Molecular analysis of a UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) gene from purple potato (Solanum tuberosum)

Characterization of key genes in anthocyanin and flavonoid biosynthesis during floral development in Rosa canina L

This study investigates the transition of Rosa canina L. petals from pink to white, driven by genetic and biochemical factors. It characterizes the expression of ten key genes involved in anthocyanin and flavonoid biosynthesis across five developmental stages, correlating gene expression with flavonoid and anthocyanin concentrations and colorimetric changes. Initially, the petals exhibit a rich flavonoid profile, dominated by Rutin and Kaempferol derivatives. The peak anthocyanin concentration, corresponding to the deepest color saturation, occurs in the subsequent stage. Advanced chromatographic analyses identify key flavonoids persisting into the final white petal stage. Notably, the ANS gene shows a dramatic 137.82-fold increase in expression at the final stage, indicating its crucial role in petal color maturation despite the absence of visible pigmentation. The study provides a comprehensive characterization of the genetic and biochemical mechanisms underlying petal pigmentation, suggesting that reduced anthocyanin synthesis and increased flavonol concentration led to white petals. It also highlights the roles of other genes such as PAL, CCD1, FLS, CHI, CHS, UFGT, F3H, DFR, and RhMYB1, indicating that post-translational modifications and other regulatory mechanisms may influence anthocyanin stability and degradation.

The PpMYB75-PpDFR module reveals the difference between 'SR' and its bud variant 'RMHC' in peach red flesh

'Red Meat Honey Crisp (RMHC)' has been widely cultivated by growers in recent years due to its early maturity, and red meat type characteristics. As a bud variant of 'Super Red (SR)' peach, red flesh is the most distinctive characteristic of 'Red Meat Honey Crisp (RMHC)'. However, the mechanism of red flesh formation in 'RMHC' remains unclear. In this study, 79 differentially produced metabolites were identified by metabolomics analysis. The anthocyanin content in 'RMHC' was significantly higher than that in 'SR' during the same period, such as cyanidin O-syringic acid and cyanidin 3-O-glucoside. Other flavonoids also increased during the formation of red flesh, including flavonols (6-hydroxykaempferol-7-O-glucoside, hyperin), flavanols (protocatechuic acid, (+)-gallocatechin), and flavonoids (chrysoeriol 5-O-hexoside, tricetin). In addition, transcriptomic analysis and RT-qPCR showed that the expression levels of the flavonoid synthesis pathway transcription factor MYB75 and some structural genes, such as PpDFR, PpCHS, PpC4H, and PpLDOX increased significantly in 'RMHC'. Subcellular localization analysis revealed that MYB75 was localized to the nucleus. Yeast single hybridization assays showed that MYB75 bound to the cis-acting element CCGTTG of the PpDFR promoter region. The MYB75-PpDFR regulatory network was identified to be a key pathway in the reddening of 'RMHC' flesh. Moreover, this is the first study to describe the cause for red meat reddening in 'RMHC' compared to 'SR' peaches using transcriptomics, metabolomics and molecular methods. Our study identified a key transcription factor involved in the regulation of the flavonoid synthetic pathway and contributes to peach breeding-related efforts as well as the identification of genes involved in color formation in other species.

Regulatory network characterization of anthocyanin metabolites in purple sweetpotato via joint transcriptomics and metabolomics

INTRODUCTION

Sweet potato is an important staple food crop in the world and contains abundant secondary metabolites in its underground tuberous roots. The large accumulation of several categories of secondary metabolites result in colorful pigmentation of the roots. Anthocyanin, is a typical flavonoid compound present in purple sweet potatoes and it contributes to the antioxidant activity.

METHODS

In this study, we developed joint omics research via by combing the transcriptomic and metabolomic analysis to explore the molecular mechanisms underlying the anthocyanin biosynthesis in purple sweet potato. Four experimental materials with different pigmentation phenotypes, 1143-1 (white root flesh), HS (orange root flesh), Dianziganshu No.88 (DZ88, purple root flesh), and Dianziganshu No.54 (DZ54, dark purple root flesh) were comparably studied.

RESULTS AND DISCUSSION

We identified 38 differentially accumulated pigment metabolites and 1214 differentially expressed genes from a total of 418 metabolites and 50893 genes detected. There were 14 kinds of anthocyanin detected in DZ88 and DZ54, with glycosylated cyanidin and peonidin as the major components. The significantly enhanced expression levels of multiple structural genes involved in the central anthocyanin metabolic network, such as chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase/leucocyanidin oxygenase (ANS), and glutathione S-transferase (GST) were manifested to be the primary reason why the purple sweet potatoes had a much higher accumulation of anthocyanin. Moreover, the competition or redistribution of the intermediate substrates (i.e. dihydrokaempferol and dihydroquercetin) between the downstream production of anthocyanin products and the flavonoid derivatization (i.e. quercetin and kaempferol) under the regulation of the flavonol synthesis (FLS) gene, might play a crucial role in the metabolite flux repartitioning, which further led to the discrepant pigmentary performances in the purple and non-purple materials. Furthermore, the substantial production of chlorogenic acid, another prominent high-value antioxidant, in DZ88 and DZ54 seemed to be an interrelated but independent pathway differentiated from the anthocyanin biosynthesis. Collectively, these data from the transcriptomic and metabolomic analysis of four kinds of sweet potatoes provide insight to understand the molecular mechanisms of the coloring mechanism in purple sweet potatoes.

Uncovering anthocyanin diversity in potato landraces (Solanum tuberosum L. Phureja) using RNA-seq

Potato (Solanum tuberosum L.) is the third largest source of antioxidants in the human diet, after maize and tomato. Potato landraces have particularly diverse contents of antioxidant compounds such as anthocyanins. We used this diversity to study the evolutionary and genetic basis of anthocyanin pigmentation. Specifically, we analyzed the transcriptomes and anthocyanin content of tubers from 37 landraces with different colorations. We conducted analyses of differential expression between potatoes with different colorations and used weighted correlation network analysis to identify genes whose expression is correlated to anthocyanin content across landraces. A very significant fraction of the genes identified in these two analyses had annotations related to the flavonoid-anthocyanin biosynthetic pathway, including 18 enzymes and 5 transcription factors. Importantly, the causal genes at the D, P and R loci governing anthocyanin accumulation in potato cultivars also showed correlations to anthocyanin production in the landraces studied here. Furthermore, we found that 60% of the genes identified in our study were located within anthocyanin QTLs. Finally, we identified new candidate enzymes and transcription factors that could have driven the diversification of anthocyanins. Our results indicate that many anthocyanins biosynthetic genes were manipulated in ancestral potato breeding and can be used in future breeding programs.

Comparative proteomics reveals biochemical changes in Salvia miltiorrhiza Bunge during sweating processing

ETHNOPHARMACOLOGICAL RELEVANCE

Salvia miltiorrhiza Bunge is a bulk medicinal material used in traditional Chinese medicine, that can cure cardiovascular diseases, neurasthenia, and other conditions. Sweating is a frequently used method of processing S. miltiorrhiza for medical applications. We previously demonstrated changes to the metabolic profile of linoleic acid, glyoxylate, and dicarboxylate after Sweating. However, this alteration has not been explained at the molecular level.

MATERIALS AND METHODS

Fresh roots of Salvia miltiorrhiza Bunge were treated by the Sweating processing, and then the tandem mass tag technique was used to compare the proteome difference between Sweating S. miltiorrhiza and non-Sweating S. miltiorrhiza.

RESULTS

We identified a total of 850 differentially expressed proteins after Sweating treatment in S. miltiorrhiza, including 529 upregulated proteins and 321 downregulated proteins. GO enrichment analysis indicated that these differentially expressed proteins are involved in external encapsulating structure, cell wall, oxidoreductase activity, ligase activity, and others. Further analysis showed that CYP450, the pathogenesis-related protein Bet v 1 family, and the peroxidase domain were the major protein domains. KEGG enrichment identified 18 pathways, of which phenylpropanoid biosynthesis is the most important one related to the metabolite profile and is the principal chemical component of S. miltiorrhiza.

CONCLUSION

This study addressed potential molecular mechanisms in S. miltiorrhiza after Sweating, and the findings provide reasons for the changes in biochemical properties and metabolites changes which might cause pharmacological variation at the proteome level.

Combination analysis of single-molecule long-read and Illumina sequencing provides insights into the anthocyanin accumulation mechanism in an ornamental grass, Pennisetum setaceum cv. Rubrum

Combination analysis of single-molecule long-read and Illumina sequencing provide full-length transcriptome information and shed new light on the anthocyanin accumulation mechanism of Pennisetum setaceum cv. 'Rubrum'. Pennisetum setaceum cv. 'Rubrum' is an ornamental grass with purple leaves widely used in landscaping. However, the current next-generation sequencing (NGS) transcriptome information of this species is not satisfactory due to the difficulties in obtaining full-length transcripts. Furthermore, the molecular mechanisms of anthocyanin accumulation in P. setaceum have not been thoroughly studied. In this study, we used PacBio full-length transcriptome sequencing (SMRT) combined with NGS technology to build and improve the transcriptomic datasets and reveal the molecular mechanism of anthocyanin accumulation in P. setaceum cv. 'Rubrum'. Therefore, 280,413 full-length non-chimeric reads sequences were obtained using the SMRT technology. We obtained 97,450 high-quality non-redundant transcripts and identified 5352 alternative splicing events. In addition, 93,066 open reading frames (ORFs), including 57,457 full ORFs and 2910 long non-coding RNA (lncRNAs) were screened out. Furthermore, 10,795 differentially expressed genes were identified using NGS. We also explored key genes, synthesis pathways, and detected lncRNA involved in anthocyanin accumulation, providing new insights into anthocyanin accumulation in P. setaceum cv. 'Rubrum'. To our best knowledge, we provided the full-length transcriptome information of P. setaceum cv. 'Rubrum' for the first time. The results of this study will provide baseline information for gene function studies and pave the way for future P. setaceum cv. 'Rubrum' breeding projects.

Metabolomic and Transcriptomic Analyses of the Flavonoid Biosynthetic Pathway for the Accumulation of Anthocyanins and Other Flavonoids in Sweetpotato Root Skin and Leaf Vein Base

Sweetpotato [Ipomoea batatas (L.) Lam.] is a major tuberous root crop that is rich in flavonoids. Here, we discovered a spontaneous mutation in the color of the leaf vein base (LVB) and root skin (RS) in the Zheshu 81 cultivar. The flavonoid and anthocyanin metabolites and molecular mechanism were analyzed using metabolome and transcriptome data. Compared to the wild type, 13 differentially accumulated metabolites (DAMs) in the LVB and 59 DAMs in the RS were all significantly downregulated. Moreover, all the anthocyanin metabolites decreased significantly. The differentially expressed genes (DEGs) encoding the key enzymes in the later enzymatic reaction of anthocyanin and flavonoid were significantly downregulated in the mutant. The expression trends of the transcription factor MYB were evidently related to the anthocyanin content. These results offer insights into the coloration in the LVB and RS and a theoretical basis for determining the regulation of flavonoid and anthocyanin synthesis in sweetpotato.

Identification of key gene networks controlling anthocyanin biosynthesis in peach flower

Flavonoids, particularly anthocyanin is the main pigment that determined the red color of peach flowers, and help the plant to attract pollinators, protect the reproductive organs of flower from photo-oxidative effects of light and various non-communicable diseases. Through weightage gene coexpression network analysis (WGCNA) we identified a network of 15 hub genes that co-expressed throughout peach flower development including 5 genes coded for the key enzymes (CHI, F3'H, DFR, LAR and UFGT) of flavonoid biosynthetic pathway and 1 gene Prupe.1G111700 identified as R2R3 family transcription factor MYB108. Over expression of PpMYB108 significantly increased anthocyanin biosynthesis in Tobacco flowers. Moreover, the expression correlation between PpMYB108 and PpDFR, suggests that PpMYB108 play the role of transcriptional activator for PpDFR. This was further supported by a 6 bp insertion of MYB biding site in the core promoter region of PpDFR in red flower. The positive interaction of PpMYB108 with PpDFR promoter from red flower was confirmed in yeast one hybrid assay. These findings may be helpful in peach breeding programs as well as in identifying anthocyanin related genes in other species.

Modifying Anthocyanins Biosynthesis in Tomato Hairy Roots: A Test Bed for Plant Resistance to Ionizing Radiation and Antioxidant Properties in Space

Gene expression manipulation of specific metabolic pathways can be used to obtain bioaccumulation of valuable molecules and desired quality traits in plants. A single-gene approach to impact different traits would be greatly desirable in agrospace applications, where several aspects of plant physiology can be affected, influencing growth. In this work, MicroTom hairy root cultures expressing a MYB-like transcription factor that regulates the biosynthesis of anthocyanins in Petunia hybrida (PhAN4), were considered as a testbed for bio-fortified tomato whole plants aimed at agrospace applications. Ectopic expression of PhAN4 promoted biosynthesis of anthocyanins, allowing to profile 5 major derivatives of delphinidin and petunidin together with pelargonidin and malvidin-based anthocyanins, unusual in tomato. Consistent with PhAN4 features, transcriptomic profiling indicated upregulation of genes correlated to anthocyanin biosynthesis. Interestingly, a transcriptome reprogramming oriented to positive regulation of cell response to biotic, abiotic, and redox stimuli was evidenced. PhAN4 hairy root cultures showed the significant capability to counteract reactive oxygen species (ROS) accumulation and protein misfolding upon high-dose gamma irradiation, which is among the most potent pro-oxidant stress that can be encountered in space. These results may have significance in the engineering of whole tomato plants that can benefit space agriculture.

Chitosan Coating Enriched With Ruta graveolens L. Essential Oil Reduces Postharvest Anthracnose of Papaya (Carica papaya L.) and Modulates Defense-Related Gene Expression

Anthracnose of papaya (Carica papaya L.) caused by the fungus Colletotrichum spp. is one of the most economically important postharvest diseases. Coating with chitosan (CS) and Ruta graveolens essential oil (REO) might represent a novel eco-friendly method to prevent postharvest anthracnose infection. These compounds show both antimicrobial and eliciting activities, although the molecular mechanisms in papaya have not been investigated to date. In this study, the effectiveness of CS and REO alone and combined (CS-REO) on postharvest anthracnose of papaya fruit during storage were investigated, along with the expression of selected genes involved in plant defense mechanisms. Anthracnose incidence was reduced with CS, REO, and CS-REO emulsions after 9 days storage at 25°C, by 8, 21, and 37%, respectively, with disease severity reduced by 22, 29, and 44%, respectively. Thus, McKinney's decay index was reduced by 22, 30, and 44%, respectively. A protocol based on reverse transcription quantitative real-time PCR (RT-qPCR) was validated for 17 papaya target genes linked to signaling pathways that regulate plant defense, pathogenesis-related protein, cell wall-degrading enzymes, oxidative stress, abiotic stress, and the phenylpropanoid pathway. CS induced gene upregulation mainly at 6 h posttreatment (hpt) and 48 hpt, while REO induced the highest upregulation at 0.5 hpt, which then decreased over time. Furthermore, CS-REO treatment delayed gene upregulation by REO alone, from 0.5 to 6 hpt, and kept that longer over time. This study suggests that CS stabilizes the volatile and/or hydrophobic substances of highly reactive essential oils. The additive effects of CS and REO were able to reduce postharvest decay and affect gene expression in papaya fruit.

Integrated Physiological and Transcriptomic Analyses Reveal a Regulatory Network of Anthocyanin Metabolism Contributing to the Ornamental Value in a Novel Hybrid Cultivar of Camellia Japonica

Camellia japonica is a plant species with great ornamental and gardening values. A novel hybrid cultivar Chunjiang Hongxia (Camellia japonica cv. Chunjiang Hongxia, CH) possesses vivid red leaves from an early growth stage to a prolonged period and is, therefore, commercially valuable. The molecular mechanism underlying this red-leaf phenotype in C. japonica cv. CH is largely unknown. Here, we investigated the leaf coloration process, photosynthetic pigments contents, and different types of anthocyanin compounds in three growth stages of the hybrid cultivar CH and its parental cultivars. The gene co-expression network and differential expression analysis from the transcriptome data indicated that the changes of leaf color were strongly correlated to the anthocyanin metabolic processes in different leaf growth stages. Genes with expression patterns associated with leaf color changes were also discussed. Together, physiological and transcriptomic analyses uncovered the regulatory network of metabolism processes involved in the modulation of the ornamentally valuable red-leaf phenotype and provided the potential candidate genes for future molecular breeding of ornamental plants such as Camellia japonica.

The style and substance of plant flavonoid decoration; towards defining both structure and function

Over 8000 different flavonoids have been described and a considerable number of new flavonoid structures are being elucidated every year. The advent of metabolomics alongside the development of phytochemical genetics - wherein the genetic basis underlying the regulation of the levels of plant metabolites is determined - has provided a massive boost to such efforts. That said our understanding of the individual function(s) of the vast majority of the metabolites that constitute this important class of phytochemicals remains unknown. Here we review what is known concerning the major decorative modifications of flavonoids in plants, namely hydroxylation, glycosylation, methylation and acylation. Our major focus is with regard to the in planta function of these modified compounds, however, we also highlight the demonstrated bioactive roles which they possess. We additionally performed a comprehensive survey of the flavonoids listed in the KNApSAcK database in order to assess the frequency of occurrence of each type of flavonoid modification. We conclude that whilst considerable research has been carried out regarding the biological roles of flavonoids most studies to date have merely provided information on the compound class or sub-classes thereof as a whole with too little currently known on the specific role of individual metabolites. We, therefore, finally suggest a framework based on currently available tools by which the relative importance of the individual compounds can be assessed under various biological conditions in order to fill this knowledge-gap.

Comparative Metabolomic Analysis Reveals Distinct Flavonoid Biosynthesis Regulation for Leaf Color Development of Cymbidium sinense 'Red Sun'

The colorful leaf is an important ornamental character of Cymbidium sinense (C. sinense), especially the red leaf, which has always been attracted by breeders and consumers. However, little is documented on the formation mechanism of the red leaf of C. sinense. In this study, the changing patterns of flavonoid-related metabolites, corresponding enzyme activities and genes expression in the leaves of C. sinense ‘Red Sun’ from red to yellow and finally to green was investigated. A total of 196 flavonoid-related metabolites including 11 anthocyanins metabolites were identified using UPLC-MS/MS-based approach. In the process of leaf color change, 42 metabolites were identified as having significantly different contents and the content of 28 differential metabolites turned to zero. In anthocyanin biosynthetic pathway, content of all 15 identified metabolites showed downregulation trend in the process of leaf color change. Among the 15 metabolites, the contents of Naringenin chalcone, Pelargonidin O-acetylhexoside and Anthocyanin 3-O-beta-d-glucoside decreased to zero in the green leaf stage. The changing pattern of enzyme activity of 10 enzymes involved in the anthocyanin biosynthetic pathway showed different trends from red leaves that have turned yellow and finally green, while the expression of genes encoding these enzymes was all down-regulated in the process of leaf color change. The results of this study revealed the types of flavonoid-related metabolites and the comprehensive analysis of metabolites content, enzyme activities and genes expression providing a new reference for breeders to improve the leaf color of C. sinense ‘Red Sun’.

Anthocyanin Accumulation in the Leaves of the Purple Sweet Potato (Ipomoea batatas L.) Cultivars

Sweet potato anthocyanins are water-soluble pigments with many physiological functions. Previous research on anthocyanin accumulation in sweet potato has focused on the roots, but the accumulation progress in the leaves is still unclear. Two purple sweet potato cultivars (Fushu No. 23 and Fushu No. 317) with large quantities of anthocyanin in the leaves were investigated. Anthocyanin composition and content were assessed with ultra-performance liquid chromatography diode-array detection (UPLC-DAD) and ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and the expressions of genes were detected by qRT-PCR. The two cultivars contained nine cyanidin anthocyanins and nine peonidin anthocyanins with an acylation modification. The acylation modification of anthocyanins in sweet potato leaves primarily included caffeoyl, p-coumaryl, feruloyl, and p-hydroxy benzoyl. We identified three anthocyanin compounds in sweet potato leaves for the first time: cyanidin 3-p-coumarylsophoroside-5-glucoside, peonidin 3-p-coumarylsophoroside-5-glucoside, and cyanidin 3-caffeoyl-p-coumarylsophoroside-5-glucoside. The anthocyanidin biosynthesis downstream structural genes DFR4, F3H1, anthocyanin synthase (ANS), and UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT3), as well as the transcription factor MYB1, were found to be vital regulatory genes during the accumulation of anthocyanins in sweet potato leaves. The composition of anthocyanins (nine cyanidin-based anthocyanins and nine peonidin-based anthocyanins) in all sweet potato leaves were the same, but the quantity of anthocyanins in leaves of sweet potato varied by cultivar and differed from anthocyanin levels in the roots of sweet potatoes. The anthocyanidin biosynthesis structural genes and transcription factor together regulated and controlled the anthocyandin biosynthesis in sweet potato leaves.

Diverse biological effects of glycosyltransferase genes from Tartary buckwheat

BACKGROUND

Tartary buckwheat (Fagopyrum tataricum) is an edible cereal crop whose sprouts have been marketed and commercialized for their higher levels of anti-oxidants, including rutin and anthocyanin. UDP-glucose flavonoid glycosyltransferases (UFGTs) play an important role in the biosynthesis of flavonoids in plants. So far, few studies are available on UFGT genes that may play a role in tartary buckwheat flavonoids biosynthesis. Here, we report on the identification and functional characterization of seven UFGTs from tartary buckwheat that are potentially involved in flavonoid biosynthesis (and have varying effects on plant growth and development when overexpressed in Arabidopsis thaliana.) RESULTS: Phylogenetic analysis indicated that the potential function of the seven FtUFGT proteins, FtUFGT6, FtUFGT7, FtUFGT8, FtUFGT9, FtUFGT15, FtUFGT40, and FtUFGT41, could be divided into three Arabidopsis thaliana functional subgroups that are involved in flavonoid biosynthesis of and anthocyanin accumulation. A significant positive correlation between FtUFGT8 and FtUFGT15 expression and anthocyanin accumulation capacity was observed in the tartary buckwheat seedlings after cold stress. Overexpression in Arabidopsis thaliana showed that FtUFGT8, FtUFGT15, and FtUFGT41 significantly increased the anthocyanin content in transgenic plants. Unexpectedly, overexpression of FtUFGT6, while not leading to enhanced anthocyanin accumulation, significantly enhanced the growth yield of transgenic plants. When wild-type plants have only cotyledons, most of the transgenic plants of FtUFGT6 had grown true leaves. Moreover, the growth speed of the oxFtUFGT6 transgenic plant root was also significantly faster than that of the wild type. At later growth, FtUFGT6 transgenic plants showed larger leaves, earlier twitching times and more tillers than wild type, whereas FtUFGT15 showed opposite results.

CONCLUSIONS

Seven FtUFGTs were isolated from tartary buckwheat. FtUFGT8, FtUFGT15, and FtUFGT41 can significantly increase the accumulation of total anthocyanins in transgenic plants. Furthermore, overexpression of FtUFGT6 increased the overall yield of Arabidopsis transgenic plants at all growth stages. However, FtUFGT15 shows the opposite trend at later growth stage and delays the growth speed of plants. These results suggested that the biological function of FtUFGT genes in tartary buckwheat is diverse.

Looking at Flavonoid Biodiversity in Horticultural Crops: A Colored Mine with Nutritional Benefits

Flavonoids represent a wide group of plant secondary metabolites implicated in many physiological roles, from the attraction of pollinators to the protection against biotic or abiotic stresses. Flavonoids are synthetized in a number of horticultural crops that are important components of our daily diet. In the last decades, the consumption of vegetables rich in antioxidants has been strongly promoted from the perspective of prevention/protection against chronic diseases. Therefore, due to their nutritional importance, several attempts have been made to enhance flavonoid levels in species of agronomic interest. In this review, we focus on the flavonoid biodiversity among the major horticultural species, which is responsible of differences among closely related species and influences the qualitative/quantitative composition. We also review the role of flavonoids in the nutritional quality of plant products, contributing to their organoleptic and nutritional properties, and the main strategies of biofortification to increase their content.

Functional characteristics of phenolic compounds accumulated in young leaves of two subtropical forest tree species of different successional stages

The abundance of phenolic compounds (including anthocyanins) in leaves is associated with photosynthetic performance, but the regulatory mechanism is unclear. Schima superba Gardn. et Champ. and Cryptocarya concinna Hance., which exhibit distinct anthocyanin accumulation patterns, are dominant tree species in the early- and late-successional stages, respectively, of subtropical forests in China. RNA-seq and analyses of phenolic concentrations, antioxidant capacity and photosynthetic characteristics were performed on young and mature leaves of these two species under contrasting light conditions. The high-light-acclimated young leaves of S. superba and C. concinna and low-light-acclimated young leaves of C. concinna were red. These red leaves had higher ratios of electron transport rate to gross photosynthesis (ETR:Pgross) and total antioxidant capacity to chlorophyll (TAC:Chl) than did the green leaves, regardless of light conditions. In addition, the red leaves had a higher expression level of the UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) gene than did the green leaves, irrespective of light conditions. Total antioxidant capacity was positively correlated with flavonoid content in C. concinna leaves and with total phenolic content in leaves of both species under both high and low light. Consistent with the measurements of photosynthetic performance and flavonoids:Chl ratio, photosynthesis-related genes were extensively downregulated and flavonoid-pathway-related genes were extensively upregulated in young leaves relative to mature leaves. Under high and low light, both non-photochemical quenching and TAC:Chl, which serve as different types of photoprotective tools, were enhanced in young leaves of S. superba, whereas only TAC:Chl was enhanced in young leaves of C. concinna. Our results indicate that the biosynthesis of phenolic compounds in young leaves is likely enhanced by an imbalance between photosynthetic electron supply and demand and that flavonoids play a larger role in meditating photoprotection in late-successional species than in early-successional ones.

Higher anthocyanin accumulation associated with higher transcription levels of anthocyanin biosynthesis genes in spinach

Spinach (Spinacia oleracea L.) is widely cultivated as an economically important green leafy vegetable crop for fresh and processing consumption. The red-purple spinach shows abundant anthocyanin accumulation in the leaf and leaf petiole. However, the molecular mechanisms of anthocyanin synthesis in this species are still undetermined. In the present study, we investigated pigment formation and identified anthocyanin biosynthetic genes in spinach. We also analyzed the expression of these genes in purple and green cultivars by quantitative PCR. The accumulation of anthocyanin showed that it was the dominant pigment resulting in the red coloration in spinach. In total, 22 biosynthesis genes and 25 regulatory genes were identified in spinach, based on the spinach genomic and transcriptomic database. Furthermore, the expression patterns of genes encoding enzymes indicated that SoPAL, SoUFGT3, and SoUFGT4 were possible candidate genes for anthocyanin biosynthesis in red-purple spinach. The expression patterns of transcription factors indicated that two SoMYB genes, three SobHLH genes, and one SoWD40 gene were drastically up-regulated and co-expression in red-purple spinach, suggesting an essential role of regulatory genes in the anthocyanin biosynthesis of spinach. These results will enhance our understanding of the molecular mechanisms of anthocyanin biosynthesis in purple spinach.

Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume)

The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot.

Characterization of Three Glucosyltransferase Genes in Tartary Buckwheat and Their Expression after Cold Stress

Anthocyanins confer the red color in the hypocotyl of tartary buckwheat sprouts. Uridine diphosphate (UDP)-glucose:flavonoid 3-O-glycosyltransferase (UFGT) stabilizes anthocyanin by attaching the glucosyl moiety from UDP-glucose to the C3 hydroxyl of anthocyanin. In this study, we characterized three UFGT-like genes, designated FtUFGT1, 2, and 3 from tartary buckwheat. The results revealed that FtUFGT1, FtUFGT2, and FtUFGT3 can convert cyanidin to cyanidin 3-O-glucoside, with specific activities of 20.01 × 10(-3), 8.93 × 10(-3), and 20.24 × 10(-3) IU/mg, respectively. The active-site residues of the C-terminal domains and the N-terminal domains are important for the donor and acceptor recognition of these proteins. The expression of the three FtUFGTs paralleled the tissue-specific anthocyanin accumulation. After cold treatment, the increased content of anthocyanin was accompanied by the up-regulated expression of the three FtUFGTs. Among these three UGFT gene members, FtUFGT3 showed the highest expression level and the highest specific activity, suggesting that FtUFGT3 might be the major gene involved in anthocyanin biosynthesis. These results suggested that the FtUFGT genes, FtUFGT3 in particular, might be important candidates for anthocyanin formation in tartary buckwheat sprouts.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.

Biochemical and Molecular Characterization of a Flavonoid 3-O-glycosyltransferase Responsible for Anthocyanins and Flavonols Biosynthesis in Freesia hybrida

The glycosylation of flavonoids increases their solubility and stability in plants. Flowers accumulate anthocyanidin and flavonol glycosides which are synthesized by UDP-sugar flavonoid glycosyltransferases (UFGTs). In our previous study, a cDNA clone (Fh3GT1) encoding UFGT was isolated from Freesia hybrida, which was preliminarily proved to be invovled in cyanidin 3-O-glucoside biosynthesis. Here, a variety of anthocyanin and flavonol glycosides were detected in flowers and other tissues of F. hybrida, implying the versatile roles of Fh3GT1 in flavonoids biosynthesis. To further unravel its multi-functional roles, integrative analysis between gene expression and metabolites was investigated. The results showed expression of Fh3GT1 was positively related to the accumulation of anthocyanins and flavonol glycosides, suggesting its potential roles in the biosynthesis of both flavonoid glycosides. Subsequently, biochemical analysis results revealed that a broad range of flavonoid substrates including flavonoid not naturally occurred in F. hybrida could be recognized by the recombinant Fh3GT1. Both UDP-glucose and UDP-galactose could be used as sugar donors by recombinant Fh3GT1, although UDP-galactose was transferred with relatively low activity. Furthermore, regiospecificity analysis demonstrated that Fh3GT1 was able to glycosylate delphinidin at the 3-, 4-', and 7- positions in a sugar-dependent manner. And the introduction of Fh3GT1 into Arabidopsis UGT78D2 mutant successfully restored the anthocyanins and flavonols phenotypes caused by lost-of-function of the 3GT, indicating that Fh3GT1 functions as a flavonoid 3-O-glucosyltransferase in vivo. In summary, these results demonstrate that Fh3GT1 is a flavonoid 3-O-glycosyltransferase using UDP-glucose as the preferred sugar donor and may involve in flavonoid glycosylation in F. hybrida.

De novo sequencing and comprehensive analysis of the mutant transcriptome from purple sweet potato (Ipomoea batatas L.)

Purple sweet potatoes, rich in anthocyanin, have been widely favored in light of increasing awareness of health and food safety. In this study, a mutant of purple sweet potato (white peel and flesh) was used to study anthocyanin metabolism by high-throughput RNA sequencing and comparative analysis of the mutant and wild type transcriptomes. A total of 88,509 unigenes ranging from 200nt to 14,986nt with an average length of 849nt were obtained. Unigenes were assigned to Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Functional enrichment using GO and KEGG annotations showed that 3828 of the differently expressed genes probably influenced many important biological and metabolic pathways, including anthocyanin biosynthesis. Most importantly, the structural and transcription factor genes that contribute to anthocyanin biosynthesis were downregulated in the mutant. The unigene dataset that was used to discover the anthocyanin candidate genes can serve as a comprehensive resource for molecular research in sweet potato.

Comparative Transcriptome Analysis of White and Purple Potato to Identify Genes Involved in Anthocyanin Biosynthesis

INTRODUCTION

The potato (Solanum tuberosum) cultivar 'Xin Daping' is tetraploid with white skin and white flesh, while the cultivar 'Hei Meiren' is also tetraploid with purple skin and purple flesh. Comparative transcriptome analysis of white and purple cultivars was carried out using high-throughput RNA sequencing in order to further understand the mechanism of anthocyanin biosynthesis in potato.

METHODS AND RESULTS

By aligning transcript reads to the recently published diploid potato genome and de novo assembly, 209 million paired-end Illumina RNA-seq reads from these tetraploid cultivars were assembled on to 60,930 transcripts, of which 27,754 (45.55%) are novel transcripts and 9393 alternative transcripts. Using a comparison of the RNA-sequence datasets, multiple versions of the genes encoding anthocyanin biosynthetic steps and regulatory transcription factors were identified. Other novel genes potentially involved in anthocyanin biosynthesis in potato tubers were also discovered. Real-time qPCR validation of candidate genes revealed good correlation with the transcriptome data. SNPs (Single Nucleotide Polymorphism) and indels were predicted and validated for the transcription factors MYB AN1 and bHLH1 and the biosynthetic gene anthocyanidin 3-O-glucosyltransferase (UFGT).

CONCLUSIONS

These results contribute to our understanding of the molecular mechanism of white and purple potato development, by identifying differential responses of biosynthetic gene family members together with the variation in structural genes and transcription factors in this highly heterozygous crop. This provides an excellent platform and resource for future genetic and functional genomic research.

Transcription factors, sucrose, and sucrose metabolic genes interact to regulate potato phenylpropanoid metabolism

Much remains unknown about how transcription factors and sugars regulate phenylpropanoid metabolism in tuber crops like potato (Solanum tuberosum). Based on phylogeny and protein similarity to known regulators of phenylpropanoid metabolism, 15 transcription factors were selected and their expression was compared in white, yellow, red, and purple genotypes with contrasting phenolic and anthocyanin profiles. Red and purple genotypes had increased phenylalanine ammonia lyase (PAL) enzyme activity, markedly higher levels of phenylpropanoids, and elevated expression of most phenylpropanoid structural genes, including a novel anthocyanin O-methyltransferase. The transcription factors Anthocyanin1 (StAN1), basic Helix Loop Helix1 (StbHLH1), and StWD40 were more strongly expressed in red and purple potatoes. Expression of 12 other transcription factors was not associated with phenylpropanoid content, except for StMYB12B, which showed a negative relationship. Increased expression of AN1, bHLH1, and WD40 was also associated with environmentally mediated increases in tuber phenylpropanoids. Treatment of potato plantlets with sucrose induced hydroxycinnamic acids, flavonols, anthocyanins, structural genes, AN1, bHLH1, WD40, and genes encoding the sucrose-hydrolysing enzymes SUSY1, SUSY4, and INV2. Transient expression of StAN1 in tobacco leaves induced bHLH1, structural genes, SUSY1, SUSY4, and INV1, and increased phenylpropanoid amounts. StAN1 infiltration into tobacco leaves decreased sucrose and glucose concentrations. In silico promoter analysis revealed the presence of MYB and bHLH regulatory elements on sucrolytic gene promoters and sucrose-responsive elements on the AN1 promoter. These findings reveal an interesting dynamic between AN1, sucrose, and sucrose metabolic genes in modulating potato phenylpropanoids.

An ankyrin repeat protein is involved in anthocyanin biosynthesis in Arabidopsis

The ankyrin domain is one of the most common protein motifs in eukaryotic proteins. Repeated ankyrin domains are ubiquitous and their mediation of protein-protein interactions is involved in a number of physiological and developmental responses such as the cell cycle, signal transduction and cell differentiation. A novel putative phytochrome-interacting ankyrin repeat protein 2 (PIA2) containing three repeated ankyrin domains was identified in Arabidopsis. An in vitro pull-down and phosphorylation assay revealed that PIA2 is phosphorylated and interacts directly with oat phytochrome A. The N-terminal domain of PIA2 was specifically phosphorylated, whereas interactions between the domains of PIA2 and phytochrome A had no Pr/Pfr preference. PIA2 was ubiquitously expressed in most tissues and was localized in both the nucleus and the cytoplasm independent of treatment with light of specific wavelengths. Anthocyanin accumulation in seedlings grown under far-red light, a typical phenotype of wild-type plants, was reduced in a loss-of-function mutant of PIA2 (pia2), whereas anthocyanin accumulation was increased in an overexpressing plant (PIA2-OX). The gene expression of UDP-flavonoid-3'-glucosyl-transferase (UF3GT), a major enzyme in the anthocyanin biosynthesis processes, was decreased in pia2 knockout plants suggesting that decreased anthocyanin was because of the decreased expression of UF3GT. Our results suggest that PIA2 plays a role in the anthocyanin biosynthesis during seedling development as a novel phytochrome-interacting protein.