these metabolites were mainly classified into ten different categories. Correlation analysis, hierarchical clustering analysis, principal component analysis and orthogonal partial least squares discriminant analysis of metabolites showed that the L-Sc samples could be clearly separated from the R-Sc samples. Differential accumulated metabolite analysis revealed that most of differential primary metabolites were significantly lower in the L-Sc than in the R-Sc. Conversely, the major differential secondary metabolites had higher levels in the L-Sc than in the R-Sc. Further analysis indicated that the flavonoids were the major putative antioxidant components and most of putative antioxidant components exhibited higher relative concentrations in the L-Sc than the R-Sc. These results improve our understanding of metabolite accumulation and provide a reference for the study of medicinal value in S. collina.

Metabolomic and Transcriptomic Profiling Provide Novel Insights into Fruit Ripening and Ripening Disorder Caused by 1-MCP Treatments in Papaya

Treatment with 1-methylcyclopropylene (1-MCP) is an effective technique to preserve fruits, but inappropriate treatment with 1-MCP causes a ripening disorder (rubbery texture) in papaya fruit. In this study, a combined metabolomic and transcriptomic analysis was conducted to reveal the possible mechanism of the ripening disorder caused by unsuitable 1-MCP in papaya. A total of 203 differential accumulated metabolites (DAMs) were identified in the metabolome analysis. Only 24 DAMs were identified in the control (CK) vs. the 1-MCP 2 h group, and they were primarily flavonoids. Ninety and 89 DAMs were identified in the CK vs. 1-MCP 16 h and 1-MCP 2 h vs. 1-MCP 16 h groups, respectively, indicating that long-term 1-MCP treatment severely altered the metabolites during fruit ripening. 1-MCP 16 h treatment severely reduced the number of metabolites, which primarily consisted of flavonoids, lipids, phenolic acids, alkaloids, and organic acids. An integrated analysis of RNA-Seq and metabolomics showed that various energy metabolites for the tricarboxylic acid cycle were reduced by long-term treatment with 1-MCP, and the glycolic acid cycle was the most significantly affected, as well as the phenylpropane pathway. These results provide valuable information for fruit quality control and new insight into the ripening disorder caused by unsuitable treatment with 1-MCP in papaya.

Systematic investigation and expression profiles of the GbR2R3-MYB transcription factor family in ginkgo (Ginkgo biloba L.)

As one of the largest families of transcription factors, the R2R3-MYB family plays a significant role in plant growth, development, and response to hormone and environmental stress. To explore its evolutionary mechanism and potential function in Ginkgo biloba, a gymnosperm of great economic and ecological value, we presented a comprehensive analysis of the R2R3-MYB genes in ginkgo. Sixty-nine GbR2R3-MYB genes were identified and these genes could be classified into 33 groups based on the characteristics of the amino acid sequence of the R2R3-MYB domain and gene structure. Syntenic analyses indicated that few tandem and segmental duplications possibly resulted in the contraction of the GbR2R3-MYB gene family. Based on the transcriptome data, expression profiles of eight different tissues and different developmental stages of leaf and kernel showed that GbR2R3-MYB genes had distinct temporal and spatial expression characteristics. Specific expression patterns of the sixteen GbR2R3-MYB genes were also identified in response to different abiotic stresses and hormonal exposures. Further investigation revealed that GbR2R3-MYB19 was located in the nucleus and possessed transcriptional activity, implying its potential roles in the regulation of multiple biological processes. Our findings provide a robust basis for future comprehensive evolutionary and functional analyses of GbR2R3-MYB genes in ginkgo.

Metabolomic and Transcriptomic Analyses of Anthocyanin Biosynthesis Mechanisms in the Color Mutant Ziziphus jujuba cv. Tailihong

The purplish-red color of "Tailihong" jujube fruit skins is caused primarily by anthocyanin accumulation, but the mechanisms that underlie anthocyanin biosynthesis in jujube fruit have rarely been studied. We performed metabolomic and transcriptomic analyses of jujube fruit skins at different developmental stages and identified a total of 158 flavonoids, among which cyanidin-3-O-rutinoside and peonidin-3,5-O-diglucoside were the primary anthocyanins. During fruit development and maturation, the anthocyanin content was strongly correlated with the expression of ZjANS and ZjUGT79B1, suggesting that these are key genes in the anthocyanin biosynthesis process. Transcriptomic analysis indicated that the transcription factors ZjMYB5, ZjTT8, and ZjWDR3 regulated anthocyanin biosynthesis in jujube fruit skins. Subcellular localization experiments confirmed that ZjANS and ZjUGT79B1 were localized to the nucleus and the endoplasmic reticulum. ZjMYB5 and ZjTT8 were found only in the nucleus, whereas strong fluorescence signals from ZjWDR3 were observed in the nucleus and cytoplasm. Prokaryotic expression and in vitro enzyme activity assays showed that the recombinant ZjANS protein catalyzed the formation of cyanidin from (+)-catechin. Secondary glycosylation by ZjUFGT79B1 modified cyanidin-3-O-glucoside to produce cyanidin-3-O-rutinoside, and ZjCCoAOMT readily catalyzed the production of the methylated anthocyanin peonidin-3,5-O-diglucoside from cyanidin 3,5-O-glucoside. Dual-Luciferase and GUS activity assays showed that the ZjANS and ZjUGT79B1 promoters were activated by ZjMYB5, ZjTT8, and ZjWDR3. All data indicated that these three transcription factors played important roles in anthocyanin biosynthesis in the color mutant Ziziphus jujuba cv. Tailihong, contributing to anthocyanin accumulation by enhancing the expression of ZjANS and ZjUGT79B1.

Metabolomic and transcriptomic analyses of mutant yellow leaves provide insights into pigment synthesis and metabolism in Ginkgo biloba

BACKGROUND

Ginkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mutants remains unclear.

RESULTS

We compared the metabolomes and transcriptomes of green and mutant yellow leaves of ginkgo over the same period in this study. The results showed that the chlorophyll content of normal green leaves was significantly higher than that of mutant yellow leaves of ginkgo. We obtained 931.52M clean reads from different color leaves of ginkgo. A total of 283 substances in the metabolic profiles were finally detected, including 50 significantly differentially expressed metabolites (DEMs). We identified these DEMs and 1361 differentially expressed genes (DEGs), with 37, 4, 3 and 13 DEGs involved in the photosynthesis, chlorophyll, carotenoid, and flavonoid biosynthesis pathways, respectively. Moreover, integrative analysis of the metabolomes and transcriptomes revealed that the flavonoid pathway contained the upregulated DEM (-)-epicatechin. Fourteen DEGs from the photosynthesis pathway were positively or negatively correlated with the DEMs.

CONCLUSIONS

Our findings suggest a complex metabolic network in mutant yellow leaves. This study will provide a basis for studies of leaf color variation and regulation.

Temporospatial Flavonoids Metabolism Variation in Ginkgo biloba Leaves

Ginkgo (Ginkgo biloba L.) is a high-value medicinal tree species characterized by its flavonoids beneficial effects that are abundant in leaves. We performed a temporospatial comprehensive transcriptome and metabolome dynamics analyses of clonally propagated Ginkgo plants at four developmental stages (time: May to August) across three different environments (space) to unravel leaves flavonoids biosynthesis variation. Principal component analysis revealed clear gene expression separation across samples from different environments and leaf-developmental stages. We found that flavonoid-related metabolism was more active in the early stage of leaf development, and the content of total flavonoid glycosides and the expression of some genes in flavonoid biosynthesis pathway peaked in May. We also constructed a co-expression regulation network and identified eight GbMYBs and combining with other TF genes (3 GbERFs, 1 GbbHLH, and 1 GbTrihelix) positively regulated the expression of multiple structural genes in the flavonoid biosynthesis pathway. We found that part of these GbTFs (Gb_11316, Gb_32143, and Gb_00128) expressions was negatively correlated with mean minimum temperature and mean relative humidity, while positively correlated with sunshine duration. This study increased our understanding of the molecular mechanisms of flavonoids biosynthesis in Ginkgo leaves and provided insight into the proper production and management of Ginkgo commercial plantations.

The Wild Rice Locus CTS-12 Mediates ABA-Dependent Stomatal Opening Modulation to Limit Water Loss Under Severe Chilling Stress

A near-isogenic line (NIL) DC90 which was generated by introgressing a wild rice (Oryza rufipogon Griff.) locus CTS-12 into the 9311(Oryza sativa L. ssp. indica) background confers chilling tolerance phenotype. Here, our pilot trials showed that chilling tolerance was positively correlated with abscisic acid (ABA) biosynthesis. To understand how CTS-12 mediated the ABA-dependent multi-levels of regulation, the integration of transcriptomic and metabolomic profiling using the two-way orthogonal projections to latent structures (O2PLS) and discriminant analysis (OPLS-DA) modeling was performed to investigate the mechanisms underlying chilling tolerance. Our results revealed that metabolic shifts, including the activation of stachyose biosynthesis, amino acid metabolism pathways, phenylpropanoid/flavonoid biosynthesis, ABA biosynthesis, and perturbation of glycolysis, occurred under chilling treatment; in the recovery period, glutamate-related pathways, β-alanine biosynthesis and degradation, and serotonin biosynthesis pathways were differentiated between 9311 and DC90. Particularly, the differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs), including galactinol, β-alanine, glutamate, naringenin, serotonin, ABA, and LOC_Os03g44380 (9-cis-epoxycarotenoid dioxygenase 3, OsNCED3), might be involved in the chilling tolerance variation of 9311 and DC90. CRISPR/Cas9-edited OsNCED3 resulted in chilling sensitive of japonica rice ZH11, demonstrating the involvement of ABA pathway in chilling stress response. In addition, chilling tolerance of rice was associated with the balance of water uptake and loss that was modulated by stomatal movement under chilling stress. Therefore, we speculated that the CTS-12-mediated ABA signaling pathway leads to transcriptional regulation of chilling-responsive genes and, in turn, triggers metabolic shifts to coordinately regulate the stomatal movement of guard cells. The results of this study improve our understanding of the multilevel regulation of wild rice in response to chilling stress.

Overexpression of GbF3'5'H1 Provides a Potential to Improve the Content of Epicatechin and Gallocatechin

The flavonoids in Ginkgo biloba L. (ginkgo) have important medicinal uses due to their antioxidant, antitumor, and blood circulation-promoting effects. However, the genetic mechanisms underlying flavonoid biosynthesis in ginkgo remain elusive. Flavonoid 3′, 5′-hydroxylase (F3′5′H) is an important enzyme in flavonoid synthesis. We detected a novel differentially expressed GbF3′5′H1 gene homologous to the F3′5′H enzyme involved in the flavonoid synthesis pathway through transcriptome sequencing. In this study, we characterized this gene, performed an expression analysis, and heterologously overexpressed GbF3′5′H1 in Populus. Our results showed that GbF3′5′H1 is abundant in the leaf and highly expressed during April. We also found four metabolites closely related to flavonoid biosynthesis. Importantly, the contents of 4′,5-dihydroxy-7-glucosyloxyflavanone, epicatechin, and gallocatechin were significantly higher in transgenic plants than in nontransgenic plants. Our findings revealed that the GbF3′5′H1 gene functions in the biosynthesis of flavonoid-related metabolites, suggesting that GbF3′5′H1 represents a prime candidate for future studies (e.g., gene-editing) aiming to optimize ginkgo flavonoid production, especially that of flavan-3-ols.