Unraveling the Regulatory Mechanism of Color Diversity in Camellia japonica Petals by Integrative Transcriptome and Metabolome Analysis

Spatial and Temporal Regulation of Flower Coloration in Cymbidium lowianum

Flower color is a crucial trait that attracts pollinators and determines the ornamental value of floral crops. Cymbidium lowianum, one of the most important breeding parent of Cymbidium hybrids, has two flower morphs (normal and albino) that differ in flower lip color. However, the molecular mechanisms underlying flower color formation in C. lowianum are not well understood. In this study, comparative metabolomic analysis between normal and albino flower lip tissues indicated that cyanidin-3-O-glucoside content was significantly higher in red epichiles than in other lip tissues. This finding suggests that cyanidin-3-O-glucoside is responsible for color variation and differentiation in the lip in C. lowianum. We also found that red coloration in C. lowianum flower is correlated with high levels of F3'H expression; further, anthocyanins, carotenoids and chlorophyll coordinate to influence sepal and petal coloration during flower development. In transgenic Arabidopsis lines, overexpression of F3'H increased anthocyanin concentration, overexpression of BCH increased carotenoid concentration, whereas overexpression of HEMG and CHLI both increased chlorophyll concentration. Identification and assessment of several transcription factors revealed that MYB308-1 activates BCH, MYB111 and PIF4-2 activate HEMG and CHLI expression during flower development. Importantly, MYB14-1 shows interaction with PIF4-2, and appears to act as a connector between anthocyanin and chlorophyll biosynthesis by either activating F3'H expression or inhibiting CHLI expression. These results indicate that, in C. lowianum, variation in flower color and differentiation of lip color patterns are primarily regulated by the types and concentrations of flavonoids; further, carotenoids and chlorophyll also influence flower coloration during development.

Integration of transcriptome, metabolome and high-throughput amplicon sequencing reveals potential mechanisms of antioxidant activity and environmental adaptation in the purple-leaf phenotype of Coffea cultivars

To understand its potential in meeting the increasing market demand for high-quality and resistant coffee varieties., the study focused on evaluating a leaf color mutation in Coffea arabica L. (purple coffee) and comparing it with the control (Catimor). Analysis of antioxidant indices revealed that purple coffee exhibited significantly higher levels of TAC (total anthocyanin content), DPPH (2,2-dyphenyl-1-picrylhydrazyl), POD (peroxidase), and PPO (polyphenol oxidase) compared to Catimor, indicating stronger antioxidant activities. Multi-omics analysis was conducted to create metabolic profiles, genetic maps, and phyllosphere microbial communities of the two Coffea genotypes. The metabolome and transcriptome results showed higher levels of flavonoids and phenolic acids in purple coffee, along with different gene expression patterns. The up-regulation of key genes in the phenylpropanoid pathway was identified to result in a notable alteration in the accumulation of flavonoids and phenolic acids. The co-occurrence network analysis of bacterial communities identified 10 keystone OTUs (operational taxonomic units), including Methylobacterium-Methylorubrum, 1174-901-12, Massilia, Comamonas, Klenkia, and Salinicola, all of which are Proteobacteria. The results of the co-analysis demonstrated a strong correlation between keystone OTUs and both phenylpropanoid metabolism and antioxidant activity. Taken together, we hypothesize that the up-regulation of key genes in the phenylpropanoid metabolite pathway in purple coffee facilitates the synthesis of flavonoids and phenolic acids, which suppresses the abundance of microbial taxa and thus enhances antioxidant activity and environment adaptability. These findings provide valuable insights for future research on the environmental adaptation of coffee and hold potential in breeding high flavonoid content coffee leaf tea.

Genome-Wide Characterization of WRKY Gene Family in Camellia chekiangoleosa Identifies Potential Regulatory Components in Pigment Biosynthesis Pathways

The WRKY gene family is essential for controlling a variety of plant physiological functions, yet the involvement of specific WRKY members in pigment biosynthesis and accumulation in Camellia chekiangoleosa remains unexplored, particularly in anthocyanins and carotenoids, which play crucial roles in the pigmentation of C. chekiangoleosa. This study systematically identified 87 WRKY genes across 15 chromosomes in C. chekiangoleosa through bioinformatic approaches. Further structural and phylogenetic analyses of these TFs enabled their classification into six different subgroups. WRKY family expansion was shown to be mostly driven by tandem duplication. W-box elements, which can be binding sites for WRKY transcription factors, were present in a number of biosynthetic genes in the pigment production pathway. Yeast one-hybrid assay confirmed that five WRKY transcription factors (CchWRKY15/24/33/47/76) directly bind to the promoter regions of two key biosynthetic genes, CchPSY1 and Cch4CL1. Intriguingly, among the five WRKYs tested, the expression levels of CchWRKY15, CchWRKY33, and CchWRKY47 showed the strongest positive associations with flavonoid accumulation (p < 0.05, Pearson correlation analysis).These findings provide novel insights into the evolutionary patterns, transcriptional regulation, and functional characteristics of CchWRKYs, while elucidating their possible regulatory mechanisms in the fruit coloration of C. chekiangoleosa.

Benzalkonium chloride disinfection increases the difficulty of controlling foodborne pathogens identified in aquatic product processing

Benzalkonium chloride (BAC) has been widely used as disinfectant in food processing, whereas there is still largely unknown concerning its profound and/or reverse effects on the pathogens control. This study was aimed to assess the effects of BAC disinfection on the controlling difficulty of foodborne pathogens, by investigating the growth rate, micromorphology, biofilm characteristics, and antibiotic resistance. The results showed that two pathogenic strains, identified as Proteus vulgaris PV29 and Bacillus cereus BC30, were residually remained on the processing utensils after BAC disinfection. Moreover, compared with the parent cells, the micromorphology of the subcutured cells under BAC stress changed, while final cell densities of P. vulgaris PV29 and B. cereus BC30 increased by 106 % and 18 %, respectively. In addition, the BAC-adapted cells formed more obvious and denser biofilms, within which the cell density doubled at most. Even worse, antibiotic resistance of the both strains to common antibiotics (including vancomycin, sulfamethoxazole, mezlocillin sodium, and minocycline) increased after prolonged BAC-adaption. In sum, the present study verified increased difficulty to control the foodborne pathogens of P. vulgaris PV29 and B. cereus BC30 with regular BAC disinfection, and enlighten future assessment on the potential risks of BAC disinfection.

Plant Tannase: Evolutionary and Functional Divergence Features

In plants, α/β-hydrolase regulates the hydrolysis of ester compounds, enriching the types and functions of specialized metabolites. In this study, three genes─CsCSE, CsCXE3, and CsTA─which encode caffeoyl shikimate esterase (CSE), carboxylesterase (CXE), and tannase (TA), respectively, were isolated from the tea plant genome through multiomics correlation analysis. Evolutionary analysis showed that CSE and CXE were ancient, whereas TA emerged in core eudicots approximately 120 million years ago. Enzyme activity assays revealed that CsCSE and CsCXE3 catalyze phenolic acid and acetate ester hydrolysis, respectively. Interestingly, CsTA not only has the catalytic function of CsCSE and CsCXE3 but also catalyzes the hydrolysis of galloylated catechin, hydrolyzable tannin, and hormone ester. Overall, CsTA is a newly derived α/β-hydrolase with evolutionary and functional divergence features. This study expands our understanding of the physiological significance of plant TA and provides insights into the potential role of CsTA in the complex metabolic processes of tea plants.

Metabolome and transcriptome analysis of anthocyanin biosynthesis reveal key metabolites and candidate genes in red-stemmed alfalfa (Medicago sativa)

BACKGROUND

Alfalfa (Medicago sativa L.) serves as a vital high-quality forage resource, especially in tropical and subtropical regions where there is a deficiency of protein-rich feed. The red pigmentation of stem of space mutated alfalfa was mainly caused by anthocyanin accumulation. However, investigations into the mechanisms governing anthocyanin biosynthesis in alfalfa stems have been scarce.

RESULT

In this study, we conducted combined transcriptome and metabolome analyses on two types of alfalfa stems: space mutation red-stemmed alfalfa and non-space mutation green-stemmed alfalfa (control). Profiling of the anthocyanin metabolome unveiled 45 metabolites linked to anthocyanin biosynthesis, with cyanidin-3-O-glucoside, pelargonidin-3-O-arabinoside, delphinidin-3-O-(6-O-acetyl)-glucoside, and kaempferol-3-O-rutinoside identified as the primary anthocyanins of red-stemmed alfalfa. Transcriptome analysis revealed 72 differentially expressed genes related to anthocyanin biosynthesis pathways, of which 54 genes were highly expressed in red stems, including 12 PALs (phenylalanine ammonia-lyase), 22 4CLs (4-coumaroyl: CoA-ligase), eight CHSs (chalcone synthase), three F3Hs (flavanone 3-hydroxylase), two ANRs (anthocyanidin reductase), three DFRs (dihydroflavonol-4-reductase), three ANSs (anthocyanidin synthase), and one FLS (flavonol synthase) gene. These genes are likely pivotal for anthocyanin biosynthesis in red-stemmed. Co-expression analysis of differentially expressed genes and relative contents of differentially expressed anthocyanin showed that each anthocyanin was closely related to multiple genes, and anthocyanin accumulation process was regulated by multiple genes. The expressions of these genes were significantly positively correlated with the relative contents of cyanidin-3-O-glucoside, pelargonin-3-O-arabinoside, and kaempferol-3-O-rutin.

CONCLUSION

Overall, the expression patterns of PAL, 4CL, CHS, F3H, ANR, DFR, ANS, and FLS structural genes in anthocyanin biosynthesis pathway were closely related to the composition and content of anthocyanins. Different anthocyanins' accumulation patterns may result in the different stem colors of alfalfa. These findings provide comprehensive insights into the molecular mechanisms for anthocyanin biosynthesis in red-stemmed alfalfa.

Metabolomic and Transcriptomic Analyses Reveal the Factors Underlying Mature Fruit Pericarp Color Variations in the 'Xinli No. 7' Pear (Pyrus sinkiangensis)

Background/Objectives: The 'Xinli No. 7' pear is a new pear variety with the advantages of early ripening, high quality, high storage resistance, and a long shelf life. Peel color is an important appearance-related trait and an important indicator of fruit quality and commercial value. Methods: In this study, we investigated the polyphenol compound biosynthesis metabolic pathway in the fruit pericarp of 'Xinli No. 7' pear using metabolomic and transcriptomic approaches, and qRT-PCR was used for the relative expression analysis of 21 DEGs associated with flavonoid biosynthesis. Results: A total of 128 phenolic compounds were identified, along with 1850 differently expressed genes (DEGs) in peels of different colors. Caftaric acid, apigenin, astragalin, phlorizin, prunin, taxifolin, rutin, naringenin, and their derivatives were abundant in the peel of 'Xinli No. 7' pear. An integrated analysis of transcriptomic and metabolomic data revealed that one PGT1, one LAR, two ANS, three 4CL, one CHS, one DFR, and one CHI gene involved in flavonoid biosynthesis exhibited markedly different expression levels in the fruit pericarp of 'Xinli No. 7' pear. Metabolic profiling of pear skin led to the identification of polyphenol substances involved in the flavonoid biosynthetic process and revealed 16 flavonoid compounds with high accumulation in pear fruit with red skin (PR). Notably, MYBs (25), bHLHs (18), WRKYs (15), NACs (15), ERFs (15), and MADs (2) may also contribute to the accumulation of flavonoid metabolites and the biosynthesis of anthocyanins in the peel of 'Xinli No. 7'. Conclusions: Therefore, our results demonstrate the key role of phenolic compounds and candidate transcription factors involved in the peel color formation of 'Xinli No. 7' pear fruit.

Integrated Metabolomics and Transcriptome Analysis of Anthocyanin Biosynthetic Pathway in Prunus serrulata

Prunus serrulata is an important landscape tree species whose flower color has high ornamental value. However, the molecular mechanisms regulating flower color in P. serrulata remain unclear. By studying the metabolomics and transcriptomics of three different color varieties under the species lineage of P. serrulata, 'Eigeng' (EG, white), 'Albo-rosea' (AR, pink), and 'Grandiflora' (GF, green), the biosynthetic mechanisms of different flower colors in P. serrulata were revealed. The results showed that the different colors of the petals were related to the content of chlorophyll and anthocyanins. Among these, cyanidin-3-O-glucoside and cyanidin-3-O-(6-O-malonyl-β-D-glucoside) were highly expressed in AR. A combined transcriptomic analysis revealed that five flavonoid structural genes, including two DFR genes and three UFGT genes, were specifically expressed. In addition, three key transcription factors, PsMYB77, PsMYB17, and PsMYB105, were identified as regulators of the structural genes DFR and UFGT and participants in the forward synthesis of anthocyanin. This study provides convincing evidence elucidating the regulatory mechanisms of anthocyanin synthesis of P. serrulata and provides a theoretical basis for the breeding and development of new varieties and germplasm resource innovation for cherry blossom.

Metabolomic and Transcriptomic Analyses of Flavonoid Biosynthesis in Different Colors of Soybean Seed Coats

Soybean has outstanding nutritional and medicinal value because of its abundant protein, oil, and flavonoid contents. This crop has rich seed coat colors, such as yellow, green, black, brown, and red, as well as bicolor variants. However, there are limited reports on the synthesis of flavonoids in the soybean seed coats of different colors. Thus, the seed coat metabolomes and transcriptomes of five soybean germplasms with yellow (S141), red (S26), brown (S62), green (S100), and black (S124) seed coats were measured. In this study, 1645 metabolites were detected in the soybean seed coat, including 426 flavonoid compounds. The flavonoids differed among the different-colored seed coats of soybean germplasms, and flavonoids were distributed in all varieties. Procyanidins A1, B1, B6, C1, and B2, cyanidin 3-O-(6″-malonyl-arabinoside), petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, and malvidin 3-laminaribioside were significantly upregulated in S26_vs._S141, S62_vs._S141, S100_vs._S141, and S124_vs._S141 groups, with a variation of 1.43-2.97 × 1013 in terms of fold. The differences in the contents of cyanidin 3-O-(6″-malonyl-arabinoside) and proanthocyanidin A1 relate to the seed coat color differences of red soybean. Malvidin 3-laminaribioside, petunidin 3-(6″-p-coumaryl-glucoside) 5-glucoside, cyanidin 3-O-(6″-malonyl-arabinoside), and proanthocyanidin A1 affect the color of black soybean. The difference in the contents of procyanidin B1 and malvidin 3-glucoside-4-vinylphenol might be related to the seed coat color differences of brown soybeans. Cyanidin 3-gentiobioside affects the color of green soybean. The metabolomic-transcriptomic combined analysis showed that flavonoid biosynthesis is the key synthesis pathway for soybean seed color formation. Transcriptome analysis revealed that the upregulation of most flavonoid biosynthesis genes was observed in all groups, except for S62_vs._S141, and promoted flavonoid accumulation. Furthermore, CHS, CHI, DFR, FG3, ANR, FLS, LAR, and UGT88F4 exhibited differential expression in all groups. This study broadens our understanding of the metabolic and transcriptomic changes in soybean seed coats of different colors and provides new insights into developing bioactive substances from soybean seed coats.

Molecular mechanisms underlying floral fragrance in Camellia japonica 'High Fragrance': a time-course assessment

Camellia japonica 'High Fragrance' is a camellia hybrid known for its unique and intense floral scent. The current understanding of the dynamic changes in its fragrance and the underlying mechanisms are still limited. This study employed a combination of metabolomic and transcriptomic approaches to reveal the characteristics of the metabolites involved in the remarkable fragrance of this camellia and their biosynthetic mechanisms along three flower developmental stages (flower bud, initial bloom, and full bloom). Among the 349 detected volatile organic compounds (VOCs), the majority were terpenes (57, 16.33%) and esters (53, 15.19%). Of these, 136 VOCs exhibited differential accumulation over time. Transcriptomic data from floral organs at different flowering stages identified 56,303 genes, with 13,793 showing significant differential expression. KEGG enrichment analysis revealed 57, 91, and 33 candidate differential genes related to the biosynthesis of terpenes, phenylpropanoids, and fatty acid derivatives, respectively. This indicates that terpenes, esters, and their related synthetic genes might play a crucial role in the formation of 'High Fragrance' characteristics. During the entire flowering process, the majority of genes exhibited an elevated expression pattern, which correlated with the progressive accumulation of VOCs. Interestingly, the expression patterns of the differentially expressed genes in the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, associated with terpene synthesis, showed opposite trends. A transcriptional-metabolic regulatory network linking terpenoid compounds, related synthetic enzymes, and potential transcription factors could be outlined for 'High Fragrance' camellia, thus providing a theoretical basis for further exploring these events and breeding more fragrant camellias.

Unravelling the physiological and molecular mechanisms of leaf color change in Acer griseum through multi-omics analysis

Paperbark maple (Acer griseum), an endemic and endangered wild plant in China, has red-colored autumn leaves of high ornamental and garden application value. Leaf color change serves as a crucial indicator for evaluating garden tree aesthetics; however, research on A. griseum's leaf color change remains limited. This study aims to elucidate the physiological and molecular mechanisms underlying leaf color change in maple leaves through physiological, transcriptional, and metabolic assays. Data analysis encompasses gene expression levels and metabolite changes in three distinct states of maple leaves: green, half-red, and red. The progessive decrease of chlorophyll and carotenoids and the continuous accumulation of anthocyanidins caused a sharp change in leaf coloration, which was most drastic in the green to half-red period. Subsequently, targeted metabolomics analysis was performed, and a total of 71 anthocyanidins were detected, and the content of eight types of anthocyanidins increased significantly in the half-red and red periods, compared with that in the green period; of which the multiplicative difference was the largest for cyanidin-3,5-O diglucoside, delivering the largest multiplicative difference. Thus, it was plausible that cyanidin-3,5-O-diglucoside-dominated compoundswere likely to be the main metabolites associated with leaf reddening. Correlation analysis revealed that 12 key transcription factors (TFs) were significantly correlated with the anthocyanin-related metabolites and structural genes, which play important regulatory roles during the biosynthesis of anthocyanosides in A. griseum. These findings offered useful insights into the molecular basis of leaf color variation in A. griseum; providing valuable information to guide targeted genetic breeding and varietal improvement strategies.

Role of anthocyanin metabolic diversity in bract coloration of Curcuma alismatifolia varieties

Anthocyanins are one of the key metabolites influencing the coloration of ornamental bracts in plants. Curcuma alismatifolia is an emerging ornamental plant, known for the rich diversity in the coloration of its bracts and the variety of anthocyanins present. However, the specific anthocyanin metabolites contributing to this diversity are not entirely clear. This study examines the bract color variation across 19 C. alismatifolia varieties using colorimetric analysis and spectrophotometric determination of total anthocyanin content. The 19 accessions were categorized into four color groups: white, light pink, pink, and purple. Further analysis using anthocyanin metabolomics and transcriptomics was conducted on five C. alismatifolia varieties with significant differences in coloration and total anthocyanin content. In addition to previously reported anthocyanins, delphinidin-3-O-glucoside and peonidin-3-O-rutinoside were identified for the first time as important contributors to the diverse bract coloration in C. alismatifolia. Fifty-three differentially expressed genes (DEGs) were identified in the anthocyanin biosynthesis pathway, and two significant gene modules were determined through WGCNA analysis. Correlation network analysis revealed two BZ1 genes that may be key terminal enzyme genes affecting anthocyanin synthesis in C. alismatifolia bracts. Multiple transcription factors, including MYB, NAC, WRKY, ERF, and bHLH, may be involved in regulating the accumulation of different anthocyanin contents in the bracts. This research sheds light on the genetic and metabolic factors that influence bract coloration in C. alismatifolia.

Understanding the molecular regulation of flavonoid 3'-hydroxylase in anthocyanin synthesis: insights from purple qingke

BACKGROUND

The Flavonoid 3'-hydroxylase gene(F3'H) is an important structural gene in the anthocyanin synthesis pathway of plants, which has been proven to be involved in the color formation of organs such as leaves, flowers, and fruits in many plants. However, the mechanism and function in barley are still unclear.

RESULTS

In order to explore the molecular mechanism of the grain color formation of purple qingke, we used the cultivated qingke variety Nierumzha (purple grain) and the selected qingke variety Kunlun 10 (white grain) to conduct transcriptomic sequencing at the early milk, late milk and soft dough stage. Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct weighted gene co-expression network related to grain color formation, and three key modules (brown, yellow, and turquoise modules) related to purple grain of qingke were selected. F3'H (HORVU1Hr1G094880) was selected from the hub gene of the module for the yeast library, yeast two-hybrid (Y2H), subcellular localization and other studies. It was found that in purple qingke, HvnF3'H mainly distributed in the cytoplasm and cell membrane and interacted with several stress proteins such as methyltransferase protein and zinc finger protein.

CONCLUSIONS

The results of this study provide reference for the regulation mechanism of anthocyanin-related genes in purple grain qingke.

Unraveling the Bioactive Potential of Camellia japonica Edible Flowers: Profiling Antioxidant Substances and In Vitro Bioactivity Assessment

In recent years, the search for novel natural-based ingredients by food and related industries has sparked extensive research aimed at discovering new sources of functional molecules. Camellia japonica, traditionally known as an ornamental plant, has gained attention due to its diverse array of bioactive compounds with potential industrial applications. Although C. japonica flowers are edible, their phytochemical profile has not been thoroughly investigated. In this study, a phenolic profile screening through an HPLC-ESI-QQQ-MS/MS approach was applied to C. japonica flower extracts, revealing a total of 36 compounds, including anthocyanins, curcuminoids, dihydrochalcones, dihydroflavonols, flavonols, flavones, hydroxybenzoic acids, hydroxycinnamic acids, isoflavonoids, stilbenes, and tyrosols. Following extract profiling, their bioactivity was assessed by means of in vitro antioxidant, antimicrobial, cytotoxic, and neuroprotective activities. The results showed a multifaceted high correlation of phenolic compounds with all the tested bioactivities according to Pearson's correlation analysis, unraveling the potential of C. japonica flowers as promising sources of nutraceuticals. Overall, these findings provide insight into the valorization of C. japonica flowers from different unexplored cultivars thus diversifying their industrial outcome.

Genome assembly and multi-omic analyses reveal the mechanisms underlying flower color formation in Torenia fournieri

Torenia fournieri Lind. is an ornamental plant that is popular for its numerous flowers and variety of colors. However, its genomic evolutionary history and the genetic and metabolic bases of flower color formation remain poorly understood. Here, we report the first T. fournieri reference genome, which was resolved to the chromosome scale and was 164.4 Mb in size. Phylogenetic analyses clarified relationships with other plant species, and a comparative genomic analysis indicated that the shared ancestor of T. fournieri and Antirrhinum majus underwent a whole genome duplication event. Joint transcriptomic and metabolomic analyses identified many metabolites related to pelargonidin, peonidin, and naringenin production in rose (TfR)-colored flowers. Samples with blue (TfB) and deep blue (TfD) colors contained numerous derivatives of petunidin, cyanidin, quercetin, and malvidin; differences in the abundances of these metabolites and expression levels of the associated genes were hypothesized to be responsible for variety-specific differences in flower color. Furthermore, the genes encoding flavonoid 3-hydroxylase, anthocyanin synthase, and anthocyanin reductase were differentially expressed between flowers of different colors. Overall, we successfully identified key genes and metabolites involved in T. fournieri flower color formation. The data provided by the chromosome-scale genome assembly establish a basis for understanding the differentiation of this species and will facilitate future genetic studies and genomic-assisted breeding.

Metabolic and molecular mechanisms of spine color formation in Chinese red chestnut

The spines of Chinese red chestnut are red and the depth of their color gradually increases with maturity. To identify the anthocyanin types and synthesis pathways in red chestnut and to identify the key genes regulating the anthocyanin biosynthesis pathway, we obtained and analyzed the transcriptome and anthocyanin metabolism of red chestnut and its control variety with green spines at 3 different periods. GO and KEGG analyses revealed that photosynthesis was more highly enriched in green spines compared with red spines, while processes related to defense and metabolism regulation were more highly enriched in red spines. The analysis showed that the change in spine color promoted photoprotection in red chestnut, especially at the early growth stage, which resulted in the accumulation of differentially expressed genes involved in the defense metabolic pathway. The metabolome results revealed 6 anthocyanins in red spines. Moreover, red spines exhibited high levels of cyanidin, peonidin and pelargonidin and low levels of delphinidin, petunidin and malvidin. Compared with those in the control group, the levels of cyanidin, peonidin, pelargonidin and malvidin in red spines were significantly increased, indicating that the cyanidin and pelargonidin pathways were enriched in the synthesis of anthocyanins in red spines, whereas the delphinidin pathways were inhibited and mostly transformed into malvidin. During the process of flower pigment synthesis, the expression of the CHS, CHI, F3H, CYP75A, CYP75B1, DFR and ANS genes clearly increased, that of CYP73A decreased obviously, and that of PAL, 4CL and LAR both increased and decreased. Notably, the findings revealed that the synthesized anthocyanin can be converted into anthocyanidin or epicatechin. In red spines, the upregulation of BZ1 gene expression increases the corresponding anthocyanidin content, and the upregulation of the ANR gene also promotes the conversion of anthocyanin to epicatechin. The transcription factors involved in color formation included 4 WRKYs.

Integrated analysis of metabolome, transcriptome, and bioclimatic factors of Acer truncatum seeds reveals key candidate genes related to unsaturated fatty acid biosynthesis, and potentially optimal production area

BACKGROUND

Lipids found in plant seeds are essential for controlling seed dormancy, dispersal, and defenses against biotic and abiotic stress. Additionally, these lipids provide nutrition and energy and are therefore important to the human diet as edible oils. Acer truncatum, which belongs to the Aceaceae family, is widely cultivated around the world for its ornamental value. Further because its seed oil is rich in unsaturated fatty acids (UFAs)- i.e. α-linolenic acid (ALA) and nervonic acid (NA)- and because it has been validated as a new food resource in China, the importance of A. truncatum has greatly risen. However, it remains unknown how UFAs are biosynthesized during the growth season, to what extent environmental factors impact their content, and what areas are potentially optimal for their production.

RESULTS

In this study, transcriptome and metabolome of A. truncatum seeds at three representative developmental stages was used to find the accumulation patterns of all major FAs. Cumulatively, 966 metabolites and 87,343 unigenes were detected; the differential expressed unigenes and metabolites were compared between stages as follows: stage 1 vs. 2, stage 1 vs. 3, and stage 2 vs. 3 seeds, respectively. Moreover, 13 fatty acid desaturases (FADs) and 20 β-ketoacyl-CoA synthases (KCSs) were identified, among which the expression level of FAD3 (Cluster-7222.41455) and KCS20 (Cluster-7222.40643) were consistent with the metabolic results of ALA and NA, respectively. Upon analysis of the geographical origin-affected diversity from 17 various locations, we found significant variation in phenotypes and UFA content. Notably, in this study we found that 7 bioclimatic variables showed considerable influence on FAs contents in A. truncatum seeds oil, suggesting their significance as critical environmental parameters. Ultimately, we developed a model for potentially ecological suitable regions in China.

CONCLUSION

This study provides a comprehensive understanding of the relationship between metabolome and transcriptome in A. truncatum at various developmental stages of seeds and a new strategy to enhance seed FA content, especially ALA and NA. This is particularly significant in meeting the increasing demands for high-quality edible oil for human consumption. The study offers a scientific basis for A. truncatum's novel utilization as a woody vegetable oil rather than an ornamental plant, potentially expanding its cultivation worldwide.

Integrative Metabolomic and Transcriptomic Analyses Reveal the Mechanism of Petal Blotch Formation in Rosa persica

Petal blotch is a specific flower color pattern commonly found in angiosperm families. In particular, Rosa persica is characterized by dark red blotches at the base of yellow petals. Modern rose cultivars with blotches inherited the blotch trait from R. persica. Therefore, understanding the mechanism for blotch formation is crucial for breeding rose cultivars with various color patterns. In this study, the metabolites and genes responsible for the blotch formation in R. persica were identified for the first time through metabolomic and transcriptomic analyses using LC-MS/MS and RNA-seq. A total of 157 flavonoids were identified, with 7 anthocyanins as the major flavonoids, namely, cyanidin 3-O-(6″-O-malonyl) glucoside 5-O-glucoside, cyanidin-3-O-glucoside, cyanidin 3-O-galactoside, cyanidin O-rutinoside-O-malonylglucoside, pelargonidin 3-O-glucoside, pelargonidin 3,5-O-diglucoside, and peonidin O-rutinoside-O-malonylglucoside, contributing to pigmentation and color darkening in the blotch parts of R. persica, whereas carotenoids predominantly influenced the color formation of non-blotch parts. Zeaxanthin and antheraxanthin mainly contributed to the yellow color formation of petals at the semi-open and full bloom stages. The expression levels of two 4-coumarate: CoA ligase genes (Rbe014123 and Rbe028518), the dihydroflavonol 4-reductase gene (Rbe013916), the anthocyanidin synthase gene (Rbe016466), and UDP-flavonoid glucosyltransferase gene (Rbe026328) indicated that they might be the key structural genes affecting the formation and color of petal blotch. Correlation analysis combined with weighted gene co-expression network analysis (WGCNA) further characterized 10 transcription factors (TFs). These TFs might participate in the regulation of anthocyanin accumulation in the blotch parts of petals by modulating one or more structural genes. Our results elucidate the compounds and molecular mechanisms underlying petal blotch formation in R. persica and provide valuable candidate genes for the future genetic improvement of rose cultivars with novel flower color patterns.

Genome-wide identification of GATA transcription factors in tetraploid potato and expression analysis in differently colored potato flesh

The GATA gene family belongs to a kind of transcriptional regulatory protein featuring a zinc finger motif, which is essential for plant growth and development. However, the identification of the GATA gene family in tetraploid potato is still not performed. In the present research, a total of 88 GATA genes in the tetraploid potato C88.v1 genome were identified by bioinformatics methods. These StGATA genes had an uneven distribution on 44 chromosomes, and the corresponding StGATA proteins were divided into four subfamilies (I-IV) based on phylogenetic analysis. The cis-elements of StGATA genes were identified, including multiple cis-elements related to light-responsive and hormone-responsive. The collinearity analysis indicates that segmental duplication is a key driving force for the expansion of GATA gene family in tetraploid potato, and that the GATA gene families of tetraploid potato and Arabidopsis share a closer evolutionary relationship than rice. The transcript profiling analysis showed that all 88 StGATA genes had tissue-specific expression, indicating that the StGATA gene family members participate in the development of multiple potato tissues. The RNA-seq analysis was also performed on the tuber flesh of two potato varieties with different color, and 18 differentially expressed GATA transcription factor genes were screened, of which eight genes were validated through qRT-PCR. In this study, we identified and characterized StGATA transcription factors in tetraploid potato for the first time, and screened differentially expressed genes in potato flesh with different color. It provides a theoretical basis for further understanding the StGATA gene family and its function in anthocyanin biosynthesis.

Integrative metabolome and transcriptome analyses reveal the coloration mechanism in Camellia oleifera petals with different color

BACKGROUND

Camellia olelfera petals are colorful, and have high ornamental value. However, the color formation mechanism of C. olelfera petals with different color is still unclear. In our study, WGCNA method was applied to integrate metabolites and transcriptomes to investigate the coloration mechanism of four C. olelfera cultivars with different petal colors.

RESULTS

Here, a total of 372 flavonoids were identified (including 27 anthocyanins), and 13 anthocyanins were significantly differentially accumulated in C. olelfera petals. Among them, cyanidin-3-O-(6''-O-p-Coumaroyl) glucoside was the main color constituent in pink petals, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, cyanidin-3-O-rutinoside, and cyanidin-3-O-(6''-O-malonyl) glucoside were the main contributors to candy pink petals, and peonidin-3-O-glucoside was the important color substance responsible for the red petals of C. oleifera. Furthermore, six structural genes (Co4CL1, CoF3H1, CoF3'H, CoANS, CoUGT75C1-4, and CoUGT75C1-5), three MYBs (CoMYB1, CoMYB4, and CoMYB44-3), three bHLHs (CobHLH30, CobHLH 77, and CobHLH 79-1), and two WRKYs (CoWRKY7 and CoWRKY22) could be identified candidate genes related to anthocyanins biosynthesis and accumulation, and lead to the pink and red phenotypes. The regulatory network of differentially accumulated anthocyanins and the anthocyanins related genes in C. olelfera petals were established.

CONCLUSIONS

These findings elucidate the molecular basis of the coloration mechanisms of pink and red color in C. olelfera petals, and provided valuable target genes for future improvement of petals color in C. olelfera.

Metabolome and Transcriptome Analyses Reveal Flower Color Differentiation Mechanisms in Various Sophora japonica L. Petal Types

Sophora japonica L. is an important landscaping and ornamental tree species throughout southern and northern parts of China. The most common color of S. japonica petals is yellow and white. In this study, S. japonica flower color mutants with yellow and white flag petals and light purple-red wing and keel petals were used for transcriptomics and metabolomics analyses. To investigate the underlying mechanisms of flower color variation in S. japonica 'AM' mutant, 36 anthocyanin metabolites were screened in the anthocyanin-targeting metabolome. The results demonstrated that cyanidins such as cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside in the 'AM' mutant were the key metabolites responsible for the red color of the wing and keel petals. Transcriptome sequencing and differentially expressed gene (DEG) analysis identified the key structural genes and transcription factors related to anthocyanin biosynthesis. Among these, F3'5'H, ANS, UFGT79B1, bHLH, and WRKY expression was significantly correlated with the cyanidin-type anthocyanins (key regulatory factors affecting anthocyanin biosynthesis) in the flag, wing, and keel petals in S. japonica at various flower development stages.

Association Analysis of Transcriptome and Targeted Metabolites Identifies Key Genes Involved in Iris germanica Anthocyanin Biosynthesis

The anthocyanin biosynthetic pathway is the main pathway regulating floral coloration in Iris germanica, a well-known ornamental plant. We investigated the transcriptome profiles and targeted metabolites to elucidate the relationship between genes and metabolites in anthocyanin biosynthesis in the bitone flower cultivar 'Clarence', which has a deep blue outer perianth and nearly white inner perianth. In this study, delphinidin-, pelargonidin-, and cyanidin-based anthocyanins were detected in the flowers. The content of delphinidin-based anthocyanins increased with the development of the flower. At full bloom (stage 3), delphinidin-based anthocyanins accounted for most of the total anthocyanin metabolites, whereas the content of pelargonidin- and cyanidin-based anthocyanins was relatively low. Based on functional annotations, a number of novel genes in the anthocyanin pathway were identified, which included early biosynthetic genes IgCHS, IgCHI, and IgF3H and late biosynthetic genes Ig F3'5'H, IgANS, and IgDFR. The expression of key structural genes encoding enzymes, such as IgF3H, Ig F3'5'H, IgANS, and IgDFR, was significantly upregulated in the outer perianth compared to the inner perianth. In addition, most structural genes exhibited their highest expression at the half-color stage rather than at the full-bloom stage, which indicates that these genes function ahead of anthocyanins synthesis. Moreover, transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) related to the regulation of anthocyanin biosynthesis were identified. Among 56 R2R3-MYB genes, 2 members belonged to subgroup 4, with them regulating the expression of late biosynthetic genes in the anthocyanin biosynthetic pathway, and 4 members belonged to subgroup 7, with them regulating the expression of early biosynthetic genes in the anthocyanin biosynthetic pathway. Quantitative real-time PCR (qRT-PCR) analysis was used to validate the data of RNA sequencing (RNA-Seq). The relative expression profiles of most candidate genes were consistent with the FPKM of RNA-seq. This study identified the key structural genes encoding enzymes and TFs that affect anthocyanin biosynthesis, which provides a basis and reference for the regulation of plant anthocyanin biosynthesis in I. germanica.

Metabolomics Analysis Reveals the Accumulation Patterns of Flavonoids and Volatile Compounds in Camellia oleifera Petals with Different Color

To systematically and comprehensively investigate the metabolic characteristics of coloring substances and floral aroma substances in Camellia oleifera petals with different colors, ultrahigh-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) and headspace solid phase microextraction and gas chromatography-mass spectrometry (HS-SPME-GC-MS) metabolomics methods were applied to determine the metabolic profiles of white, candy-pink and dark-red petals. The results revealed that 270 volatile organic compounds were detected, mainly terpenoids, heterocyclic, esters, hydrocarbons, aldehydes, and alcohols, in which phenylethyl alcohol, lilac alcohol, and butanoic acid, 1-methylhexyl ester, hotrienol, alpha-terpineol and 7-Octen-4-ol, 2-methyl-6-methylene-, (S)-, butanoic acid, 2-methyl-, 2-methylbutyl ester, 2,4-Octadienal, (E,E)- could act as the floral scent compounds. A total of 372 flavonoid compounds were identified, and luteolin, kaempferol, cyanidin and peonidin derivatives were considered as the main coloring substances for candy-pink and dark-red petal coloration. In conclusion, this study intuitively and quantitatively exhibited the variations in flower color and floral scent of C. oleifera petal with different colors caused by changes in variations of flavonoids and volatile organic compound composition, and provided useful data for improving the sensory quality and breeding of C. oleifera petals.

Functional Characterization of AP2/ERF Transcription Factors during Flower Development and Anthocyanin Biosynthesis Related Candidate Genes in Lycoris

The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and plant stress responses. To date, there has been little investigation into how the AP2/ERF genes influence flower formation and anthocyanin biosynthesis in Lycoris. Herein, 80 putative LrAP2/ERF transcription factors (TFs) with complete open reading frames (ORFs) were retrieved from the Lycoris transcriptome sequence data, which could be divided into five subfamilies dependent on their complete protein sequences. Furthermore, our findings demonstrated that genes belonging to the same subfamily had structural similarities and conserved motifs. LrAP2/ERF genes were analyzed for playing an important role in plant growth, water deprivation, and flower formation by means of gene ontology (GO) enrichment analysis. The expression pattern of the LrAP2/ERF genes differed across tissues and might be important for Lycoris growth and flower development. In response to methyl jasmonate (MeJA) exposure and drought stress, the expression of each LrAP2/ERF gene varied across tissues and time. Moreover, a total of 20 anthocyanin components were characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, and pelargonidin-3-O-glucoside-5-O-arabinoside was identified as the major anthocyanin aglycone responsible for the coloration of the red petals in Lycoris. In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. These findings provide the basic conceptual groundwork for future research into the molecular underpinnings and regulation mechanisms of AP2/ERF TFs in anthocyanin accumulation and Lycoris floral development.

Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data

Pinellia ternata (Thunb.) Breit. (Araceae), a significant medicinal plant, has been used to treat various diseases for centuries. Terahertz radiation (THZ) is located between microwaves and infrared rays on the electromagnetic spectrum. THZ possesses low single-photon energy and a spectral fingerprint, but its effects on plant growth have not yet been investigated. The study's primary objective was to examine the transcriptome and metabolome databases of the SY line to provide a new perspective for identifying genes associated with resistance and growth promotion and comprehending the underlying molecular mechanism. Variations in the biological characteristics of P. ternata grown under control and experimental conditions were analyzed to determine the effect of THZ. Compared with the control group, phenotypic variables such as leaf length, petiole length, number of leaves, leaf petiole diameter, and proliferation coefficient exhibited significant differences. P. ternata response to THZ was analyzed regarding the effects of various coercions on root exudation. The experimental group contained considerably more sugar alcohol than the control group. The transcriptome analysis revealed 1,695 differentially expressed genes (DEGs), including 509 upregulated and 1,186 downregulated genes. In the KEGG-enriched plant hormone signaling pathway, there were 19 differentially expressed genes, 13 of which were downregulated and six of which were upregulated. In the metabolomic analysis, approximately 416 metabolites were uncovered. There were 112 DEMs that were downregulated, whereas 148 were upregulated. The P. ternata leaves displayed significant differences in phytohormone metabolites, specifically in brassinolide (BR) and abscisic acid (ABA). The rise in BR triggers alterations in internal plant hormones, resulting in faster growth and development of P. ternata. Our findings demonstrated a link between THZ and several metabolic pathway processes, which will enhance our understanding of P. ternata mechanisms.

Transcriptome and metabolome analysis reveals the effect of flavonoids on flower color variation in Dendrobium nobile Lindl

Introduction

Dendrobium nobile L. is a rare orchid plant with high medicinal and ornamentalvalue, and extremely few genetic species resources are remaining in nature. In the normal purple flower population, a type of population material with a white flower variation phenotype has been discovered, and through pigment component determination, flavonoids were preliminarily found to be the main reason for the variation.

Methods

This study mainly explored the different genes and metabolites at different flowering stages and analysed the flower color variation mechanism through transcriptome- and flavonoid-targeted metabolomics. The experimental materials consisted of two different flower color phenotypes, purple flower (PF) and white flower (WF), observed during three different periods.

Results and discussion

The results identified 1382, 2421 and 989 differentially expressed genes (DEGs) in the white flower variety compared with the purple flower variety at S1 (bud stage), S2 (chromogenic stage) and S3 (flowering stage), respectively. Among these, 27 genes enriched in the ko00941, ko00942, ko00943 and ko00944 pathways were screened as potential functional genes affecting flavonoid synthesis and flower color. Further analysis revealed that 15 genes are potential functional genes that lead to flavonoid changes and flower color variations. The metabolomics results at S3 found 129 differentially accumulated metabolites (DAMs), which included 8 anthocyanin metabolites, all of which (with the exception of delphinidin-3-o-(2'''-o-malonyl) sophoroside-5-o-glucoside) were found at lower amounts in the WF variety compared with the PF variety, indicating that a decrease in the anthocyanin content was the main reason for the inability to form purple flowers. Therefore, the changes in 19 flavone and 62 flavonol metabolites were considered the main reasons for the formation of white flowers. In this study, valuable materials responsible for flower color variation in D. nobile were identified and further analyzed the main pathways and potential genes affecting changes in flavonoids and the flower color. This study provides a material basis and theoretical support for the hybridization and molecular-assisted breeding of D. nobile.

Characterization Variation of the Differential Coloring Substances in Rapeseed Petals with Different Colors Using UPLC-HESI-MS/MS

Rapeseed's (Brassica napus L.) colorful petals have important ornamental values. However, the mechanisms of regulating petals coloration in rapeseed are still unknown. In our study, we investigated the key differential coloring substances in nine rapeseed cultivars with different petal colors, and 543 metabolites were detected and characterized through UPLC-HESI-MS/MS. Among them, the kinds and contents of flavonols, flavones, and anthocyanidins were the main contributors to petals' coloration. Tamarixetin-, quercetin-, butin-, naringenin- and luteolin-derivates were the main pigment bases in white and yellow petals. Peonidin-3,5-O-diglucoside, peonidin-3-O-(6″-O-caffeoyl)glucoside, and quercetin-derivatives were the main coloring substances in pink petals. Acylated cyanidin derivatives might lead to a series of different purple petal colors. Glycosylated anthocyanins were responsible for the coloration of rapeseed red petals, and peonidin-3-O-glucoside and kaempferol-derivatives were mainly detected from the red petals. These results provide comprehensive insights into the difference in flavonoid metabolites in rapeseed petals with different colors and supply theoretical supports for the breeding of novel colorful rapeseed cultivars.

Camellia japonica Flowers as a Source of Nutritional and Bioactive Compounds

In recent decades, plants have strengthened their relevance as sources of molecules potentially beneficial for health. This underpinning effect also arises from the extensive research that has been conducted on plants that are typically undervalued, besides being scarcely used. This is the case with Camellia japonica in Galicia (NW Spain), where, despite its abundance, it is exclusively used for ornamental purposes and has been studied only for its proximate composition. Thus, the present study was conducted on several additional parameters in the flowers of eight C. japonica varieties. Our results show that camellia has a high nutritional value, with carbohydrates as the most abundant macronutrients followed by a moderate protein content (4.4-6.3 g/100 g dry weight) and high levels of polyunsaturated fatty acids (especially ω-3 fatty acids, which represent 12.9-22.7% of the total fatty acids), raising its potential for use for nutritional purposes. According to the thermochemical characterization and elemental composition of camellia, the raw material has poor mineralization and low nitrogen content, but high percentages of volatile matter and high carbon-fixation rates, making it a promising alternative for biofuel production. Furthermore, preliminary analysis reveals a high concentration of different bioactive compounds. As a result of these findings, camellias can be used as food or functional ingredients to improve the nutritional quality of food formulations.

Metabolite Profiling of External and Internal Petals in Three Different Colors of Tea Flowers (Camellia sinensis) Using Widely Targeted Metabolomics

The flower is the reproductive organ of the tea plant, while it is also processed into different kinds of products and thus of great significance to be utilized. In this study, the non-volatile secondary metabolites in the internal and external petals of white, white and pink, and pink tea flowers were studied using a widely targeted metabolomics method with ultra-high liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). A total of 429 metabolites were identified, including 195 flavonoids, 121 phenolic acids, 40 alkaloids, 29 lignans and coumarins, 19 tannins, 17 terpenoids, and 8 other metabolites. The metabolites in the internal and external petals of different colored flowers showed great changes in flavonoids. Most flavonoids and all tannins in the internal petals were higher compared with the external petals. Some phenolic acids were more accumulated in the external petals, while others showed opposite trends. The pink tea flower contained more flavonoids, alkaloids, lignans, coumarins, terpenoids, and tannins compared with white tea flowers. In addition, cyanidin-3-O-glucoside was more accumulated in the external petals of the pink flower, indicating that anthocyanin may be the main reason for the color difference between the pink and white tea flower. The enriched metabolic pathways of different colored flowers were involved in flavonoid biosynthesis, glycine, serine and threonine metabolism, glycerophospholipid metabolism, and phenylpropanoid biosynthesis. The findings of this study broaden the current understanding of non-volatile compound changes in tea plants. It is also helpful to lay a theoretical foundation for integrated applications of tea flowers.

Exogenous γ-aminobutyric acid (GABA) alleviates nitrogen deficiency by mediating nitrate uptake and assimilation in Andrographis paniculata seedlings

γ-Aminobutyric acid (GABA) plays significant metabolic and signaling roles in plant stress responses. Recent studies have proposed that GABA alleviates plant nitrogen (N) deficient stress; however, the mechanism by which GABA mediates plant N deficiency adaptation remains not yet well understood. Herein we found in a medicinal plant Andrographis paniculata that 5 mmol L^-1 exogenous GABA promoted plant growth under N deficient (1 mmol L^-1 NO₃^-) condition, with remarkably increments in total N and NO₃^- concentrations in plants. GABA increased N assimilation and protein synthesis by up-regulating the activities and expression of N metabolic enzymes. GABA also increased the accumulation of α-ketoglutarate and malate, which could facilitate the assimilation of NO₃^-. Inhibition of NR by Na₂WO₄ counteracted the promoting effects of GABA on plant growth, and the effects of GABA were not affected by L-DABA and 3-MP, the inhibitors of GABA transaminase (GABA-T) and glutamate decarboxylase (GAD), respectively. These results suggested that the nutritional role of GABA was excluded in promoting plant growth under low N condition. The results of ¹⁵N isotopic tracing and NRTs transcription indicated that exogenous GABA could up-regulate NRT2.4 and NRT3.2 to increase plant NO₃^- uptake under N deficient condition. Interestingly, primidone, an inhibitor of GABA receptor, impeded the effects of GABA on plant growth and N accumulation. Thus, our results revealed that exogenous GABA acted as a signal to up-regulate NRTs via its receptor to increase NO₃^- uptake, and subsequently promoted NO₃^- assimilation to alleviate N deficiency in A. paniculata.

Cloning and functional analysis of GhDFR1, a key gene of flavonoid synthesis pathway in naturally colored cotton

BACKGROUND

The naturally colored brown cotton fiber is the most widely used environmentally friendly textile material, which primarily contains proanthocyanidins and their derivatives. Many structural genes in the flavonoid synthesis pathway are known to improve the genetic resources of naturally colored cotton. Among them, DFR is a crucial late enzyme to synthesis both anthocyanins and proanthocyanidins in the plant flavonoid pathway.

METHODS

The protein sequences of GhDFRs were analyzed using bioinformatic tools. The expression levels of GhDFRs in various tissues and organs of upland cotton Zongxu1 (ZX1), were analyzed by quantitative real-time PCR, and the expression pattern of GhDFR1 during fiber development of white cotton and brown cotton was analyzed further. The function of GhDFR1 in NCC ZX1 was preliminarily analyzed by virus induced gene silencing (VIGS) technology.

RESULTS

Bioinformatic analysis revealed that GhDFRs sequences in upland cotton genome were extremely conserved. Furthermore, evolutionary tree analysis revealed that the functions of GhDFR1 and GhDFR2, and GhDFR3 and GhDFR4, presented different and shared some similarities. Our study showed GhDFR1 and GhDFR2 were specifically expressed in fibers, while GhDFR3 and GhDFR4 were specifically expressed in petals. GhDFR1 was exclusively expressed in brown cotton fiber at various stages of development and progressively increased with the growth of fiber, but the trend of expression in white cotton was quite the opposite. We silenced GhDFR1 expression in brown cotton fiber using VIGS technology, and observed the VIGS-interference plants. After reducing the expression level of GhDFR1, the period for significant GhDFR1 expression in the developing fibers changed, reducing the content of anthocyanins, and lightening the color of mature cotton fibers.

CONCLUSION

GhDFR1 was preferentially expressed in brown cotton during fiber development. The timing of GhDFR1 expression for flavonoid synthesis altered, resulting in anthocyanin contents reduced and the fiber color of the GhDFR1i lines lightened. These findings showed the role of GhDFR1 in fiber coloration of NCC and provided a new candidate for NCC genetic improvement.

The lineage-specific evolution of the oleosin family in Theaceae

Oleosins play essential roles in stabilization of lipid droplets (LDs) and seed oil production. However, evolution of this gene family has not been reported in Theaceae, a large plant family that contains many important tea and oil tea species. In this study, a total of 65 oleosin genes were identified in nine genome-sequenced Theaceae species. Among these genomes, the gene number of oleosin showed significant difference, with Camellia sinensis var. sinensis cv. Shuchazao and Camellia lanceoleosa displayed more oleosin numbers than other species. Phylogenetic analyses revealed that Theaceae oleosin genes were classified into three clades (U, SL, SH) respectively. Proteins within the same clade had similar gene structure and motif composition. Segmental duplication was the primary driving force for the evolution of oleosin genes in Shuchazao (SCZ), Huangdan (HD), C.lanceoleosa (Cla), and wild tea (DASZ). Synteny analysis showed that most oleosin genes displayed inter-species synteny among tea and oil tea species. Expression analysis demonstrated that oleosin genes were specifically expressed in seed and kernel of Huangdan (HD) and C.lanceoleosa. Moreover, expression divergence was observed in paralogous pairs and ∼1-2 oleosin genes in each clade have become activate. This study leads to a comprehensive understanding of evolution of oleosin family in Theaceae, and provides a rich resource to further address the functions of oleosin in tea and oil tea species.

Cyanidin-3-O-glucoside Contributes to Leaf Color Change by Regulating Two bHLH Transcription Factors in Phoebe bournei

Anthocyanins produce different-colored pigments in plant organs, which provide ornamental value. Thus, this study was conducted to understand the mechanism of anthocyanin synthesis in ornamental plants. Phoebe bournei, a Chinese specialty tree, has high ornamental and economic value due to its rich leaf color and diverse metabolic products. Here, the metabolic data and gene expression of red P. bournei leaves at the three developmental stages were evaluated to elucidate the color-production mechanism in the red-leaved P. bournei species. First, metabolomic analysis identified 34 anthocyanin metabolites showing high levels of cyanidin-3-O-glucoside (cya-3-O-glu) in the S1 stage, which may suggest that it is a characteristic metabolite associated with the red coloration of the leaves. Second, transcriptome analysis showed that 94 structural genes were involved in anthocyanin biosynthesis, especially flavanone 3'-hydroxy-lase (PbF3'H), and were significantly correlated with the cya-3-O-glu level. Third, K-means clustering analysis and phylogenetic analyses identified PbbHLH1 and PbbHLH2, which shared the same expression pattern as most structural genes, indicating that these two PbbHLH genes may be regulators of anthocyanin biosynthesis in P. bournei. Finally, overexpression of PbbHLH1 and PbbHLH2 in Nicotiana tabacum leaves triggered anthocyanin accumulation. These findings provide a basis for cultivating P. bournei varieties that have high ornamental value.

Novel insight into anthocyanin metabolism and molecular characterization of its key regulators in Camellia sasanqua

Flower color is a trait that affects the ornamental value of a plant. Camellia sasanqua is a horticultural plant with rich flower color, but little is known about the regulatory mechanism of color diversity in this plant. Here, the anthocyanin profile of 20 C. sasanqua cultivars revealed and quantified 11 anthocyanin derivatives (five delphinidin-based and six cyanidin-based anthocyanins) for the first time. Cyanidin-3-O-(6-O-(E)-p-coumaroyl)-glucoside was the main contributor to flower base color, and the accumulation of cyanidin and delphinidin derivatives differed in the petals. To further explore the molecular mechanism of color divergence, a transcriptome analysis was performed using C. sasanqua cultivars 'YingYueYe', 'WanXia', 'XueYueHua', and'XiaoMeiGui'. The co-expression network related to differences in delphinidin and cyanidin derivatives accumulation was identified. Eleven candidate genes encoding key enzymes (e.g., F3H, F3'H, and ANS) were involved in anthocyanin biosynthesis. Moreover, 27 transcription factors were screened as regulators of the two types of accumulating anthocyanins. The association was suggested by correlation analysis between the expression levels of the candidate genes and the different camellia cultivars. We concluded that cyanidin and delphinidin derivatives are the major drivers of color diversity in C. sasanqua. This finding provides valuable resources for the study of flower color in C. sasanqua and lays a foundation for genetic modification of anthocyanin biosynthesis.

Characterization of the WRKY Gene Family Related to Anthocyanin Biosynthesis and the Regulation Mechanism under Drought Stress and Methyl Jasmonate Treatment in Lycoris radiata

Lycoris radiata, belonging to the Amaryllidaceae family, is a well-known Chinese traditional medicinal plant and susceptible to many stresses. WRKY proteins are one of the largest families of transcription factors (TFs) in plants and play significant functions in regulating physiological metabolisms and abiotic stress responses. The WRKY TF family has been identified and investigated in many medicinal plants, but its members and functions are not identified in L. radiata. In this study, a total of 31 L. radiata WRKY (LrWRKY) genes were identified based on the transcriptome-sequencing data. Next, the LrWRKYs were divided into three major clades (Group I-III) based on the WRKY domains. A motif analysis showed the members within same group shared a similar motif component, indicating a conservational function. Furthermore, subcellular localization analysis exhibited that most LrWRKYs were localized in the nucleus. The expression pattern of the LrWRKY genes differed across tissues and might be important for Lycoris growth and flower development. There were large differences among the LrWRKYs based on the transcriptional levels under drought stress and MeJA treatments. Moreover, a total of 18 anthocyanin components were characterized using an ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis and pelargonidin-3-O-glucoside-5-O-arabinoside as well as cyanidin-3-O-sambubioside were identified as the major anthocyanin aglycones responsible for the coloration of the red petals in L. radiata. We further established a gene-to-metabolite correlation network and identified LrWRKY3 and LrWRKY27 significant association with the accumulation of pelargonidin-3-O-glucoside-5-O-arabinoside in the Lycoris red petals. These results provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in anthocyanin biosynthesis and in response to drought stress and MeJA treatment.

Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes

Vitis adenoclada is a wild grape unique to China. It exhibits well resistance to heat, humidity, fungal disease, drought, and soil infertility. Here, we report the high-quality, chromosome-level genome assembly of GH6 (V. adenoclada). The 498.27 Mb genome contained 221.78 Mb of transposable elements, 28,660 protein-coding genes, and 481.44 Mb of sequences associated with 19 chromosomes. GH6 shares a common ancestor with PN40024 (Vitis vinifera) from approximately 4.26-9.01 million years ago, whose divergence occurred later than Vitis rotundifolia and Vitis riparia. Widely-targeted metabolome and transcriptome analysis revealed that the profiles and metabolism of phenolic compounds in V. adenoclada varieties significantly were differed from other grape varieties. Specifically, V. adenoclada varieties were rich in phenolic acids and flavonols, whereas the flavan-3-ol and anthocyanin content was lower compared with other varieties that have V. vinifera consanguinity in this study. In addition, ferulic acid and stilbenes content were associated with higher expressions of COMT and STSs in V. adenoclada varieties. Furthermore, MYB2, MYB73-1, and MYB73-2 were presumably responsible for the high expression level of COMT in V. adenoclada berries. MYB12 (MYBF1) was positively correlated with PAL, CHS, FLS and UFGT.Meanwhile, MYB4 and MYBC2-L1 may inhibit the synthesis of flavan-3-ols and anthocyanins in two V. adenoclada varieties (YN2 and GH6). The publication of the V. adenoclada grape genome provides a molecular foundation for further revealing its flavor and quality characteristics, is also important for identifying favorable genes of the East Asian species for future breeding.

Metabolic profile and transcriptome reveal the mystery of petal blotch formation in rose

BACKGROUND

Petal blotch is a unique ornamental trait in angiosperm families, and blotch in rose petal is rare and has great esthetic value. However, the cause of the formation of petal blotch in rose is still unclear. The influence of key enzyme genes and regulatory genes in the pigment synthesis pathways needs to be explored and clarified.

RESULTS

In this study, the rose cultivar 'Sunset Babylon Eyes' with rose-red to dark red blotch at the base of petal was selected as the experimental material. The HPLC-DAD and UPLC-TQ-MS analyses indicated that only cyanidin 3,5-O-diglucoside (Cy3G5G) contributed to the blotch pigmentation of 'Sunset Babylon Eyes', and the amounts of Cy3G5G varied at different developmental stages. Only flavonols but no flavone were found in blotch and non-blotch parts. As a consequence, kaempferol and its derivatives as well as quercetin and its derivatives may act as background colors during flower developmental stages. Despite of the differences in composition, the total content of carotenoids in blotch and non-blotch parts were similar, and carotenoids may just make the petals show a brighter color. Transcriptomic data, quantitative real-time PCR and promoter sequence analyses indicated that RC7G0058400 (F3'H), RC6G0470600 (DFR) and RC7G0212200 (ANS) may be the key enzyme genes for the early formation and color deepening of blotch at later stages. As for two transcription factor, RC7G0019000 (MYB) and RC1G0363600 (WRKY) may bind to the promoters of critical enzyme genes, or RC1G0363600 (WRKY) may bind to the promoter of RC7G0019000 (MYB) to activate the anthocyanin accumulation in blotch parts of 'Sunset Babylon Eyes'.

CONCLUSIONS

Our findings provide a theoretical basis for the understanding of the chemical and molecular mechanism for the formation of petal blotch in rose.

Anthocyanins from Malus spp. inhibit the activity of Gymnosporangium yamadae by downregulating the expression of WSC, RLM1, and PMA1

Malus plants are frequently devastated by the apple rust caused by Gymnosporangium yamadae Miyabe. When rust occurs, most Malus spp. and cultivars produce yellow spots, which are more severe, whereas a few cultivars accumulate anthocyanins around rust spots, forming red spots that inhibit the expansion of the affected area and might confer rust resistance. Inoculation experiments showed that Malus spp. with red spots had a significantly lower rust severity. Compared with M. micromalus, M. 'Profusion', with red spots, accumulated more anthocyanins. Anthocyanins exhibited concentration-dependent antifungal activity against G. yamadae by inhibiting teliospores germination. Morphological observations and the leakage of teliospores intracellular contents evidenced that anthocyanins destroyed cell integrity. Transcriptome data of anthocyanins-treated teliospores showed that differentially expressed genes were enriched in cell wall and membrane metabolism-related pathways. Obvious cell atrophy in periodical cells and aeciospores was observed at the rust spots of M. 'Profusion'. Moreover, WSC, RLM1, and PMA1 in the cell wall and membrane metabolic pathways were progressively downregulated with increasing anthocyanins content, both in the in vitro treatment and in Malus spp. Our results suggest that anthocyanins play an anti-rust role by downregulating the expression of WSC, RLM1, and PMA1 to destroy the cell integrity of G. yamadae.

ERF subfamily transcription factors and their function in plant responses to abiotic stresses

Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K⁺ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.

Transcriptome and chemical analyses revealed the mechanism of flower color formation in Rosa rugosa

Rosa rugosa is a famous Chinese traditional flower with high ornamental value and well environmental adapt ability. The cultivation of new colorful germplasms to improve monotonous flower color could promote its landscape application. However, the mechanism of flower color formation in R. rugosa remains unclear. In this study, combined analyses of the chemical and transcriptome were performed in the R. rugosa germplasms with representative flower colors. Among the identified anthocyanins, cyanidin 3,5-O-diglucoside (Cy3G5G) and peonidin 3,5-O-diglucoside (Pn3G5G) were the two dominant anthocyanins in the petals of R. rugosa. The sum content of Cy3G5G and Pn3G5G was responsible for the petal color intensity, such as pink or purple, light- or dark- red. The ratio of Cy3G5G to Pn3G5G was contributed to the petal color hue, that is, red or pink/purple. Maintaining both high relative and high absolute content of Cy3G5G may be the precondition for forming red-colored petals in R. rugosa. Cyanidin biosynthesis shunt was the dominant pathway for anthocyanin accumulation in R. rugosa, which may be the key reason for the presence of monotonous petal color in R. rugosa, mainly pink/purple. In the upstream pathway of cyanidin biosynthesis, 35 differentially expressed structural genes encoding 12 enzymes co-expressed to regulate the sum contents of Cy3G5G and Pn3G5G, and then determined the color intensity of petals. RrAOMT, involved in the downstream pathway of cyanidin biosynthesis, regulated the ratio of Cy3G5G to Pn3G5G via methylation and then determined the color hue of petals. It was worth mentioning that significantly higher delphinidin-3,5-O-diglucoside content and RrF3'5'H expression were detected from deep purple-red-flowered 8-16 germplasm with somewhat unique and visible blue hue. Three candidate key transcription factors identified by correlation analysis, RrMYB108, RrC1, and RrMYB114, might play critical roles in the control of petal color by regulating the expression of both RrAOMT and other multiple structural genes. These results provided novel insights into anthocyanin accumulation and flower coloration mechanism in R. rugosa, and the candidate key genes involved in anthocyanin biosynthesis could be valuable resources for the breeding of ornamental plants in future.

Metabolomic and transcriptomic analyses reveal a MYB gene, CsAN1, involved in anthocyanins accumulation separation in F1 between 'Zijuan' (Camellia sinensis var. assamica) and 'Fudingdabaicha' (C. sinensis var. sinensis) tea plants

'Zijuan' (Camellia sinensis var. assamica), a somatic mutant with purple foliage and stem selected from the Yunnan Daye cultivar, has been well developed owing to abnormal pattern of anthocyanin accumulation. However, the genetic basis for the specific accumulation of phloem glycosides is not clear. Tea plants are self-incompatible, so parents with large differences in foliage color were used for crosses to investigate the genetic mechanism of anthocyanins. In this study, 'Zijuan' and green foliage cultivar 'Fudingdabaicha' (C. sinensis var. sinensis) were used as female and male parents, respectively, to generated F1 hybrid progenies with various anthocyanin contents. In order to decipher the genetic rules of anthocyanins accumulation, we performed widely targeted metabolic and transcriptomic profiling. The results showed that cyanidin-3-O-galactoside, delphinidin-3-O-galactoside and petunidin-3-O-galactoside were the major types of anthocyanins and factors directly led to the color variation between parents and F1 plants. Transcriptomic analyses suggested the significant up-regulation of anthocyanidin synthase gene (CsANS1) and CsAN1, a MYB family gene positively regulated the expression of CsANS1, in anthocyanin-rich tea plants. Furthermore, the deletion mutation of CsAN1 was found by cloning and alignment in anthocyanin-lacking cultivars. Taken together, the function deficiency of CsAN1 is predominantly responsible for the inability of anthocyanins accumulation, and this trait is heritable in progenies through hybridization. The present study elucidated the molecular basis of leaf purple trait formation in 'zijuan' and 'Fudingdabaicha' and their F1 plants, which helps to elucidate the genetic mechanism of leaf anthocyanin accumulation regulation in tea plants, and the results provide a research reference for the selection and breeding of high anthocyanin type tea varieties.

Decoding the formation of diverse petal colors of Lagerstroemia indica by integrating the data from transcriptome and metabolome

Lagerstroemia indica has great economic value due to its ecological, medicinal, and ornamental properties. Because its bloom color is one of the most essential characteristics, research into its color development is a hot topic. In this study, five representative colored cultivars were chosen, each representing a different color, such as white, red, pink, violet, and purple. Fully bloomed flowers were used to detect flavonoids in the petals. Anthocyanin is the main factor for the color formation of L. indica. 14 anthocyanins were discovered among the 299 flavonoids. Among 14 anthocyanins, malvidin-3,5-di-O-glucoside varied greatly among four colored samples and is the main contributor to color diversity. Transcriptome sequencing revealed that compared to white flowers, Anthocyanin pathway genes appear to be more active in colored samples. Analyzing the correlation network between metabolites and differential expressed genes, 53 key structural genes, and 24 TFs were detected that may play an essential role in the formation of color in L. indica flowers. Among these, the differential expression of F3'5'H and F3'H between all samples are contributors to color diversity. These findings lay the foundation for discovering the molecular mechanism of L. indica flower color diversity.

Comparative Metabolome and Transcriptome Analysis of Anthocyanin Biosynthesis in White and Pink Petals of Cotton (Gossypium hirsutum L.)

Upland cotton (Gossypium hirsutum L.) is one of the important fiber crops. Cotton flowers usually appear white (or cream-colored) without colored spots at the petal base, and turn pink on the next day after flowering. In this study, using a mutant showing pink petals with crimson spots at their base, we conducted comparative metabolome and transcriptome analyses to investigate the molecular mechanism of coloration in cotton flowers. Metabolic profiling showed that cyanidin-3-O-glucoside and glycosidic derivatives of pelargonidins and peonidins are the main pigments responsible for the coloration of the pink petals of the mutant. A total of 2443 genes differentially expressed (DEGs) between the white and pink petals were identified by RNA-sequencing. Many DEGs are structural genes and regulatory genes of the anthocyanin biosynthesis pathway. Among them, MYB21, UGT88F3, GSTF12, and VPS32.3 showed significant association with the accumulation of cyanidin-3-O-glucoside in the pink petals. Taken together, our study preliminarily revealed the metabolites responsible for the pink petals and the key genes regulating the biosynthesis and accumulation of anthocyanins in the pink petals. The results provide new insights into the biochemical and molecular mechanism underlying anthocyanin biosynthesis in upland cotton.

Transcriptomic and metabolomic profiling of flavonoid biosynthesis provides novel insights into petals coloration in Asian cotton (Gossypium arboreum L.)

BACKGROUND

Asian cotton (Gossypium arboreum L.), as a precious germplasm resource of cotton with insect resistance and stress tolerance, possesses a broad spectrum of phenotypic variation related to pigmentation. Flower color affects insect pollination and the ornamental value of plants. Studying flower color of Asian cotton varieties improves the rate of hybridization and thus enriches the diversity of germplasm resources. Meanwhile, it also impacts the development of the horticultural industry. Unfortunately, there is a clear lack of studies concerning intricate mechanisms of cotton flower-color differentiation. Hereby, we report an integrative approach utilizing transcriptome and metabolome concerning flower color variation in three Gossypium arboreum cultivars.

RESULTS

A total of 215 differentially accumulated metabolites (DAMs) were identified, including 83 differentially accumulated flavonoids (DAFs). Colorless kaempferol was more abundant in white flowers, while gossypetin-fer showed specificity in white flowers. Quercetin and gossypetin were the main contributors to yellow petal formation. Pelargonidin 3-O-beta-D-glucoside and cyanidin-3-O-(6''-Malonylglucoside) showed high accumulation levels in purple petals. Quercetin and gossypetin pigments also promoted purple flower coloration. Moreover, 8178 differentially expressed genes (DEGs) were identified by RNA sequencing. The correlation results between total anthocyanins and DEGs were explored, indicating that 10 key structural genes and 29 transcription factors promoted anthocyanin biosynthesis and could be candidates for anthocyanin accumulation. Ultimately, we constructed co-expression networks of key DAFs and DEGs and demonstrated the interactions between specific metabolites and transcripts in different color flowers.

CONCLUSION

This study provides new insights into elucidating the regulatory mechanisms of cotton flower color and lays a potential foundation for generate cotton varieties with highly attractive flowers for pollinators.

Insight into the molecular mechanisms of leaf coloration in Cymbidium ensifolium

Cymbidiumensifolium L. is a significant ornamental plant in Orchidaceae. Aside from its attractive flowers, its leaf coloration is also an important ornamental trait. However, there is an apparent lack of studies concerning the intricate mechanism of leaf coloration in C. ensifolium. In this study, we report a systematic evaluation of leaf coloration utilizing transcriptome and metabolome profiles of purple, yellow, and green leaves. In total, 40 anthocyanins and 67 flavonoids were quantified along with chlorophyll content. The tissue–transcriptome profile identified 26,499 differentially expressed genes (DEGs). The highest chlorophyll contents were identified in green leaves, followed by yellow and purple leaves. We identified key anthocyanins and flavonoids associated with leaf coloration, including cyanidin-3-O-sophoroside, naringenin-7-O-glucoside, delphinidin, cyanidin, petunidin, and quercetin, diosmetin, sinensetin, and naringenin chalcone. Moreover, genes encoding UDP-glucoronosyl, UDP-glucosyl transferase, chalcone synthesis, flavodoxin, cytochrome P450, and AMP-binding enzyme were identified as key structural genes affecting leaf coloration in C. ensifolium. In summary, copigmentation resulting from several key metabolites modulated by structural genes was identified as governing leaf coloration in C. ensifolium. Further functional verification of the identified DEGs and co-accumulation of metabolites can provide a tool to modify leaf color and improve the aesthetic value of C. ensifolium.

Metabolome and transcriptome analyses of the flavonoid biosynthetic pathway for the efficient accumulation of anthocyanins and other flavonoids in a new duckweed variety (68-red)

Duckweed is a kind of aquatic plant with the characteristics of high nutritional value and medicinal benefits. However, most researches focused on the natural germplasms. The underlying metabolic pathway remains to be systematically elaborated in duckweed. In our laboratory, one reddish-purple mutant with high-flavonoids was screened from a mutant library of Spirodela polyrhiza 6068, named 68-red. The content of anthocyanins and proanthocyanidins in 68-red mutant increased by 563.47% and 231.19%, respectively, compared to wild type. It is interesting that cynaroside and orientin content were significantly increased, in contrast, apigetrin and vitexin were decreased in 68-red mutant. Considering this, metabolome and transcriptome were employed to explore the flavonoids biosynthetic pathway. Here, a total of 734 metabolites were identified in the wild type and 68-red mutant. Among which, cyanidin-3-O-glucoside, cyanidin-3-O-galactoside, pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside were significantly accumulated, which were positively correlated with deep reddish-purple of 68-red mutant. In addition, proanthocyanidins (B1, B2, B3, B4, C1, C2), flavonoid and its glycosides (11 luteolin and its glycosides, 14 quercetin and its glycosides, 14 kaempferol and its glycosides, 2 apigenin glycosides) were significantly accumulated, 2 apigenin glycosides were down-regulated in 68-red mutant. The transcriptome data and qRT-PCR indicated that 16 enzyme genes in flavonoids biosynthetic pathway (PAL, C4H, CHSs, F3H, ANS, ANR, F3'Hs, DFRs, LAR, GT1, BZ1) were significantly up-regulated in 68-red mutant. Correlation analysis found that three copies of F3'H gene play important roles in the synthesis of anthocyanins, luteolin and apigenin glycosides. In conclusion, the 68-red mutant is a high quality germplasm resources for food and medical industry. Metabolome and transcriptome provide new insight for exploring the enzyme genes and functional metabolites in duckweed.

Response of Anthocyanin Accumulation in Pepper (Capsicum annuum) Fruit to Light Days

Light is the key factor affecting the synthesis of anthocyanins in pepper. In this study, pepper fruit under different light days was used as experimental material to explore the synthesis of anthocyanins in purple pepper. A total of 38 flavonoid metabolites were identified in the purple pepper germplasm HNUCA21 by liquid chromatography–tandem mass spectrometry (LC-MS/MS), of which 30 belong to anthocyanins. The detected anthocyanin with the highest content was Delphinidin-3-O-glucoside (17.13 µg/g), which reached the maximum after 168 h of light treatment. Through weighted gene co-expression network analysis (WGCNA), the brown module was identified to be related to the early synthesis of anthocyanins. This module contains many structural genes related to flavonoid synthesis, including chalcone synthase (CHS 107871256, 107864266), chalcone isomerase (CHI 107871144, 107852750), dihydroflavonol 4-reductase (DFR 107860031), flavonoid 3′ 5′-hydroxylase (F3’5’H 107848667), flavonoid 3′-monooxygenase (F3M 107862334), leucoanthocyanidin dioxygenase (LDOX 107866341), and trans-cinnamate 4-monooxygenase (TCM 107875406, 107875407). The module also contained some genes related to anthocyanin transport function, such as glutathione S-transferase (GST 107861273), anthocyanidin 3-O-glucosyltransferase (UDPGT 107861697, 107843659), and MATE (107863234, 107844661), as well as some transcription factors, such as EGL1 (107865400), basic helix-loop-helix 104 (bHLH104 107864591), and WRKY44 (107843538, 107843524). The co-expression regulatory network indicated the involvement of CHS, DFR, CHI, and EGL1, as well as two MATE and two WRKY44 genes in anthocyanin synthesis. The identified genes involved in early, middle, and late light response provided a reference for the further analysis of the regulatory mechanism of anthocyanin biosynthesis in pepper.

Combined Analysis of the Transcriptome and Metabolome Revealed the Mechanism of Petal Coloration in Bauhinia variegata

Bauhinia variegata petals are colorful, rich in anthocyanins, and have ornamental, nutritional, and medicinal value. However, the regulatory mechanism of anthocyanin accumulation in B. variegata remains unclear. In this study, a combined analysis of the metabolome and transcriptome was performed in red and white B. variegata cultivars in the early, middle, and blooming stages. A total of 46 different anthocyanins were identified, of which 27 showed marked differences in accumulation between the two cultivars, and contribute to their different petal colors. Malvidin 3-O-galactoside, peonidin 3-O-galactoside, cyanidin 3-O-glucoside, cyanidin 3-O-galactoside, and malvidin 3-O-glucoside were much more abundant in the second stage of flowering. In the blooming stage, except for the anthocyanins mentioned, delphinidin 3-O-galactoside and petunidin 3-O-galactoside were the most abundant anthocyanins in the red flowers, indicating that malvidin, peonidin, cyanidin, delphinidin, and petunidin were all responsible for the red color of petals in B. variegata. RNA sequencing identified 2,431 differentially expressed genes (DEGs), of which 26 were involved in the anthocyanin synthesis pathway. Correlations between the anthocyanin biosynthesis-related DEGs and anthocyanin contents were explored, and the DEGs involved in anthocyanin accumulation in B. variegata petals were identified. Eighteen of these DEGs encoded key catalytic enzymes, such as anthocyanidin reductase (ANR) and flavonoid-3'5'-hydroxylase (F3'5'H), and 17 of them encoded transcription factors (TFs) belonging to 14 families (including MYB, NAC, SPL, ERF, and CHR28). These results improve our understanding of the roles of anthocyanins, catalytic enzymes, and TFs in B. variegata petal-color expression.

Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity

Simple Summary

The Theaceae includes more than 300 species of great morphological diversity and has immense economic, cultural, and ornamental values. However, the evolutionary history of this family remains elusive. We integrated 91 genomes and transcriptome datasets of Theaceae and successfully resolved the phylogeny of Theaceae including relatives of cultivated tea plants from both extensive low-copy and multi-copy nuclear gene markers. Bayes-based molecular dating revealed that the ancestor of the tea family originated slightly earlier than the K-Pg boundary (Mass extinction events including the extinction of dinosaurs) with early diversification of three tribes associated with the Early Eocene Climatic Optimum. Further speciation analysis suggested a sole significant diversification shift rate in the common ancestor of Camellia associated with the Mid-Miocene Climatic Optimum. Collectively, polyploidy events, and key morphological innovation characters, such as pericarp with seed coat hardening, could possibly contribute to the Theaceae species diversity.

Abstract

Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.