Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids

Ethylene promotes anthocyanin synthesis in 'Viviana' lily via the LvMYB5-LvERF113-LvMYB1 module

Ethylene (ET) influences the synthesis of anthocyanins, although its regulatory effects can differ significantly across various plant species. In apples (Malus domestica), ET promotes anthocyanin synthesis, whereas in Arabidopsis thaliana, it inhibits its accumulation. Our research showed that ethephon (Eth), an ET derivative, promotes anthocyanin synthesis in 'Viviana' lilies, which has great potential in the cut flower industry. The regulatory mechanism whereby ET influences anthocyanin synthesis in lilies remains unclear. In this study, we screened and characterized an ET-induced ET response factors (ERFs), LvERF113, with inhibitory function. Our analyses suggested that LvERF113 could inhibit the negative regulatory function of LvMYB1 at transcriptional and posttranslational levels, promoting anthocyanin synthesis in 'Viviana' lily tepals. In addition, LvERF113 is positively regulated by LvMYB5, forming the LvMYB5-LvERF113-LvMYB1 module controlling anthocyanin synthesis by ET in 'Viviana' lily. These findings offer new insights into the ET regulatory network of anthocyanin synthesis and provide a theoretical basis for the application of ET derivatives in the cut flower industry.

Widely targeted metabolomics analysis flavonoid metabolites in different purple teas

Purple teas are gaining popularity due to their significant health benefits. This study analyzed flavonoid metabolites in the second leaves of three purple tea varieties with stable purple shoots-'Hongfei' (HF), 'Danfei' (DF), and 'Ziya 24' (ZY24)-using UPLC-MS/MS, with 'Yinghong 9' (YH9), a green tea, as the control. The most abundant anthocyanins were cyanidin-3-O-glucoside, cyanidin-O-syringic acid, and pelargonidin-3-O-glucoside in HF, while ZY24 and DF accumulated additional delphinidin and petunidin derivatives. DF also contained malvidin-3-O-galactoside. Furthermore, 22 significantly enriched non-anthocyanin flavonoids were identified as potential co-pigments contributing to the vibrant leaf coloration. These findings reveal key anthocyanin and flavonoid profiles responsible for the distinct purple hues in the tender shoots of different purple tea varieties.

Transcontinental patterns in floral pigment abundance among animal-pollinated species

Flower color arises primarily from pigments that serve dual functions: attracting pollinators and mitigating environmental stresses. Among major pigment types, anthocyanins and UV-absorbing phenylpropanoids (UAPs) fulfill one or both roles and should be widespread. Our review of the UV-vis absorption profiles of major floral pigments demonstrates that UAPs are the primary UV protectants. Next, we analyzed the floral pigment composition of 926 animal-pollinated species from California, Southern Spain, and Southeastern Brazil. UAPs were ubiquitous (the "dark matter" of the flower). Among the remaining pigment types, ~ 56% of species had anthocyanins, ~ 37% had carotenoids, and ~ 17% had chlorophylls (some species had > 1 pigment type). Pigment abundance varied in response to abiotic and biotic factors, particularly with pollinator type in California. Despite regional differences in environmental filtering, pollination guilds, and relatedness, UAPs are omnipresent and there is a transcontinental stable distribution of flower colors and their underlying floral pigments.

Enhanced pigment production from plants and microbes: a genome editing approach

Pigments are known for their vital roles in the growth and development of plants and microbes. In addition, they are also an imperative component of several industries, including textiles, foods, and pharmaceuticals, owing to their immense colours and therapeutic potential. Conventionally, pigments are obtained from plant resources, and the advent of in-vitro propagation techniques boosted the massive production. However, it could not meet the booming demand, leading to the incorporation of new genetic engineering tools. This review focuses on the role of various genetic engineering techniques in enhancing pigment production in plants and microorganisms. It also critically analyzes the efficacy and bottlenecks of these techniques in augmenting pigment biosynthesis. Furthermore, the use of microbes as pigment biofactories and the prospects in the field of genome editing to augment pigment synthesis are discussed. The limitations in the existing techniques underline the need for advanced genome editing strategies to broaden the mass production of pigments to meet the surging needs.

Two tandem R2R3 MYB transcription factor genes cooperatively regulate anthocyanin accumulation in potato tuber flesh

Anthocyanin biosynthesis and accumulation determines the colour of tuber flesh in potato (Solanum tuberosum) and influences nutritional quality. However, the regulatory mechanism behind anthocyanin biosynthesis in potato tuber flesh remains unclear. In this study, we identified the Pigmented tuber flesh (Pf) locus through a genome-wide association study using 135 diploid potato landraces. Genome editing of two tandem R2R3 MYB transcription factor genes, StMYB200 and StMYB210, within the Pf locus demonstrated that both genes are involved in anthocyanin biosynthesis in tuber flesh. Molecular and biochemical assays revealed that StMYB200 promotes StMYB210 transcription by directly binding to a 1.7-kb insertion present in the StMYB210 promoter, while StMYB210 also regulates its own expression. Furthermore, StMYB200 and StMYB210 both activated the expression of the basic helix-loop-helix transcription factor gene StbHLH1 and interacted with StbHLH1 to regulate anthocyanin biosynthesis. An analysis of the StMYB210 promoter in different diploid potato accessions showed that the 1.7-kb insertion is associated with flesh colour in potato. These findings reveal the genetic and molecular mechanism by which the Pf locus regulates anthocyanin accumulation in tuber flesh and provide an important reference for breeding new potato varieties with colourful flesh.

Occurrence of White Flesh Color and Refreshing Flavor Following Phytoene Synthase 2A Gene Variation in Loquat Fruit

Loquat fruits from the apple tribe of Rosaceae ripen from late spring to early summer, when most fresh fruits are out of season. Compared with the orange-fleshed varieties, the white-fleshed varieties are usually preferentially chosen by consumers for a more favorable flavor. Though the breeding of white-fleshed cultivars with large fruit size greatly promoted the development of loquat production, the mechanisms of how fruits with lighter pigments are generated and how fruit flavor changes following flesh color shifting remain to be elucidated. Pigment measurements indicated carotenoids as the dominant pigment underlying the change in flesh color changing. Genotyping and haplotyping of 807 loquat accessions revealed that the rise of PSY2Ad-PSY2Ad genotype blocks carotenoids accumulation and confers to white flesh color of loquat fruit. Analysis of widely targeted metabolomes on 18 representative cultivars identified 1420 metabolites, with 223 differentially accumulated metabolites between the two groups. Further metabolite comparison demonstrated that low levels of bitter or astringent compounds, such as flavonoids, lignans and coumarins, phenolic acids, nucleotides, alkaloids, and terpenoids, may confer to a refreshing flavor of white-fleshed fruits. Furthermore, 18 metabolic biomarkers were identified by machine learning to distinguish fruits with diverse flesh colors. This work gives insights into the understanding of how fruit color variation associated with flavor and also promotes white-fleshed loquat breeding by genus-wide genotyping.

Metabolomic and transcriptomic analyses provide insights into the role of MiMYB114 and MiMYC2 in the MeJA-induced regulatory network for mango pericarp coloration

The color of mango fruit peel is a critical factor influencing consumer preference and market value. MeJA can enhance mango pericarp coloration, but its effects on different pigments accumulation and the underlying molecular mechanisms remain unclear. In this study, exogenous treatment of 4 mmol/L MeJA enhances the red and yellow pigments in the pericarp of mango cultivar 'Guifei'. Metabolomic analysis revealed that MeJA significantly increases anthocyanin and carotenoid accumulation while accelerating chlorophyll degradation. Transcriptomic analysis indicated that MeJA promotes the expression of genes involved in anthocyanin biosynthesis (e.g., MiPAL, MiC4H, MiF3H, and MiUFGT), chlorophyll degradation (MiSGRs, MiPPHs, MiPAO, and MiRCCRs), and carotenoid biosynthesis (MiPSY, MiLCYB, MiBCH, and MiZEP). Furthermore, the transcription factors (MYBs, AP2-ERFs, bHLHs, WRKYs, and TIFYs) were induced by MeJA. Of these, transient expression assays suggested that MiMYB114 mediates anthocyanin accumulation by enhancing the expression of MiF3H and MiUFGT, and the bHLH transcription factor MiMYC2 regulates chlorophyll degradation and carotenoid biosynthesis by promoting the expression of MiSGR, MiRCCR, MiPSY, and MiBCH. Our results provide new insights into the regulatory roles of MeJA treatment in mango pericarp coloration.

CRY1-GAIP1 complex mediates blue light to hinder the repression of PIF5 on AGL5 to promote carotenoid biosynthesis in mango fruit

Carotenoids are essential natural pigments that not only determine the commercial value of horticultural crops through colouration but also serve as vital antioxidants and provitamin A precursors in the human diet. Our previous research has demonstrated that blue light induces carotenoid biosynthesis in mango fruit. However, a critical knowledge gap remains regarding how blue light regulates carotenoid biosynthesis in fruit. In this study, blue light-induced MiAGL5 was identified to promote carotenoid biosynthesis by activating the promoters of MiBCH1 and MiZEP. Subsequently, MiPIF5, a phytochrome interacting factor, transcriptionally inhibited MiAGL5 expression. MiGAIP1, a DELLA protein, promoted carotenoid biosynthesis by interacting with MiPIF5 and preventing its repression of MiAGL5. Furthermore, blue light stabilized MiGAIP1 protein through MiCRY1-MiGAIP1 interaction and reduced MiGAIP1 degradation by decreasing GA content in mango fruit. Additionally, MiGAIP1 mediated the antagonistic effects between blue light and GA in regulating carotenoid biosynthesis. Collectively, these results demonstrate that blue light induces carotenoid biosynthesis through a mechanism involving MiCRY1-MiGAIP1 complex-mediated inhibition of MiPIF5 repression on MiAGL5. Our work provides solid evidence for CRY-DELLA-PIF-AGL cross-talk in plant metabolism and establishes a new paradigm for light-hormone antagonism in the regulation of specialized metabolites.

Resequencing and Functional Analysis Revealed That BsDFR4 Could Cause the Formation of Different Flower Colors in Bletilla striata (Orchidaceae)

The formation of flower color is closely related to anthocyanin synthesis. In this study, flowers of Bletilla striata (Orchidaceae) exhibiting distinct color morphs were collected and analyzed. The HPLC results showed significantly higher total flavonoid and anthocyanin contents in purple flowers compared to pink counterparts, with increases of 2.20-fold (p < 0.01) and 15.22-fold (p < 0.01), respectively. Cyanidin was the predominant anthocyanin in B. striata. Resequencing analyses highlighted SNP as the primary variation associated with color divergence. A comprehensive screen identified 61 genes encoding enzymes critical to the flavonoid and anthocyanin biosynthesis pathways in B. striata. Among these, 16 flower-specific genes exhibited high expression levels and harbored SNP variations. Notably, a premature stop codon was identified in a gene encoding dihydroflavonol 4-reductase (DFR), leading to truncated protein synthesis and potential disruption of anthocyanin production. Further, the heterologous overexpression of BsDFR4 in Phalaenopsis aphrodite changed petal color from white to yellow-green, demonstrating that it indeed played a regulatory role in the formation of flower color. Furthermore, yeast one-hybrid assays confirmed that transcription factors BsMYB36 and BsMYB51 could directly bind to the BsDFR4 promoter, suggesting their synergistic regulation of anthocyanin biosynthesis. These results provided a conceptual basis for insights into the formation of different flower colors in Orchidaceae.

Molecular mechanism of differences in anthocyanin components between pericarp and red hairy root of early maturing litchi cultivars

Glycosylation of anthocyanin plays an important role in increasing its stability and diversity in plants. Here, we identified a glucosyltransferase gene responsible for the anthocyanin components in Litchi chinensis Sonn. Cyanidin-3-rutinoside is the main anthocyanins of pericarps and red hairy roots overexpressing MYB transcription factor LcMYB1 in the late maturing cultivars. However, in the early maturing cultivars, the anthocyanins in the pericarps is dominated by cyanidin-3-glucoside, and the anthocyanins in the red hairy roots overexpressing LcMYB1 is dominated by cyanidin-3-rutinoside. Enzyme assays highlighted notable differences in flavonoid 3-O-rhamnosyltransferase (F3RT) activity between the pericarps and red hairy roots overexpressing LcMYB1 in the early maturing cultivars. Two differentially expressed genes (DEGs), LcF3RT1 and LcF3RT2, were significantly up-regulated in the red hairy roots overexpressing LcMYB1. Yeast one-hybrid and dual luciferase reporter assays revealed that LcMYB1 could bind to the promoter of LcF3RT2 and significantly activate its expression. Functional validation showed that LcF3RT2 could catalyze the conversion of cyanidin-3-glucoside into cyanidin-3-rutinoside, leading to the differences on anthocyanin components in pericarps and red hairy roots of early maturing litchi cultivars. Our results will provide insights into the regulation and glycosylation modification of anthocyanins in litchi as well as in other plants.

Chromatic symphony of fleshy fruits: functions, biosynthesis and metabolic engineering of bioactive compounds

Fleshy fruits are popular among consumers due to their significant nutritional value, which includes essential bioactive compounds such as pigments, vitamins, and minerals. Notably, plant-derived pigments are generally considered safe and reliable, helping to protect humans against various inflammatory diseases. Although the phytochemical diversity and their biological activities have been extensively reviewed and summarized, the status of bioactive nutrients in fleshy fruits, particularly with a focusing on different colors, has received less attention. Therefore, this review introduces five common types of fleshy fruits based on coloration and summarizes their major bioactive compounds. It also provides the latest advancements on the function, biosynthesis, and metabolic engineering of plant-derived pigments. In this review, we emphasize that promoting the consumption of a diverse array of colorful fruits can contribute to a balanced diet; however, optimal intake levels still require further clinical validation. This review may serve as a useful guide for decisions that enhance the understanding of natural pigments and accelerate their application in agriculture and medicine.

Gretchen Hagen 3.6-like promotes anthocyanin accumulation by negatively regulating the expression of basic helix-loop-helix transcription factor 106 in grapevine

Anthocyanins are mainly synthesized from flavonoid precursors in plants. Although there have been numerous studies on the biosynthesis of anthocyanins, few have sought to explore how Gretchen Hagen 3 (GH3) genes regulate the production of anthocyanins. In this study, a VaGH3.6-like gene was identified, and its overexpression in grapevine callus tissues and berry skins promoted significant accumulation of anthocyanins and reduced endogenous IAA content under light conditions, whereas callus tissues transformed with a mutant VaGH3.6-like showed the opposite results. The overexpression of VaGH3.6-like was observed to directly promote the accumulation of flavonoids under dark conditions, whereas the accumulation was significantly reduced in mutants. In addition, the VabHLH106 transcription factor, a negative regulator of VaGH3.6-like, was screened via RNA-seq. Subsequent analyses using Y2H, Y1H, DLR™, and EMSA analyses revealed that VabHLH106 represses VaGH3.6-like expression by directly binding to two E-box elements in its promoter region. Interestingly, VaGH3.6-like overexpression regulates VabHLH106 expression via a negative feedback mechanism, attenuating the repressive effect of VabHLH106 on the downstream genes VvLDOX, VvCYP75B2, and VvCYP73A3, thus leading to an increasing in the synthesis of anthocyanins in grapes. These findings provide a new theoretical basis for further understanding the molecular mechanisms underlying accumulation of anthocyanins in grapes.

Effect of Light Intensity on Anthocyanin Synthesis Assessed Using Leaves of Aglaonema commutatum

BACKGROUND

Plant anthocyanins are a secondary metabolite widely distributed in the roots, stems, leaves, flowers, and fruits of plants, and their synthesis is significantly affected by light intensity. To investigate the synthesis of anthocyanins in Aglaonema commutatum's leaves under different light intensities is essential.

METHODS

Using the commonly colored leaf A. commutatum variety 'Emerald' as the control group, and the red-leaf varieties 'Red Ruyi', 'Angel', and 'Gilly Red' as the experimental material, three light intensities were set: 254~368 μmol·m-2·s-1 (CK), 588~678 μmol·m-2·s-1 (T1), and 1125~1267 μmol·m-2·s-1 (T2).

RESULTS

The changes in anthocyanin content and anthocyanin-related gene expression in the leaves of A. commutatum with different leaf colors under different light intensities were studied. The results show that the anthocyanin content of A. commutatum leaves had a different trend compared to A. commutatum with increasing light intensity, and the appropriate light intensity could significantly promote anthocyanin synthesis after a certain time, and vice-versa. The anthocyanin content of CK and the T1 treatment was 1.14-3.72 times that of the T2 treatment; the photosensitive genes PHYB, CRY, and UVR8 were correlated with the anthocyanin synthesis of 'Angel' and 'Gilly Red'. The anthocyanin structural genes PAL, DFR, and ANS were correlated with the anthocyanin synthesis of 'Red Ruyi', 'Angel', and 'Gilly Red'. The anthocyanin transcription factor bHLH was strongly correlated with the anthocyanin synthesis of 'Angel'.

CONCLUSIONS

As a byproduct from A. commutatum leaves with ornamental value and potential economic value, this study was helpful to understand the potential mechanism of A. commutatum's leaves where light intensity regulates anthocyanin synthesis and accumulation.

Unravel the molecular basis underlying inflorescence color variation in Macadamia based on widely targeted metabolomics

Macadamia integrifolia, a perennial evergreen crop valued for its nutritious nuts, also exhibits a diverse range of inflorescence colors that possess both ornamental and biological significance. Despite the economic importance of macadamia, the molecular mechanisms regulating flower coloration remain understudied. This study employed a combination of metabolomic and biochemical approaches to analyze metabolites present in inflorescences from 11 Macadamia cultivars, representing distinct color phenotypes. A total of 787 metabolites were identified through the use of ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), the majority of which were phenolic acids, flavonoids, and flavonols. Principal component analysis and clustering yielded a classification of the samples into three major flower color groups. The differential metabolites were found to be enriched in pathways such as flavonoid, flavonol, and phenylpropanoid biosynthesis, which have been demonstrated to be key contributors to color variation. Moreover, weighted gene co-expression network analysis (WGCNA) identified metabolite modules that were strongly associated with specific flower colors. This revealed that key compounds, including kaempferol, quercetin derivatives, and anthocyanins, were the primary drivers of pigmentation. This study provides a comprehensive framework for understanding the genetic, biochemical, and environmental factors influencing macadamia flower color. These findings contribute to the theoretical understanding of macadamia reproductive biology and have practical implications for molecular breeding, ornamental enhancement, and optimizing pollinator attraction to improve crop yield and ecological sustainability.

Storage Properties of Double-Layer Films Enriched with Phytolacca americana L. Extract as Active Packaging for African Catfish, with a New Approach to Antioxidant Film Assay and Additional Analysis of P. americana Extract Toxicity on Human Cell Lines

Novel double-layer films based on furcellaran (FUR) and gelatin (GEL) with the addition of Phytolacca americana L. (PA) extract were used as active packaging for African catfish fillets. Films with PA extract have been shown to minimize the catfish spoilage effects, expressed as odor reduction compared to control samples; however, neither the films nor the PA extract exhibited antimicrobial activity against tested groups of microorganisms (fungi, lactic acid bacteria, Enterobacterales and psychrotrops) or specified microorganisms (E. coli, S. aureus, S. cerevisiae). The tested films demonstrated antioxidant activity determined by the DPPH, ABTS, FRAP, CUPRAC and Folin-Ciocâlteu methods. Cytotoxicity analysis showed that the PA extract affected tested cell lines (PNT2-prostate epithelial cells, HepG2-human liver cells, HaCaT-normal human keratinocytes and Nty-hori 3-1) only to a small extent-the calculated IC50 values exceeded the maximal tested concentration of 500 µg/mL.

Transcriptomic Analysis of Gibberellin-Mediated Flower Opening Process in Tree Peony (Paeonia suffruticosa)

Gibberellin (GA3) plays a crucial role in regulating the flowering time of tree peony (Paeonia suffruticosa Andr.). However, its function on flower opening after dormancy release remains unclear, and its molecular mechanism need further study. We investigated the effects of exogenous GA3 treatments at 800 mg/L, 900 mg/L, and 1000 mg/L on the flowering process of five-year-old peony plants ('Luhehong') under greenhouse conditions. Our results showed that exogenous GA3 significantly accelerated the flower opening process. Specifically, flower buds treated with 800 mg/L and 900 mg/L GA3 bloomed after 42 and 45 days, respectively. In contrast, all flower buds treated with 1000 mg/L GA3 aborted, while only one flower bud in the control group bloomed after 56 days. Furthermore, analysis of endogenous hormone levels revealed that GA3 treatment rapidly increased endogenous GA3 levels, decreased ABA levels, and gradually increased IAA levels. Transcriptomic analysis of flower buds released from dormancy following GA3 treatment identified multiple key genes involved in the flower opening process of peony. Notably, members of the C2H2, C3H, ERF, bHLH, MYB, bZIP, NAC, and WRKY families showed significant differential expression. Moreover, several key genes involved in GA3, ABA, and IAA hormone signaling pathways were also differentially expressed. Our findings suggested that an appropriate concentration of exogenous GA3 treatment could accelerate the flower opening process in tree peony through multiple pathways, which would provide valuable insights into the molecular mechanisms underlying the gibberellin-mediated flower opening process in tree peony.

LcbHLH107 actively suppresses the expression of LcDFR to repress anthocyanin biosynthesis in Litchi chinensis Sonn

Basic helix-loop-helix (bHLH) proteins have been recognized as activators of anthocyanin in many plant species, but their role as inhibitors of anthocyanin is seldom reported. In this study, LcbHLH107 was identified as a transcription repressor regulating anthocyanin biosynthesis in litchi. LcbHLH107 was up-regulated in the red hairy roots overexpressing LcMYB1, which was the key transcription activator in litchi anthocyanin biosynthesis. Dual luciferase assay and yeast one-hybrid assay confirmed that LcbHLH107 was regulated by LcMYB1. LcbHLH107 could suppresses anthocyanin accumulation through transient transformation in petunia leaves and overexpression in litchi callus. Moreover, LcbHLH107 directly bound to the promoter of LcDFR, and inhibited its expression. Furthermore, protein sequence mutation and functional verification revealed that the EAR motif was essential for the inhibitory function of LcbHLH107. In summary, LcbHLH107 is a repressor that inhibits anthocyanin biosynthesis in litchi, providing a negative feedback mechanism to regulate anthocyanin accumulation at transcriptional level.

Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Lagerstroemia indica petals

BACKGROUND

Lagerstroemia indica is an ornamental plant with high economic and ecological values. However, the mechanism underlying the regulation of L. indica petal color variation remains unclear. We used LC-MS/MS and RNA-seq to uncover the genetic basis of flower colour variation with the help of the metabolome and transcriptome of three varieties with different colored petal, 'Huahai', 'Zhuimeng', 'Zixian'.

RESULTS

A total of 54 anthocyanidins were identified, 11 peonidin derivatives, 10 cyanidin derivatives, 9 delphinidin derivatives, 5 petunidin derivatives, 5 malvidin derivatives, 4 pelargonidin derivatives, 2 procyanidin derivatives, and 8 other flavonoids. Delphinidin-3-O-glucoside, Malvidin-3-O-glucoside, Petunidin-3-O-glucoside were abundant in petals of all three varieties. 28 differentially accumulated metabolites, including peonidin, cyanidins and flavonoids, were common to 'Zixian' vs. 'Huahai' and 'Zhuimeng' vs. 'Huahai'. Malvidin-3-O-glucoside, Peonidin-3-O-glucoside varied greatly among three varieties. A total of 9923 genes were found to be differentially expressed between red and other colored petals. The upregulation of the expression of ANS (LOC116213234), CHI (LOC116194939), CHI (LOC116196656), F3H (LOC116211316), F3'H (LOC116198721), UGT (LOC104445830) and UGT (LOC116210262) in 'Huahai' was consistent with the contents of cyanidin derivatives, delphinidin derivatives, kaempferol derivatives, naringenin, peonidin derivatives and petunidin derivatives. Regarding transcription factors associated with the anthocyanin pthway, the MYB gene family had the highest number of DEGs, followed by the bHLH gene family, bZIP gene family, WRKY gene family, and MADS box gene family.

CONCLUSION

Malvidin-3-O-glucoside and Peonidin-3-O-glucoside may contribute to variation of petal color in the three varieties. The upregulation of ANS, CHI, F3H, F3'H and UGT expression is involved in anthocyanin biosynthesis of the red pigmentation in the L. indica variety. Expression of twelve transcription factor genes has a strongly positive correlation with expression of structural genes. Collectively, our results may facilitate the genetic breeding and cultivation of L. indica with enhanced red pigmentation.

Identification and characterization of anthocyanins' composition and regulatory genes involved in anthocyanins biosynthesis in water dropwort (Oenanthe javanica)

MAIN CONCLUSION

This study showed that anthocyanin was the main pigments related to purple stem and OjUFGT1 is involved in anthocyanin glycosylation in water dropwort. Water dropwort is a kind of aquatic vegetable with many medicinal values. In the study, the green-stem water dropwort 'FQ1H' and purple-stem water dropwort 'Sq013' were selected as plant materials. The anthocyanins composition was determined by UPLC-MS/MS and the transcript profile was analyzed based on RNA-seq in water dropwort. Nine anthocyanins were identified from water dropwort by UPLC-MS/MS. Petunidin and anthocyanin have higher content, which play a crucial role in the formation of purple stem. In total, 20,478 DEGs were identified in the purple stem, which might have a high correlation with anthocyanin accumulation. The expressions of 26 DEGs encoding anthocyanin biosynthesis structural genes were determined. Furthermore, co-expression analysis indicated that many R2R3-MYB and bHLH transcription factors were potentially involved in anthocyanin biosynthesis. In vitro enzyme activity assay showed that glycosyltransferase OjUFGT1 recognizes UDP-galactose as glycosyl donor and converts cyanidin to cyanidin-3-O-galactoside. In summary, these results may facilitate the development of our breeding and utilization for the high-anthocyanin water dropwort in the future.

Differential Analysis of Anthocyanins in Red and Yellow Hawthorn (Crataegus pinnatifida) Peel Based on Ultra-High Performance Liquid Chromatography-Electrospray Ionization Tandem Mass Spectrometry

Anthocyanins constitute the primary pigment components in hawthorn (Crataegus pinnatifida) peel, yet their specific composition and concentration profiles remain poorly characterized. This study employed ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based metabolomics to systematically compare anthocyanin profiles between red-peel (CPR) and yellow-peel (CPY) hawthorn cultivars. Our analysis identified 26 anthocyanin metabolites in CPR and 24 in CPY, with cyanidin-3-O-galactoside and cyanidin-3-O-arabinoside being the predominant compounds in both. Multivariate analysis revealed seven significantly differential metabolites, including cyanidin-3-O-galactoside, cyanidin-3-O-arabinoside, pelargonidin-3-O-galactoside, pelargonidin-3-O-glucoside, pelargonidin-3-O-arabinoside, and peonidin-3-O-galactoside. Notably, all the differential metabolites exhibited reductions in CPY compared to CPR. Chromatic analysis demonstrated that CPR possessed highly significantly lower hue angle values (hab) than CPY (47.7093 ± 4.1706, 83.6427 ± 1.4604, p < 0.01), showing strong negative correlations with key anthocyanins. These findings enhance the scientific understanding of anthocyanin biosynthesis in hawthorn peel and provide a certain reference for the development and utilization of anthocyanins in hawthorn peel.

Metabolic fingerprinting reveals roles of Arabidopsis thaliana BGLU1, BGLU3, and BGLU4 in glycosylation of various flavonoids

Flavonoids are specialized metabolites that play important roles in plants, including interactions with the environment. The high structural diversity of this metabolite group is largely due to enzyme-mediated modifications of flavonoid core skeletons. In particular, glycosylation with different sugars is very common. In this study, the functions of the Arabidopsis thaliana glycoside hydrolase family 1-type glycosyltransferase proteins BGLU1, BGLU3, and BGLU4 were investigated, using a reverse genetics approach and untargeted metabolic fingerprinting. We screened for metabolic differences between A. thaliana wild type, loss-of-function mutants, and overexpression lines and partially identified differentially accumulating metabolites, which are putative products and/or substrates of the BGLU enzymes. Our study revealed that the investigated BGLU proteins are glycosyltransferases involved in the glycosylation of already glycosylated flavonoids using different substrates. While BGLU1 appears to be involved in the rhamnosylation of a kaempferol diglycoside in leaves, BGLU3 and BGLU4 are likely involved in the glycosylation of quercetin diglycosides in A. thaliana seeds. In addition, we present evidence that BGLU3 is a multifunctional enzyme that catalyzes other metabolic reactions with more complex substrates. This study deepens our understanding of the metabolic pathways and enzymes that contribute to the high structural diversity of flavonoids.

The basic helix-loop-helix transcription factor PpeUNE12 regulates peach ripening by promoting polyamine catabolism and anthocyanin synthesis

The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in various plant developmental and biological processes. However, the precise mechanisms by which bHLH TFs regulate fruit ripening warrant further investigation. Polyamine oxidase (PAO) is crucial for polyamine (PA) catabolism and plays crucial roles in fruit ripening. However, the regulatory mechanism of PAO gene expression during fruit ripening remains largely unexplored. In this study, we identified a peach bHLH TF, PpeUNE12, which directly binds to and activates the promoter of PpePAO1. Silencing PpeUNE12 substantially increased PA accumulation and delayed peach fruit ripening, while overexpressing PpeUNE12 decreased PA accumulation and accelerated peach fruit ripening. Additionally, anthocyanin content decreased in PpeUNE12-silenced fruits but increased in PpeUNE12-overexpressing peach fruits compared to the control. RNA-seq and RT-qPCR analyses revealed that the majority of genes involved in anthocyanin biosynthesis, including PpeF3H, PpeCHS, PpeDFR, PpeUFGT and PpeMYB10.1 exhibited down-regulation in fruits with silenced PpeUNE12, while these genes were up-regulated in fruits overexpressing PpeUNE12. Although PpeUNE12 exhibited no direct binding to the promoters of PpeUFGT and PpeMYB10.1, it substantially activated their activity. This investigation is the first to provide evidence that bHLH regulates fruit maturation via promoting both PA catabolism and anthocyanin synthesis. It reveals a novel mechanism of bHLH in regulating fruit ripening and enhances our comprehension of the regulatory mechanism of PA catabolism and anthocyanin synthesis during fruit maturation.

Differential gene expression and metabolic pathways in Toona sinensis: Influence on colour and aroma

Toona sinensis, a plant species renowned for its culinary and medicinal properties, exhibits diverse colour variations that contribute to its aesthetic appeal and commercial value. Understanding the molecular mechanisms underlying colour and aroma traits in Toona sinensis is crucial for breeding programs and quality regulation in agriculture and the food industry. The present investigation included a comprehensive analysis of the transcriptomic and metabolomic profiles of Toona sinensis with different colours, including green, red, and red leaves with green stems. Metabolic analysis revealed that the flavonoid biosynthesis pathway governs the colour distinction between green and red Toona sinensis. The top 10 metabolites influenced by transcriptome include terpenoids (5), heterocyclic compounds (1), phenol (1), ketone (1), aldehyde (1), and alcohol (1). Fifteen highly expressed genes impacted by phenylpropanoid, sesquiterpenoid, and triterpenoid biosynthesis in coloured Toona sinensis. Functional annotation and pathway analysis revealed that terpene metabolites are predominantly synthesized via terpene metabolic pathway, involving eight key gene families. This study underscores the importance of multi-omics approaches in unravelling the genetic and metabolic basis of phenotypic traits in plant species aimed at improving colour, aroma, and nutritional quality in plants and derived products. HIGHLIGHTS: Flavonoid biosynthesis pathway governs the colour distinction between green and red Toona sinensis. The top 10 metabolites influenced by transcriptome include five terpenoids, one heterocyclic compound, one phenol, one ketone, one aldehyde, and one alcohol. Fifteen highly expressed genes impacted by phenylpropanoid, sesquiterpenoid, and triterpenoid biosynthesis in coloured Toona sinensis. Terpene metabolites are predominantly synthesized via the terpene metabolic pathway, involving eight key gene families. The net photosynthetic rate and intercellular CO2 concentration are relatively high in the red Toon sinensis morph.

When the sand blossoms: Phylogeny, trait evolution, and geography of speciation in Linanthus

PREMISE

Understanding how plants successfully diversified in novel environments is a central question in evolutionary biology. Linanthus occurs in arid areas of western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences in blooming time, and variation in life history strategies. We reconstructed the evolutionary history of this genus.

METHODS

We generated restriction-site associated (ddRAD) sequences for 180 individuals and target capture (TC) sequences for 63 individuals, with complete species sampling. Using maximum likelihood and pseudo-coalescent approaches, we inferred phylogenies of Linanthus and used them to model the evolution of phenotypic traits and investigate the genus's geographic speciation history.

RESULTS

Relationships are consistent and well supported with both ddRAD and TC data. Most species are monophyletic despite extensive local sympatry and range overlap, suggesting strong isolating barriers. The non-monophyly of the night-blooming and perennial species may be due to rapid speciation or cryptic diversity. Perenniality likely evolved from annuality, a rare shift in angiosperms. Night-blooming evolved three times independently. Flower color polymorphism is an evolutionarily labile trait that is likely ancestral. No single geographic mode of speciation characterizes this diversification, but most species overlap in range, which suggests that they evolved in parapatry.

CONCLUSIONS

Our results illustrate the complexity of phylogenetic inference for recent radiations, even with multiple sources of genomic data and extensive sampling. This analysis provides a foundation for understanding aridity adaptations, such as evolution of flower color polymorphisms, night-blooming, and perenniality, as well as speciation mechanisms.

MsERF17 Promotes Ethylene-Induced Anthocyanin Biosynthesis Under Drought Conditions in Malus spectabilis Leaves

Drought is an important factor that affects plant anthocyanin biosynthesis. However, the underlying molecular mechanisms remain elusive. Ethylene response factors (ERFs) are pivotal regulators in plant growth and environmental responses, particularly in anthocyanin biosynthesis. This study investigated the leaf colour transition from green to red in Malus spectabilis under drought conditions. This transition was primarily attributed to the accumulation of anthocyanins, specifically cyanidin-3,5-diglucoside and cyanidin-3-O-galactoside. Our findings elucidate the pivotal role of MsERF17 in drought-induced anthocyanin biosynthesis. Biochemical and molecular analyses showed that MsERF17 positively regulates anthocyanin synthesis by binding to promoters of MsbHLH3 and MsF3' H, thereby activating their expression. Moreover, transient overexpression and virus-induced gene silencing of MsERF17 in fruit peel and leaves, respectively, regulated anthocyanin synthesis. The stable transformation of calli further corroborated the positive regulatory function of MsERF17 in anthocyanin biosynthesis. Our results provide novel insights into the mechanism by which MsERF17, induced by ethylene, promotes anthocyanin accumulation through the positive regulation of MsbHLH3 and MsF3'H expression under drought conditions in M. spectabilis leaves.

Genome-wide identification, characterization and expression analysis of the chalcone synthase gene family in Chinese cabbage

BACKGROUND

Chalcone synthase (CHS) is a key rate-limiting enzyme in the flavonoid synthesis pathway. Flavonoids are crucial secondary metabolites that play significant roles in plant growth, development, and stress resistance. The CHS gene (BrCHS) family in Chinese cabbage has not yet been studied.

RESULTS

We identified 10 BrCHS genes distributed across 7 chromosomes in the Chinese cabbage genome. Their encoded proteins all contain the Chal_Sti_Synt_C (PF02797) and Chal_Sti_Synt_N (PF00195) domains and can be classified into two groups based on systematic evolution analysis. These BrCHS genes contain 2-4 exons and numerous cis-acting elements responsive to light, hormones, stress, growth and development in the BrCHS gene promoters. We also revealed that the expression of BrCHS2 and BrCHS8 increased under treatment with methyl jasmonate, salt, or drought stress. Virus-induced gene silencing (VIGS) of BrCHS4 inhibited the expression of BrCHS4 and reduced the flavonoid and anthocyanin contents in leaves.

CONCLUSIONS

Ten BrCHS family genes are present in the genome of Chinese cabbage. These BrCHS genes seemingly maintained similar characteristics and functionalities during evolution. Our results demonstrated that BrCHS4 is involved in flavonoid and anthocyanin accumulation in Chinese cabbage and identified candidate genes for purple Chinese cabbage breeding.

Transcriptome and Metabolome Analyses Reveal the Mechanism of Color Differences in Pomegranate (Punica granatum L.) Red and White Petals

Pomegranate (Punica granatum L.) is an important economic tree, possessing both edible and ornamental value. Flower color is an important ornamental trait of pomegranate, but the color formation pattern and related molecular mechanisms of pomegranate petals are still unclear. In this study, we conducted physiological, transcriptomic, and metabolomic studies on the petals of Tunisia and White pomegranate varieties during the blooming stage. The results showed that compared to White petals, the contents of anthocyanin, carotenoid, and sucrose in Tunisia petals were significantly increased, while the flavonoid content was significantly decreased. Through RNA-seq, 23 DEGs were identified in the anthocyanin synthesis, and 3 DEGs were identified in the carotenoid synthesis. Transcription factor genes such as MYB, bHLH, WRKY, and MADS were identified as key candidates for regulating anthocyanin metabolism. Metabolomic analysis revealed that eight DEMs are associated with anthocyanin synthesis and three DEMs are associated with carotenoid synthesis. In addition, caffeic acid and its derivatives were significantly upregulated in Tunisia petals. In summary, we propose the following hypothesis: the accumulation of anthocyanins and carotenoids is the reason for the red color of Tunisian petals, and the upregulation of structural genes, including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, DFR, ANS, PSY, and LCYB, leads to an increase in their content. Transcription factor genes such as MYB, bHLH, bZIP, MADS, and WRKY may also play a positive role in anthocyanin accumulation. The research results provide a basis for the theory of pomegranate petal color formation.

Structure and evolution of the Forsythieae genome elucidated by chromosome-level genome comparison of Abeliophyllum distichum and Forsythia ovata (Oleaceae)

Abeliophyllum distichum and Forsythia ovata are two closely related ornamental species of the tribe Forsythieae (Oleaceae) native to Korea. Here we report their genomic characteristics, highlighting genetic differences contributing to variations in corolla coloration, genomic variations associated with heterostyly, and the reconstruction of their ancestral karyotypes. Genome comparison revealed that A. distichum had a more compact organization of gene space than F. ovata. Centromeres of both species were enriched in Forsythieae-specific satellite repeats, hAT-Ac and MuLE-MuDR DNA transposons, and OTA-Athila Ty3/Gypsy retrotransposons. Transcriptome analysis revealed spatially differential expression of carotenoid biosynthesis-related genes in A. distichum, with downregulation in the white lobe and upregulation in the yellow base. Genome-wide analysis of structural variation in A. distichum identified retrotransposon insertions in the promoter region of an AGAMOUS homolog in the thrum plant, which showed significant downregulation of the gene compared to the pin plant. Evolutionary analyses suggested that the Oleaceae genomes evolved from 13 ancestral karyotypes via lineage-specific genomic events, including chromosome recombination, rearrangement, and whole-genome duplication followed by diploidization. The divergence of A. distichum and F. ovata was estimated to have occurred 13.87 million years ago during the Miocene epoch.

AoMYB114 transcription factor regulates anthocyanin biosynthesis in the epidermis of tender asparagus stems

Introduction

Asparagus is a valuable vegetable, and its edible part is a tender stem. The color of the tender stem epidermis is an important trait. In particular, purple asparagus is rich in anthocyanins. However, the molecular mechanisms underlying anthocyanin accumulation in purple asparagus remains unclear.

Methods

The white variety 'Jinguan' (JG), the green variety 'Fengdao 2' (FD), and the purple variety 'Jingzilu 2' (JZ) were compared using physiological and transcriptomic analysis. High-performance liquid chromatography and real-time quantitative polymerase chain reaction were employed to detect anthocyanins and validate gene expression.

Results

Cyanidin 3-glucoside and cyanidin 3-rutinoside were detected as the main anthocyanins in JZ. Transcriptome data demonstrated that 4,694 and 9,427 differentially expressed genes (DEGs) were detected in the JZ versus FD and JZ versus JG control groups, respectively. These DEGs were significantly enriched in pathways associated with anthocyanin accumulation, including phenylalanine metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis. A total of 29 structural genes related to anthocyanin biosynthesis were identified. The expression of these structural genes was higher in JZ than in FD and JG, thereby activating the anthocyanin biosynthesis pathway. Additionally, a candidate gene, AoMYB114, was identified based on transcriptomic data. The expression of AoMYB114 was associated with anthocyanin accumulation in different tissues. Further research found that overexpression of AoMYB114 activated the anthocyanin biosynthesis pathway. It promoted leaf pigment accumulation in transgenic Arabidopsis.

Discussion

These findings demonstrate that AoMYB114 positively regulated anthocyanin biosynthesis. This study elucidates the molecular mechanism underlying purple coloration in asparagus. It provides important insights for improving asparagus quality and for breeding high-anthocyanin varieties.

PKS1 involved in anthocyanin accumulation in red-skinned pear fruit

KEY MESSAGE

PcPKS1 can prevent PcCSN5a from acting as an inhibitor of anthocyanin synthesis by binding to PcCSN5a, ultimately leading the accumulation of anthocyanins. Light is a crucial environmental factor that regulates anthocyanin accumulation in plants. However, the molecular mechanisms by which light signals influence anthocyanin accumulation in fruits have not yet been fully elucidated. We identified the differentially expressed gene Pyrus communis PHYTOCHROME KINASE SUBSTRATE 1 (PcPKS1), which is associated with anthocyanin accumulation in plants, in a previous study. Through measurements of the expression of PcPKS1 in 'Starkrimson' and 'Red Bartlett' pear fruit at various developmental stages and in different pear varieties, quantitative and transient expression experiments conducted on red and green skin tissues confirmed the relationship between PcPKS1 and anthocyanin accumulation. Pyrus communis COP9 SIGNALOSOME COMPLEX SUBUNIT 5A (PcCSN5a) protein, which interacts with PcPKS1, was identified from a yeast library screening. The interaction between the two proteins was validated through yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and split-luciferase (Split-LUC) experiments. Subcellular localization and co-localization experiments revealed that PcPKS1 was localized to the cell membrane, whereas PcCSN5a was localized to the cell membrane and nucleus, with PcPKS1 and PcCSN5a co-localized on the cell membrane. Transient expression in strawberry fruit indicated that PcPKS1 positively regulated anthocyanin accumulation, whereas PcCSN5a negatively regulated anthocyanin accumulation and diminished the capacity of PcPKS1 to promote anthocyanin accumulation. This study provides novel insights into the molecular mechanisms underlying light-regulated anthocyanin accumulation in red-skinned pear fruit.

Eco-friendly extension of postharvest longevity in Alstroemeria cut flowers using melatonin and putrescine treatments

Postharvest longevity is the most important factor concerning the commercial value of cut flowers. Alstroemeria 'Amatista' is one of the most valued species for its ornamental appeal and it has been often reported to suffer from premature senescence. The present study was undertaken to establish the efficacy of melatonin (100 and 200 μM) and putrescine (1.5 and 3 mM) as enviro-friendly compounds applied into the vase solution in extending the vase life of cut flowers of Alstroemeria by assessing different physiological parameters. Results showed that melatonin at 100 and 200 μM and putrescine at 1.5 mM significantly extended the flower vase life from 12 to 13 days (control) to 20-21 days. More precisely, both melatonin and putrescine lowered electrolyte leakage (EL) and increased relative water content (RWC), relative fresh weight (RFW), and relative solution uptake (RSU) of flowers. In addition, both compounds enhanced the total anthocyanin content, phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO) activities, and reduced malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) content, which implies the decline in oxidative stress. These results confirm that both melatonin and putrescine act as effective and environmental-friendly exogenous applications to improve postharvest quality and extend the vase life of Alstroemeria cut flowers. The study provides important information for possible applications in the floriculture industry.

Integrated transcriptomic and metabolomic analyses reveal the molecular mechanism of flower color differentiation in Orychophragmus violaceus

Introduction

Orychophragmus violaceus is a popular horticultural plant because of its bright purple flowers that are commonly found in parks and green belts. However, three flower colors (purple, light purple, and white) were observed in the wild-type O. violaceus. The molecular mechanism underlying the formation of these intriguing flower colors remains unknown.

Methods

Here, we combined metabolomics and transcriptomics to identify a pathway cascade leading to anthocyanin biosynthesis associated with flower color formation in O. violaceus.

Results and discussion

A total of 152 flavonoid metabolites were identified based on metabolomic data, most of which were quercetin and kaempferol. Comparative analysis of the metabolites among the three flower samples revealed that two anthocyanins, peonidin-3-glucoside and delphinidin 3-(6''-malonyl-glucoside), are the pigments most likely responsible for the coloration of the petals of O. violaceus. Subsequent transcriptomic analysis revealed 5,918 differentially expressed genes among the three groups of flowers, 87 of which encoded 13 key enzymes in the anthocyanin biosynthetic pathway. Moreover, the high expression of two transcription factors, OvMYB and OvbHLH, in purple flowers suggests their role in the regulation of anthocyanin biosynthesis. By integrating metabolomic and transcriptomic data, OvANS, which encodes anthocyanidin synthase, was significantly upregulated in purple flowers. OvANS is the enzyme responsible for the transformation of colorless leucoanthocyanidins to colored anthocyanidins. This study provides novel insights into the molecular mechanism of flower color development in O. violaceus, laying the foundation for flower color breeding.

Differential Expression of Amaranth AtrDODA Gene Family Members in Betalain Synthesis and Functional Analysis of AtrDODA1-1 Promoter

Betalains differ from anthocyanins, and they cannot coexist in the same plant under natural conditions. The L-DOPA 4,5-dioxygenase encoded by the DODA gene is a key step in the pathway of betalain biosynthesis in Caryophyllales plants. Amaranth is an important resource for the study and extraction of betalains. In order to clarify the function of AtrDODA family genes in betalain biosynthesis, we screened out three AtrDODA family gene members associated with betalains based on a genome database and RNA-seq databases of Amaranthus tricolor. Their characterization and expression pattern were further analyzed. The result of subcellular localization showed that all three AtrDODA members were located in the nucleus. Betacyanin and betaxanthin were promoted by paclobutrazol treatment in the leaves and stems of 'Suxian No.1' (red), while they were inhibited by gibberellin and darkness, which were consistent with the gene expression pattern of AtrDODAs. After heterologous transformation of the AtrDODA1-1 promoter into tobacco with GUS staining analysis, the promoter activity of AtrDODA1-1 of 'Suxian No.1' (red) amaranth was significantly higher than that of 'Suxian No.2' (green) amaranth. Furthermore, we analyzed the promoter activity of AtrDODA1-1 by GUS staining and qRT-PCR after sprayed exogenous MeJA and GA3 on the AtrDODA1-1 promoter transformed tobacco plants. The results showed that AtrDODA1-1 responded to plant hormones. This study could lay a foundation for revealing the biological functions of the amaranth DODA gene family, and provide new clues for the molecular mechanism of betalain synthesis.

Integrated physiological and transcriptomic data revealed the cold-resistant mechanisms in reproductive organs of the 'Jinguang' pear cultivar

The Pyrus spp. (pears) are crucial for the fruit industry; however, low spring temperatures can cause frost damage to their reproductive organs, which poses challenges to the final yields. In this study, we evaluated the response of the flowers and young fruits of the 'Jinguang' pear cultivar to low temperatures from integrated phenotypic, physiological, and molecular approaches. We found that the flowers were less sensitive to low temperatures than the young fruits, of which their over-cooling points were -5.6°C and -5.0°C, respectively. Transcriptomic data showed that the differentially expressed genes from flowers and young fruits compared to the control conditions were primarily involved in the biosynthesis of flavonoids, phenylalanine, and tyrosine. Further weighted gene co-expression network analysis uncovered the core transcription factors that may be potentially involved in the pear cold resistance, including MYB20, WRKY53, and WRKY30. Our findings provide valuable insights and candidate gene resources for further exploration of the molecular mechanisms underlying cold resistance in pear trees.

Metabolomics and Transcriptomics Jointly Explore the Mechanism of Pod Color Variation in Purple Pod Pea

Although the pod color was one of the seven characteristics Mendel studied in peas, the mechanism of color variation in peas with purple pods has not been reported. This study systemically analyzed the difference between two pea accessions with green pods (GPs) and purple pods (PPs) at two pod developmental stages from the metabolome and transcriptome levels, aiming to preliminarily explore the mechanism and of color variation in PPs and screen out the candidate genes. A total of 180 differentially accumulated metabolites (DAMs) belonged to seven flavonoid subgroups and 23 flavonoid-related differentially expressed genes (DEGs) were identified from the analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, respectively. Among the 180 flavonoid metabolites, ten anthocyanin compounds, which were the principal pigments in PPs and might be the major reason for the purple color formation, were significantly up-accumulated in both of the different pod development stages of PPs. A transcriptome analysis revealed that eight genes encoding enzymes (C4H, CHI, F3H, F3'H, F3'5'H, DFR, ANS, and FLS) involved in the flavonoid synthesis pathway were significantly upregulated in PPs and finally resulted in the significant accumulation of flavonoid and anthocyanin metabolites. The joint analysis of two omics and a weighted gene co-expression network analysis (WGCNA) also screened out that the WD-40 protein-encoding gene, one WRKY and three MYB transcription factor genes exhibited significant upregulation in PPs, and highly correlated with several structural genes in flavonoid synthesis pathways, indicating that these genes are involved in the regulation of pod color formation in PPs. Overall, the results of this study first explored the mechanism underlying the purple color variation between PPs and GPs, and then preliminarily screened out some candidate genes responsible for the pod color formation in PPs.

The inhibition effect of high temperature stress on potato tuber skin coloring mainly occurred in the belowground part of the plant

High temperature stress leads to a dramatic reduction of both the anthocyanin concentration and the appearance quality of colored potatoes. However, it remains uncertain if the high temperature impacts potato tuber skin coloring through only the aerial or belowground parts of the plant, or through their interaction; and it's underlying reason is still unclear. In this study, the red-skin cultivar Qingshu9 (Qs9) was exposed to the high-temperature (30 °C) treatment on the belowground part alone (BH), aerial part alone (AH) and entire plant (EH), and the normal-temperature treatment on entire plant (EN) as control. The results indicated that the total anthocyanin content in tuber skin of the BH treatment was significantly lower than the EN and AH treatment, and there was no accumulation of cyanidin and pelargonidin in BH treatment, only peonidin. Compared with the EN treatment, the decrease rate of total anthocyanin content of the AH treatment was much smaller than the BH treatment, and the composition of anthocyanin did not change. Transcriptome analysis showed the downregulated DEGs of BH vs EN, BH vs AH and AH vs EN were significantly associated with the anthocyanin synthesis and metabolism pathway. High temperature inhibited anthocyanin synthesis by reducing the expression of key genes (StPAL, StF3H, StF3'H, StF3'5'H, StDFR and StANS) in the anthocyanin synthesis pathway. In summary, high temperature inhibits anthocyanin synthesis in tuber skin by downregulating key genes, and this inhibitory effect mainly occurs through the belowground part of the plant.

Lily (Lilium spp.) LhERF061 suppresses anthocyanin biosynthesis by inhibiting LhMYBSPLATTER and LhDFR expression and interacting with LhMYBSPLATTER

Ethylene has an essential function in the biosynthesis of anthocyanin. However, the molecular mechanism through which ethylene impacts the color of lily flower remains little appreciated. This study identified LhERF061, a dehydration-responsive element-binding (DREB family) transcription factor that suppresses anthocyanin biosynthesis in response to ethylene in lilies. Transient LhERF061 overexpression caused a dramatic decrease in anthocyanin levels and downregulated both anthocyanin structural genes and positive regulators in lily tepals. Heterologous LhERF061 expression in Arabidopsis and tobacco also suppressed anthocyanin accumulation. Mechanistically, LhERF061 was found to bind to the promoters of LhMYBSPLATTER (a positive regulator of the biosynthesis of anthocyanin) and LhDFR (an anthocyanin structural gene), thereby inhibiting their transcriptional activity. Further investigation indicated that LhERF061 physically interacted with LhMYBSPLATTER, thereby interfering with the MYB-bHLH-WD40 (MBW) complex responsible for anthocyanin regulation, providing multiple mechanisms for inhibiting the biosynthesis of anthocyanin. These results provide insights into how ethylene mediates the biosynthesis of anthocyanin and increase understanding of the regulatory network of the biosynthesis of anthocyanin in lily.

DcWRKY15 positively regulates anthocyanin biosynthesis during petal coloration in Dianthus caryophyllus

Petal pigmentation in carnations is closely associated with the biosynthesis of anthocyanins. This biosynthetic process is tightly regulated by transcription factors, which activate or repress key genes involved in anthocyanin production. Here, we aim to explore the mechanisms involved in the transcriptional regulation of anthocyanin biosynthesis in carnation petals. We identified DcWRKY15 as a critical regulator influencing anthocyanin production in these petals. DcWRKY15 expression showed a strong correlation with the expression levels of genes associated with anthocyanin biosynthesis, peaking during early petal development stages. The findings from the dual-LUC, VIGS, Y1H and EMSA assays demonstrated that DcWRKY15 played a positive regulatory role in anthocyanin biosynthesis. DcWRKY15 achieved this by binding directly to the promoters of DcCHS and DcF3H, thereby enhancing their expression. Additionally, DcWRKY15 interacts with the repressor DcMYB2, which reduces its capacity to enhance anthocyanin biosynthesis, particularly during the later stages of petal development. These findings offer new insights into the molecular mechanisms responsible for petal coloration in carnations, highlighting the complex interplay between activator and repressor transcription factors.

PyWRKY40 negatively regulates anthocyanin synthesis in pear fruit

The deposition of anthocyanin plays a crucial role in fruit pigmentation and serves as the primary determinant of pear quality. Various factors influence the synthesis of anthocyanins, with salicylic acid playing a significant role among them. However, the mechanism by which salicylic acid affects anthocyanin synthesis remains unclear. Our study identifies the transcription factor PyWRKY40 as a pivotal regulator of SA-mediated anthocyanin synthesis in the nucleus. The negative regulatory function of this factor lies in its ability to suppress anthocyanin synthesis, thereby exerting an influence on fruit coloration. We have confirmed the direct binding of PyWRKY40 to the PyDFR promoter through Y1H and EMSA experiments. The findings elucidate a signaling regulatory module, PyWRKY40-PyDFR, which is responsive to SA and enhances fruit pigmentation by modulating anthocyanin metabolism. This insight offers a viable approach to enhancing fruit coloration and improving the overall quality of pear fruits.

BAHD acyltransferase from dragon fruit enables production of phyllocactin in engineered yeast

Microbial fermentation can provide a sustainable and cost-effective alternative to traditional plant extraction to produce natural food colours. Betalains are a class of yellow to red water-soluble pigments. Even though over 80 betalain variants are known, betanin is the only betalain available as a food colourant on the market. Many variants are acylated, which can enhance their stability and change the hue, but very few acyltransferases responsible for the acylation are known. Therefore, we mined the transcriptomes of Celosia argentea var. cristata and Hylocereus polyrhizus for BAHD acyltransferases, enzymes likely involved in betalain acylation. In vivo screening of the enzymes in betanin-producing Saccharomyces cerevisiae revealed that the acyltransferase HpBAHD3 from H. polyrhizus malonylates betanin, forming phyllocactin (6'-O-malonyl-betanin). This is the first identification of a BAHD acyltransferase involved in betalain biosynthesis. Expression of HpBAHD3 in a Yarrowia lipolytica strain engineered for high betanin production led to near-complete conversion of betanin to phyllocactin. In fed-batch fermentation, the strain produced 1.95 ± 0.024 g/l phyllocactin in 60 h. This study expands the range of natural food colourants produced through microbial fermentation and contributes to elucidating the biosynthesis pathway of acylated betalains.

Oleraceins from Portulaca oleracea leaves: Quali-quantitative determination and antioxidant potential

Portulaca oleracea L. (purslane) is a spontaneous herb whose shoots are appreciated in the Mediterranean and Asian diets for their fresh flavor and crunchy texture. In addition to PUFA (PolyUnsaturated Fatty Acids), it contains unusual polyphenolic alkaloids called oleraceins. This work aimed at investigating the oleracein profile of different 'green' extracts of the leaves of Portulaca oleracea and evaluating their antioxidant capacity. An LC-MS screening of different extracts revealed the infusion as the extract richest in oleraceins. Qualitative and quantitative analysis of oleraceins in this extract resulted in the identification of three polyphenolic alkaloids never reported before and in the definition of oleracein A as the most abundant alkaloid. An oleracein-enriched fraction from the infusion and its hydrolysed derivative exhibited radical scavenging activity in vitro and led to activation of the Nrf2 pathway in cells without apparent cytotoxicity. Thus, its oleracein content may make purslane a potential nutraceutical for alleviating redox distress.

Emerging Trends in Secondary Metabolite Research in Caryophyllales: Betalains and Their Roles in Plant Adaptation and Defense Mechanisms

Betalains, a distinctive group of nitrogen-containing pigments exclusive to the Caryophyllales order, possess diverse biological activities such as antioxidant, anti-inflammatory, and antimicrobial properties, making them highly valuable for applications in food, nutraceutical, and pharmaceutical industries. This Review provides a comprehensive analysis of betalain biosynthesis, structural diversity, and ecological significance, highlighting their roles in enhancing stress resilience, adaptation mechanisms, and plant evolutionary strategies. The evolutionary development of betalains is explored, revealing their emergence through gene duplication events and providing insights into their mutual exclusivity with anthocyanins. This study utilizes comparative genetics and advanced molecular tools to uncover the intricate regulatory networks involving transcription factors such as MYB, bHLH, WRKY, and SPL, which govern betalain biosynthesis. Furthermore, the Review discusses innovative transgenic studies that introduce betalains into non-native species, demonstrating their potential to enhance stress tolerance and boost agricultural productivity. While significant progress has been made in understanding betalain biosynthesis pathways, the evolutionary relationships with anthocyanins and the specific ecological functions of betalains in plants remain areas of ongoing exploration. Future research directions include integrating chemotaxonomic studies, molecular phylogenetics, and multiomics approaches to unravel the full spectrum of betalain functions and regulatory mechanisms. Such studies are essential to deepening our understanding of these vibrant pigments and their evolutionary implications, offering new opportunities for biotechnological innovations and sustainable agricultural practices. This Review stands out by combining genetic, ecological, and evolutionary perspectives, providing novel insights into the multifunctionality of betalains and their potential to drive future advancements in plant science and biotechnology.

3'-Caffeoylquercetin Glycosides and 4'-Caffeoylkaempferol Glycosides-Novel Antioxidant Flavonoids Discovered in the Freesia Yellow Flowers

The petals of flowering plants should retain unique antioxidants that have not been found in the fruits, as the petals need to stay open to attract pollinators against photooxidation and devise a solution to avoid eating attacks. We reported that the yellow petals of freesia cultivars (Freesia x hybrida) accumulated original apocarotenoids, mono- and di-neapolitanosyl crocetin. Here, in the yellow petals, we discovered eight novel flavonoids by their structural determination, including four 3'-caffeoylquercetin 3,7-glycosides, one 3'-caffeoylquercetin 3-glycoside, and three 4'-caffeoylkaempferol 3,7-glycosides. The 3-carbon sugar part was a minor hexose dimer [D-glucosyl-D-glucoside or D-glucosyl-L-rhamnoside] with the β1,2-linkage, while the 7-carbon was usually O-glycosylated with D-glucose, L-rhamnose, or D-glucuronic acid. Such caffeoyl-flavonol glycosides were also present in freesia white petals, regardless of the cultivars and wild species. When dihydroflavonols, the last common precursors between flavonols and anthocyanins, switch to the flavonol route, these caffeoyl-flavonol glycosides are likely to be synthesized via quercetin or kaempferol. All the eight flavonoids exerted in vitro antioxidant activities against both lipid peroxidation and radical generation. Specifically, 3'-caffeoylquercetin 3-sophoroside and its 7-glucuronide showed superior antioxidant activity. Freesia yellow and white flowers have been utilized as edible flowers, indicating the importance of evaluating the human benefits and risks of newly identified flavonoids.

Regulation of Flavonoid Biosynthesis by the MYB-bHLH-WDR (MBW) Complex in Plants and Its Specific Features in Cereals

Flavonoids are a large group of secondary metabolites, which are responsible for pigmentation, signaling, protection from unfavorable environmental conditions, and other important functions, as well as providing numerous benefits for human health. Various stages of flavonoid biosynthesis are subject to complex regulation by three groups of transcription regulators-MYC-like bHLH, R2R3-MYB and WDR which form the MBW regulatory complex. We attempt to cover the main aspects of this intriguing regulatory system in plants, as well as to summarize information on their distinctive features in cereals. Published data revealed the following perspectives for further research: (1) In cereals, a large number of paralogs of MYC and MYB transcription factors are present, and their diversification has led to spatial and biochemical specialization, providing an opportunity to fine-tune the distribution and composition of flavonoid compounds; (2) Regulatory systems formed by MBW proteins in cereals possess distinctive features that are not yet fully understood and require further investigation; (3) Non-classical MB-EMSY-like complexes, WDR-independent MB complexes, and solely acting R2R3-MYB transcription factors are of particular interest for studying unique regulatory mechanisms in plants. More comprehensive understanding of flavonoid biosynthesis regulation will allow us to develop cereal varieties with the required flavonoid content and spatial distribution.

Integrated Genetic Diversity and Multi-Omics Analysis of Colour Formation in Safflower

Safflower (Carthamus tinctorius L.) is a medicinal and edible cash crop that is widely cultivated worldwide. However, the genetic diversity of safflower germplasm resources and the reasons for the variations in safflower flower colour remain unclear. In this study, we used a combination of agronomic traits and Indel markers to assess the genetic diversity of 614 safflower germplasm resources. The results showed that most of the evaluated agronomic traits had high variability. The mean values of the Shannon's information index (I) and polymorphism information content (PIC) in 50 pairs of Indel markers were 0.551 and 0.296, respectively. The population structure, neighbour-joining phylogeny, and principal coordinate analyses classified all genotypes into four subgroups, and 214 safflower core germplasms were constructed. Multiple analyses of genetic diversity parameters, range conformity, and the percentage of variance difference showed that the core germplasm did not differ significantly and could represent the original germplasm better. Transcriptome and metabolome analyses revealed that flavonoid synthesis-related genes, including CHS, F3H, ANS, and BZ1, were differentially expressed in different coloured safflowers. Most significantly, different genes and metabolite compounds in white safflowers were enriched upstream from the phenylpropanoid metabolic pathway to the production of naringenin, whereas those in red safflowers were concentrated in the downstream pathway from eriodictyol. Meanwhile, the preliminary quantification of anthocyanins and carotenoids extracted from red, orange, and white types of safflower showed that the level of both anthocyanins and carotenoids were highest in red types. This work provides new insights into the formation of different safflower flower colours and in the conservation and management of safflower germplasm.

Fade into you: genetic control of pigmentation patterns in red-flesh apple (Malus domestica)

The genetic basis of type 1 red-flesh color development in apple (Malus domestica) depends upon a particular allele of the MdMYB10 gene. Interestingly, type 1 red-flesh apples are fully red after fruit set, but anthocyanin pigmentation in apple fruit cortex may decrease during fruit growth and maturation, leading to variable red patterning and intensities in the mature cortical flesh. We developed a histogram-based color analysis method to quantitatively estimate pigmentation patterns. This methodology was applied to investigate the phenotypic diversity in four hybrid F1 families segregating for red-flesh color. Pigmentation patterns were found to be heritable allowing the identification of a new locus by QTL analysis. To further investigate the mechanisms involved in the spatial deposition of anthocyanin, metabolome, transcriptome and methylome comparisons between white and red flesh areas within the red-flesh genotype cv. 'R201' exhibiting flesh pigmentation patterns, was performed. Wide-targeted analysis showed that white-flesh areas accumulate more dihydrochalcones and hydroxycinnamic acids than red-flesh areas while red-flesh areas accumulate more flavonoids. Anthocyanin biosynthesis genes and anthocyanin positive regulators (MBW complex) were up-regulated in red-flesh areas, while a reduction in anthocyanin storage, transport and stability (increase of pH, down-regulation of MdGSTU22) and an increase in phenolic catabolism were concomitant with color fading process in white-flesh areas. Expression of MdGSTU22 was linked to a differentially methylated region (DMR) suggesting a potential environmental effect on the epigenetic control of gene expression involved in color fading. Altogether, these results provide the first characterization and functional identification of color fading in apple fruit flesh.

Integrative Omics Analysis Reveals Mechanisms of Anthocyanin Biosynthesis in Djulis Spikes

Djulis (Chenopodium formosanum Koidz.), a member of the Amaranthaceae family plant, is noted for its vibrant appearance and significant ornamental value. However, the mechanisms underlying color variation in its spikes remain unexplored. This research initially detected the anthocyanin content at different developmental stages of the spike and subsequently utilized an integrative approach, combining targeted metabolomics, transcriptomics, and untargeted metabolomics analyses, to elucidate the mechanisms of anthocyanin biosynthesis in the spikes of djulis. The results of the combined multi-omics analysis showed that the metabolites associated with anthocyanin synthesis were mainly enriched in the flavonoid biosynthesis pathway (ko00941) and the anthocyanin biosynthesis pathway (ko00942). With the maturation of djulis spikes, a total of 28 differentially expressed genes and 17 differentially expressed metabolites were screened during the transition of spike color from green (G) to red (R) or orange (O). Twenty differentially expressed genes were selected for qRT-PCR validation, and the results are consistent with transcriptome sequencing. The upregulation of seven genes, including chalcone synthase (CfCHS3_1, CfCHS3_2, CfCHS3_3), flavanone 3-hydroxylase (CfF3H_3), flavonoid 3'5'-hydroxylase (CfCYP75A6_1), dihydroflavonol reductase (CfDFRA), and glucosyltransferase (Cf3GGT), promotes the formation and accumulation of delphinidin 3-sambubioside and peonidin 3-galactoside. The research results also showed that anthocyanins and betalains can coexist in the spike of djulis, and the reason for the change in spike color during development may be the result of the combined action of the two pigments. A possible regulatory pathway for anthocyanin biosynthesis during the spike maturation was constructed based on the analysis results. The results provide a reference and theoretical basis for further studying the molecular mechanism of anthocyanin regulation of color changes in Amaranthaceae plants.

From White to Reddish-Brown: The Anthocyanin Journey in Stropharia rugosoannulata Driven by Auxin and Genetic Regulators

Stropharia rugosoannulata, or wine-cap Stropharia, is a well-known edible mushroom cultivated globally. The pileipellis color is a crucial quality attribute of S. rugosoannulata, exhibiting significant variation throughout its developmental stages. However, the pigment types and regulatory mechanisms behind color variation remain unclear. The metabolome analysis found that the anthocyanin biosynthesis pathway was significantly enriched and anthocyanins accumulated steadily in fruiting bodies during three developmental stages. The pileipellis pigment was extracted, and HPLC-MS confirmed the presence of anthocyanins. Notably, significant differences in anthocyanin content were observed among the various colored varieties. Thus, anthocyanins contribute to the pileipellis color of S. rugosoannulata. Through further investigation, this study elucidated, for the first time, the relationship between the "SrNFYA-SrDRF2" regulatory module and anthocyanin accumulation. Combined multiomics assays and HPLC analysis revealed that auxin functions as a signaling molecule that regulates the accumulation of anthocyanins in the pileipellis. Subsequently, the hub gene of anthranilate synthase for auxin synthesis was identified as SrTRP1, and the transcription factor SrMYB1 was verified as a regulator of SrTRP1, influencing auxin accumulation. These findings provide a valuable resource for the targeted enhancement of the quality of S. rugosoannulata.

Comparative transcriptome and metabolome analysis of sweet potato (Ipomoea batatas (L.) Lam.) tuber development

Introduction

Sweet potato is an important food, feed and industrial raw material, and its tubers are rich in starch, carotenoids and anthocyanins.

Methods

To elucidate the gene expression regulation and metabolic characteristics during the development of sweet potato tubers, transcriptomic and metabolomic analyses were performed on the tubers of three different sweet potato varieties at three developmental stages (70, 100, and 130 days (d)).

Results

RNA-seq analysis revealed that 16,303 differentially expressed genes (DEGs) were divided into 12 clusters according to their expression patterns, and the pathways of each cluster were annotated. A total of 9118 DEGs were divided into three categories during the same developmental period. A total of 1566 metabolites were detected, which were mainly divided into 12 categories. DEGs and differentially regulated metabolites (DRMs) were significantly enriched in the starch and sucrose metabolism and flavonoid biosynthesis pathways. The DEGs associated with the flavonoid pathway showed greater expression with the development of tubers, with the highest expression occurring at 130 d; chalcone isomerase (CHI) was a key gene associated with 11 flavonoid compounds. The DEGs associated with the starch pathway presented relatively low expression during the development of tubers, with the highest expression occurring at 70 d; UDP-glucose pyrophosphorylase 2 (UPG2) and glycogen synthase (glgA) were able to regulate the key genes of 8 metabolites related to the starch biosynthesis pathway. The anthocyanin content is directly related to changes in the content of peonidin-3-O-(6"-O-feruloyl)sophoroside-5-O-glucoside, which is regulated by the IbCHI gene. The abundance of this starch is directly related to changes in the content of D-glucose 6-phosphate and is regulated by the IbUGP2 and IbglgA genes. A total of 14 candidate genes related to starch, carotenoids and anthocyanins in sweet potato tubers, including the IbCHI, IbUGP2 and IbglgA genes, were identified via weighted correlation network analysis (WGCNA).

Conclusion

This research provides fresh insights into the levels of anthocyanins, starch, and carotenoids throughout the growth of sweet potato tubers and sheds light on the potential regulatory pathways and candidate genes involved in this developmental progression.

MdFC2, a ferrochelatase gene, is a positive regulator of ALA-induced anthocyanin accumulation in apples

5-Aminolevulinic acid (ALA), a key biosynthetic precursor of tetrapyrrole compounds, significantly induces anthocyanin accumulation in apple (Malus × domestica Borkh.) as well as other fruits. Although the molecular mechanisms of ALA-induced anthocyanin accumulation have been reported, it remains unknown whether the metabolism of ALA is involved in ALA-induced anthocyanin accumulation. Here, we found that MdFC2, a gene encoding ferrochelatase (MdFC2), which catalyzes the generation of heme from protoporphyrin lX (PPIX), may play an important role in ALA-induced apple anthocyanin accumulation. Exogenous ALA induced the MdFC2 expression as well as anthocyanin accumulation in apple leaves, calli, and isolated fruits. MdFC2 overexpression in apple leaves or calli significantly enhanced anthocyanin accumulation as well as the expression of genes involved in anthocyanin biosynthesis, while RNA interference MdFC2 inhibited anthocyanin accumulation and the expression of genes involved in anthocyanin biosynthesis. When 2,2'-dithiodipyridine, an inhibitor of MdFC2, was added, ALA-induced anthocyanin accumulation was blocked. These results suggest that ALA-induced anthocyanin accumulation of apple may be regulated by heme or its biosynthesis, among which MdFC2 or MdFC2 may play a critical positive regulatory role. This finding provides a novel insight to explore the mechanisms of ALA-regulating physiological processes and better application of ALA in high-quality fruit production.