Molecular Mechanisms Of Flavonoid Biosynthesis Research Articles

Integrated Untargeted Metabolome, Full-Length Sequencing and Transcriptome Analyses Reveal the Mechanism of Flavonoid Biosynthesis in Blueberry (Vaccinium spp.) Fruit.

As a highly economic berry fruit crop, blueberry is enjoyed by most people and has various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids. To obtain more accurate and comprehensive transcripts, the full-length transcriptome of half-highbush blueberry (Vaccinium corymbosum/angustifolium cultivar Northland) obtained using single molecule real-time and next-generation sequencing technologies was reported for the first time. Overall, 147,569 consensus transcripts (average length, 2738 bp; N50, 3176 bp) were obtained. After quality control steps, 63,425 high-quality isoforms were obtained and 5030 novel genes, 3002 long non-coding RNAs, 3946 transcription factor genes (TFs), 30,540 alternative splicing events, and 2285 fusion gene pairs were identified. To better explore the molecular mechanism of flavonoid biosynthesis in mature blueberry fruit, an integrative analysis of the metabolome and transcriptome was performed on the exocarp, sarcocarp, and seed. A relatively complete biosynthesis pathway map of phenylpropanoids, flavonoids, and proanthocyanins in blueberry was constructed. The results of the joint analysis showed that the 228 functional genes and 42 TFs regulated 78 differentially expressed metabolites within the biosynthesis pathway of phenylpropanoids/flavonoids. O2PLS analysis results showed that the key metabolites differentially accumulated in blueberry fruit tissues were albireodelphin, delphinidin 3,5-diglucoside, delphinidin 3-O-rutinoside, and delphinidin 3-O-sophoroside, and 10 structural genes (4 Vc4CLs, 3 VcBZ1s, 1 VcUGT75C1, 1 VcAT, and 1 VcUGAT), 4 transporter genes (1 VcGSTF and 3 VcMATEs), and 10 TFs (1 VcMYB, 2 VcbHLHs, 4 VcWD40s, and 3 VcNACs) exhibited strong correlations with 4 delphinidin glycosides. These findings provide insights into the molecular mechanisms of flavonoid biosynthesis and accumulation in blueberry fruit.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids—quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.

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

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

Full-length transcriptome analysis provides insights into flavonoid biosynthesis in Ranunculus japonicus.

Ranunculus japonicus Thunb. is a traditional Chinese herb. Plants in the genus Ranunculus are generally rich in flavonoids, which have antibacterial, anti-infective, and other pharmacological effects. However, owing to the lack of reference genomes, little is known about the flavonoid biosynthetic pathway in R. japonicus. In this study, PacBio isoform sequencing (PacBio iso-seq) and DNA nanoball sequencing (DNB-seq) were combined to build a full-length transcriptome database for three different tissues of R. japonicus. A total of 395,402 full-length transcripts were obtained, of which 308,474 were successfully annotated. A Kyoto Encyclopedia of Genes and Genomes analysis identified 29 differentially expressed genes encoding nine key enzymes for flavonoid biosynthesis. Correlation analysis indicated that flavanone 3-hydroxylase and flavonol synthase genes might have key roles in the accumulation of flavonoid substances in the different tissues of R. japonicus. The structures of chalcone synthase and chalcone isomerase enzymes were spatially modeled. Reverse-transcription quantitative PCR was used to verify gene expression levels of key enzymes associated with flavonoid biosynthesis. In addition, 22 MYB transcription factors involved in flavonoid biosynthesis and phenylpropanoid biosynthesis were discovered. The reliable transcriptomic data from this study provide genetic information about R. japonicus as well as insights into the molecular mechanism of flavonoid biosynthesis. The results also provide a basis for developing the medicinal value R. japonicus. This article is protected by copyright. All rights reserved.

Widely targeted metabolomic profiling combined with transcriptome analysis sheds light on flavonoid biosynthesis in sweet orange 'Newhall' (C. sinensis) under magnesium stress.

Sweet orange 'Newhall' peels (SOPs) are abundant in flavonoids, making them increasingly popular in the realms of nutrition, food, and medicine. However, there is still much unknown about flavonoid components in SOPs and the molecular mechanism of flavonoid biosynthesis when subjected to magnesium stress. The previous experiment conducted by the research group found that the total flavonoid content of Magnesium deficiency (MD) was higher than Magnesium sufficiency (MS) in SOPs. In order to study the metabolic pathway of flavonoids under magnesium stress, an integrative analysis of the metabolome and transcriptome was performed in SOPs at different developmental stages, comparing MS and MD. A comprehensive analysis revealed the identification of 1,533 secondary metabolites in SOPs. Among them, 740 flavonoids were classified into eight categories, with flavones identified as the dominant flavonoid component. The influence of magnesium stress on flavonoid composition was evaluated using a combination of heat map and volcanic map, which indicated significant variations between MS and MD varieties at different growth stages. The transcriptome detected 17,897 differential genes that were significantly enriched in flavonoid pathways. Further analysis was performed using Weighted gene correlation network analysis (WGCNA) in conjunction with flavonoid metabolism profiling and transcriptome analysis to identify six hub structural genes and ten hub transcription factor genes that play a crucial role in regulating flavonoid biosynthesis from yellow and blue modules. The correlation heatmap and Canonical Correspondence Analysis (CCA) results showed that CitCHS had a significant impact on the synthesis of flavones and other flavonoids in SOPs, as it was the backbone gene in the flavonoid biosynthesis pathway. The qPCR results further validated the accuracy of transcriptome data and the reliability of candidate genes. Overall, these results shed light on the composition of flavonoid compounds in SOPs and highlight the changes in flavonoid metabolism that occur under magnesium stress. This research provides valuable insights for improving the cultivation of high-flavonoid plants and enhancing our understanding of the molecular mechanisms underlying flavonoid biosynthesis.

Transcriptome-wide expression analysis of MYB gene family leads to functional characterization of flavonoid biosynthesis in fruit coloration of Ziziphus Mill.

The Ziziphus mauritiana Lam. and Z. jujuba Mill. are the two most economically important members of the genus Ziziphus. The fruit color of Z. mauritiana remains green throughout fruit development in the majority of commercial cultivars, whereas its close relative, Z. jujuba Mill. turns from green to red in all cultivars. However, the lack of transcriptomic and genomic information confines our understanding of the molecular mechanisms underlying fruit coloration in Z. mauritiana (Ber). In the present study, we performed the transcriptome-wide analysis of MYB transcription factors (TFs) genes in Z. mauritiana and Z. jujuba, and identified 56 ZmMYB and 60 ZjMYB TFs in Z. mauritiana and Z. jujuba, respectively. Through transcriptomic expression analysis, four similar MYB genes (ZmMYB/ZjMYB13, ZmMYB/ZjMYB44, ZmMYB/ZjMYB50, and ZmMYB/ZjMYB56) from Z. mauritiana and Z. jujuba were selected as candidate key genes regulating flavonoid biosynthesis. Among these genes, the ZjMYB44 gene was transiently highly expressed in fruit, and flavonoid content accumulation also increased, indicating that this gene can influence flavonoid content during the period of fruit coloration in Z. jujuba. The current study adds to our understanding of the classification of genes, motif structure, and predicted functions of the MYB TFs, as well as identifying MYBs that regulate flavonoid biosynthesis in Ziziphus (Z. mauritiana and Z. jujuba). Based on this information, we concluded that MYB44 is involved in the flavonoids biosynthesis pathway during the fruit coloring of Ziziphus. Our research results provide an important understanding of the molecular mechanism of flavonoid biosynthesis resulting in fruit coloration and laying a foundation for further genetic improvement of fruit color in Ziziphus.

GbFLSa overexpression negatively regulates proanthocyanin biosynthesis.

Flavonoids are important secondary metabolites with extensive pharmacological functions. Ginkgo biloba L. (ginkgo) has attracted extensive attention because of its high flavonoid medicinal value. However, little is understood about ginkgo flavonol biosynthesis. Herein, we cloned the full-length gingko GbFLSa gene (1314 bp), which encodes a 363 amino acid protein that has a typical 2-oxoglutarate (2OG)-Fe(II) oxygenase region. Recombinant GbFLSa protein with a molecular mass of 41 kDa was expressed in Escherichia coli BL21(DE3). The protein was localized to the cytoplasm. Moreover, proanthocyanins, including catechin, epicatechin, epigallocatechin and gallocatechin, were significantly less abundant in transgenic poplar than in nontransgenic (CK) plants. In addition, dihydroflavonol 4-reductase, anthocyanidin synthase and leucoanthocyanidin reductase expression levels were significantly lower than those of their CK counterparts. GbFLSa thus encodes a functional protein that might negatively regulate proanthocyanin biosynthesis. This study helps elucidate the role of GbFLSa in plant metabolism and the potential molecular mechanism of flavonoid biosynthesis.

Integrative transcriptomic and metabolomic analyses reveal the flavonoid biosynthesis of Pyrus hopeiensis flowers under cold stress

Low temperature is among the most restrictive factors to limit the yield and distribution of pear. Pyrus hopeiensis is a valuable wild resource. PCA showed that P. hopeiensis had strong cold resistance. In this study, the mRNA and metabolome sequencing of P. hopeiensis flower organs exposed to different low temperatures were performed to identify changes of genes and metabolites in response to low-temperature stress. A total of 4 851 differentially expressed genes (DEGs) were identified. Trend analysis showed that these DEGs were significantly enriched in profiles 19, 18, 7, 14, 1, 4 and 11. And the KEGG enrichment analysis showed that the DEGs in profile 18 were significantly enriched in flavone and flavonol biosynthesis. Besides, the expressed trends as well as GO and KEGG functional enrichment analyses of DEGs under cold and freezing stress showed significantly difference. Analyses of flavonoid-related pathways indicated that flavonoid structural genes had undergone significant changes. Correlation analysis showed that bHLH and MYB TFs may affect flavonoid biosynthesis by regulating structural gene expression. And PhMYB308 and PhMYB330 were likely candidate repressors of flavonoid biosynthesis by binding to a specific site in bHLH proteins. In total, 92 differentially accumulated metabolites (DAMs) were identified in P. hopeiensis flowers including 12 flavonoids. WGCNA results showed that coral 1, pink and brown 4 modules were closely associated with flavonoids and 11 MYBs and 15 bHLHs among the three modules may activate or inhibit the expression of 23 structural genes of flavonoid biosynthesis. Taken together, the results of this study provided a theoretical basis for further exploration of the molecular mechanisms of flavonoid biosynthesis and cold resistance of P. hopeiensis flower organs and our findings laid a foundation for further molecular breeding in cold-resistant pear varieties.

Dynamic metabolic and transcriptomic profiling reveal synthetic characters and regulators of flavonoid biosynthesis in Camellia oleifera seeds

Flavonoids are natural bioactive substances with beneficial health effects against chronic diseases. Camellia oleifera Abel. ( C. oleifera ) has attracted attention because its seeds contain high levels of unsaturated fatty acids . Actually, flavonoids are also abundant in the C. oleifera seeds. However, the composition and distribution of flavonoid and overall molecular mechanism of flavonoid biosynthesis in the C. oleifera seeds have not been fully uncovered. To this end, metabolome , transcriptome , high-performance liquid chromatography, microscopic, and exogenous methyl jasmonate treatment analyses of C. oleifera seeds at different developmental stages were performed. Results revealed that the differential metabolites and genes were enriched in the flavonoid biosynthesis pathways in C. oleifera seeds. Flavonoid profiles presented dynamic patterns that changed with seed development, consistent with the pattern of gene regulation in the corresponding pathways. In total, 52 differentially accumulated flavonoids and 124 differentially expressed structural genes involved in flavonoid biosynthesis were identified. After weighted gene co-expression network analysis, three modules were highly interrelated with the accumulation of flavonoid components. The co-expression networks of these three modules were used to identify key candidate transcription factors associated with flavonoid biosynthesis, such as MYC2 , bHLH3 , bHLH18 , MYB44 , MYB86 , WRKY26 , and WRKY32 . Based on these differentially accumulated flavonoids and key genes, the genetic and metabolic regulatory networks of flavonoid biosynthesis was proposed. Moreover, exogenous methyl jasmonate influenced the accumulation of diverse flavonoids in C . oleifera seeds. Potential regulatory factors identified in this study will contribute to the provision of molecular traces for in-depth research on flavonoid biosynthesis and product development for C. oleifera with higher value. • In total, 148 flavonoids were identified in Camellia oleifera seeds. • Differentially expressed genes were enriched in the flavonoid biosynthesis pathways. • Seven key transcription factors related to flavonoid biosynthesis were screened. • A model was proposed in which flavonoid biosynthesis is induced by methyl jasmonate.

Integrative Analysis of the Metabolome and Transcriptome Provides Insights into the Mechanisms of Flavonoid Biosynthesis in Quinoa Seeds at Different Developmental Stages.

Quinoa (Chenopodium quinoa Willd.) is a crop with high nutritional and health benefits. Quinoa seeds are rich in flavonoid compounds; however, the mechanisms behind quinoa flavonoid biosynthesis remain unclear. We independently selected the high-generation quinoa strain ‘Dianli-3260′, and used its seeds at the filling, milk ripening, wax ripening, and mature stages for extensive targeted metabolome analysis combined with joint transcriptome analysis. The results showed that the molecular mechanism of flavonoid biosynthesis in quinoa seeds was mainly concentrated in two pathways: “flavonoid biosynthesis pathway” and “flavone and flavonol biosynthesis pathway”. Totally, 154 flavonoid-related metabolites, mainly flavones and flavonols, were detected in the four development stages. Moreover, 39,738 genes were annotated with KEGG functions, and most structural genes of flavonoid biosynthesis were differentially expressed during grain development. We analyzed the differential flavonoid metabolites and transcriptome changes between the four development stages of quinoa seeds and found that 11 differential flavonoid metabolites and 22 differential genes were the key factors for the difference in flavonoid biosynthesis. This study provides important information on the mechanisms underlying quinoa flavonoid biosynthesis, the screening of potential quinoa flavonoid biosynthesis regulation target genes, and the development of quinoa products.

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

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

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.

Integrative analysis of the metabolome and transcriptome provides novel insights into the mechanisms of flavonoid biosynthesis in Camellia lanceoleosa

Flavonoids, the effective material basis for the anti-thrombotic, anti-myocardial ischemia, and anti-dementia drug system framework, are one class of the main bioactive compounds in tea-oil Camellia. However, the molecular mechanism of the transcription regulation of flavonoid biosynthesis in tea-oil Camellia has not been fully investigated. Camellia lanceoleosa (C. lanceoleosa) is a diploid species of section Oleifera with genomic information, which has high value in scientific research and application. To comprehend the molecular mechanism of flavonoid biosynthesis in C. lanceoleosa, five different tissues (roots, stems, leaves, flower buds, and seeds) were used to perform an integrated analysis of the metabolome and transcriptome. Overall, 1,437 metabolites were identified and quantified, among which 488 common metabolites and 92 tissue-specific metabolites were detected in different tissues of C. lanceoleosa. Notably, the most abundant metabolite class was the flavonoids in the detected tissues of C. lanceoleosa. Furthermore, the differential metabolites and genes were also mainly enriched in flavonoid biosynthesis. A total of 145 differentially accumulated flavonoids and 65 differentially expressed structural genes were found within the biosynthesis of flavonoid in C. lanceoleosa. The expression patterns of most genes were consistent with the flavonoid accumulation patterns in the corresponding pathways. Using weighted gene coexpression network analysis, five gene modules and several candidate hub genes involved in flavonoid biosynthesis were investigated in different tissues of C. lanceoleosa, these genes included differentially expressed structural genes (PAL, CHS, DFR, and ANR) and transcription factors (bHLHs, MYBs, WRKYs, NACs, and SPL6). These results provide useful genetic resources for studying the molecular insights into the regulatory network of flavonoid biosynthesis in C. lanceoleos.

Comparative Transcriptome Analysis Reveals Differential Regulation of Flavonoids Biosynthesis Between Kernels of Two Pecan Cultivars.

Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high (“YLC28”) and a low (“Oconee”) flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in “YLC28” were 1.76- and 2.67-fold higher levels than that of “Oconee” on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in “YLC28” were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3’,5’-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in “YLC28.” A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in blackberry

Blackberry fruit is rich in anthocyanins, showing incomparable nutritional and health value. Anthocyanins are flavonoids that are downstream products of the flavonoid biosynthesis pathway. They are important secondary metabolites with antioxidant and anticancer functions. Therefore, we performed combined transcriptome and metabolome analyses of unripe and ripe blackberry fruits to identify the molecular mechanisms of flavonoid biosynthesis. Herein, we identified 997 differentially expressed metabolites (DEMs) in positive-ion mode, 411 DEMs in negative-ion mode, and 17,566 differentially expressed genes (DEGs). Eight DEMs and 16 DEGs were annotated to the flavonoid biosynthesis pathway. Four DEGs related to flavonoids (unigene 0028088, unigene 0039337, unigene 0063209, and unigene 0014842) were positively correlated with related flavonoid DEMs. Interestingly, 8 DEGs and 11 flavonoid-related DEMs showed significant negative correlations. This study lays a foundation for further research on the biosynthesis and metabolism of flavonoid, providing a reference for the future breeding and cultivation of excellent high-flavonoid germplasm resources and the blackberry-related pharmaceutical industry.

Flavonoid biosynthesis in four Dendrobium species based on transcriptome sequencing and metabolite analysis.

Dendrobium is a genus of plants used as traditional Chinese herbal medicines, with high economic and medicinal value. To reveal the mechanism of flavonoid biosynthesis in Dendrobium, the metabolites and transcriptomes of four Dendrobium species (D. chrysotoxum, D. nobile, D. fimbriatum, and D. denneanum) were analyzed comprehensively. Ultra-high-performance liquid chromatography-tandem mass spectrometry analysis revealed ten flavonoid compounds in Dendrobium. In total, 100,096 unigenes were obtained from the transcript database of the four Dendrobium species. Among the identified differentially expressed genes, 51 were associated with flavonoid biosynthesis, and 670 differentially expressed transcription factors were predicted, including 194 MYB, 87 bHLH, and 100 WRKY family transcription factors, respectively. Transcriptome analysis showed that the expression levels of structural genes such as chalcone synthase (CHS), cinnamate-4-hydroxylase (C4H), and flavonoid 3'-hydroxylase (F3'H) were lower in D. chrysotoxum, D. nobile, and D. fimbriatum than those in D. denneanum, which may be the main reason for the low flavonoid contents in D. chrysotoxum, D. nobile, and D. fimbriatum. The expression level of structural genes corresponded to the accumulation level of flavonols in the different Dendrobium species. The results deepen the understanding of the molecular mechanism of flavonoid biosynthesis in Dendrobium and provide novel insights into the synthesis and accumulation of flavonoids in Dendrobium.

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

BackgroundAlpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant.ResultsIn all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves.ConclusionThe DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.

Metabolic and transcriptomic analyses reveal different metabolite biosynthesis profiles between leaf buds and mature leaves in Ziziphus jujuba mill

Jujube leaf is well known for its high nutritional value and medicinal benefits. However, a thorough and dynamic assessment of the metabolites present in jujube leaves is lacking. Here, the primary and secondary metabolites from purple leaf buds and green mature leaves were investigated using ultra-high-performance liquid chromatography/tandem mass spectrometry. A total of 778 metabolites were characterized and more than 700 compounds were reported for the first time. Analysis of differentially accumulated metabolites showed that the flavonoids were the major differential metabolites and determined the leaf coloration. The transcriptome data indicated that 20 flavonoid structural genes and three main types of flavonoid regulatory genes were significantly differentially expressed. Moreover, light had a significant influence on flavonoid accumulation. These results improve our understanding of metabolite accumulation and the molecular mechanisms of flavonoid biosynthesis in jujube leaf.

Comparative transcriptome profiling reveals differentially expressed genes involved in flavonoid biosynthesis between biennial and triennial Sophora flavescens

Flavonoids are a primary bioactive component of Sophora flavescens, which is widely used in traditional Chinese medicine. Understanding flavonoid biosynthesis is of great importance for improving the production of active compounds. In this study, both the total flavonoid content and the contents of six main flavonoid (namely, genistin, trifolirhizin, maackiain, kushenol I, kurarinone, and nor-kurarinone) were significantly higher in triennial S. flavescens than in biennial plants, and the flavonoid content of lateral roots was higher than that of taproots. We attempted to generate exhaustive molecular information on the flavonoid secondary metabolite pathway and to increase the genomic resources for S. flavescens. De novo transcriptome data provided 643,251 unigenes, and 365,572 (56.83 %) were successfully annotated in five public protein databases. The gene expression profiles of taproots and lateral roots clustered with each other and were separated by the cultivation period; the other expression profiles were clustered according to tissue pattern. The differentially expressed unigenes (DEGs) in the lateral roots, taproots and stems between biennial and triennial S. flavescens were identified and subjected to functional annotation enrichment. A total of 92 unigenes encoding well-known enzymes involved in flavonoid biosynthesis were found to show differential expression between biennial and triennial S. flavescens. Furthermore, the comparative expression results of eight unigenes were validated by real-time quantitative PCR (qRT-PCR). The most abundant transcription factors (TFs) that were differentially expressed in S. flavescens were those belonging to the bHLH-, NAC-, ERF- and MYB-related families, and these TFs were identified regardless of the tissue or cultivation period. Our study provides important resources of gene sequences and expression and insights into the molecular mechanism of flavonoid biosynthesis during S. flavescens cultivation.

Integrated metabolomic and transcriptomic strategies to understand the effects of dark stress on tea callus flavonoid biosynthesis

Flavonoid biosynthesis is a crucial secondary metabolism process for tea plants. Its metabolism is affected by multiple environmental factors, especially light. Shade, also known as dark stress (DS), is generally used during cultivation to improve tea quality by influencing the flavonoid accumulation. To explore the molecular mechanisms of flavonoid biosynthesis under DS, metabolomics and transcriptomics (METR) analyses were performed in tea callus via culturing the plants in vitro using 12 h light/12 h dark cycles (A) or completely dark (B) conditions for 30 days. In total, 161 differential metabolic products (DMPs) and 3592 differential expression genes (DEGs) were identified. The major flavonoids including epicatechin gallate, catechin gallate, gallocatechin-catechin, cyanidin 3-O-glucoside and the total of catechin, anthocyanin and proanthocyanidin contents were all remarkably down-regulated in tea callus under DS. Meanwhile, 9 genes including CsPAL, Cs4CL, CsCHS, CsFLS, CsDFR, CsANS, CsLAR, CsANR, and CsUFGT determined to be responsible for the flavonoid biosynthesis. In addition, 2 transcription factors (TFs) including CsMYBT1 and CsMYBT2 verified to play key role in regulation the flavonoid biosynthesis. These results helped us further understand the underlying molecular mechanism of flavonoid metabolism in tea plants.