McMYB12 Transcription Factors Co-regulate Proanthocyanidin and Anthocyanin Biosynthesis in Malus Crabapple

How the tulip breaking virus creates striped tulips

The beauty of tulips has enchanted mankind for centuries. The striped variety has attracted particular attention for its intricate and unpredictable patterns. A good understanding of the mechanism driving the striped pattern formation of broken tulips has been missing since the 17th century. It has been known since 1928 that these patterned tulips suffer from a viral infection by the tulip breaking virus. Here, we present a mathematical model to understand how a virus infection of the petals can lead to stripes, thereby providing a possible explanation of a 350 year-old mystery. The model, which describes the viral inhibition of pigment expression (anthocyanins) and their interaction with viral reproduction, incorporates a pattern formation mechanism identified as an activator-substrate mechanism, similar to the well-known Turing instability, working together with Wolpert's positional information mechanism. The model is solved on a growing tulip petal-shaped domain, whereby we introduce a new method to describe the tulip petal growth explicitly. This work shows how a viral infection that inhibits pigment production can lead to beautiful tulip patterns.

Loss-of-function mutation in anthocyanidin reductase activates the anthocyanin synthesis pathway in strawberry

Fruit color substantially affects consumer preferences, with darker red strawberries being economically more valuable due to their higher anthocyanin content. However, the molecular basis for the dark red coloration remains unclear. Through screening of an ethyl methanesulfonate mutant library, we identified a rg418 mutant, that demonstrated anthocyanin accumulation during early fruit development stages. Furthermore, the ripening fruits of this mutant had higher anthocyanin content than wild-type (WT) fruits. An analysis of flavonoid content in WT and rg418 mutant fruits revealed substantial changes in metabolic fluxes, with the mutant exhibiting increased levels of anthocyanins and flavonols and decreased levels of proanthocyanidins. Bulked sergeant analysis sequencing indicated that the mutant gene was anthocyanidin reductase (ANR), a key gene in the proanthocyanidin synthesis pathway. Furthermore, transcriptome sequencing revealed the increased expression of MYB105 during the early development stage of mutant fruits, which promoted the expression of UFGT (UDP-glucose flavonoid 3-O-glucosyltransferase), a key gene involved in anthocyanin synthesis, thus substantially enhancing the anthocyanin content in the mutant fruits. Additionally, mutating ANR in a white-fruited strawberry variant (myb10 mutant) resulted in appealing pink-colored fruits, suggesting the diverse roles of ANR in fruit color regulation. Our study provides valuable theoretical insights for improving strawberry fruit color.

Chromosomal level genome assemblies of two Malus crabapple cultivars Flame and Royalty

Malus hybrid 'Flame' and Malus hybrid 'Royalty' are representative ornamental crabapples, rich in flavonoids and serving as the preferred materials for studying the coloration mechanism. We generated two sets of high-quality chromosome-level and haplotype-resolved genome of 'Flame' with sizes of 688.2 Mb and 675.7 Mb, and those of 'Royalty' with sizes of 674.1 Mb and 663.6 Mb, all anchored to 17 chromosomes and with a high BUSCO completeness score nearly 99.0%. A total of 47,833 and 47,307 protein-coding genes were annotated in the two haplotype genomes of 'Flame', and the numbers of 'Royalty' were 46,305 and 46,920 individually. The assembled high-quality genomes offer new resources for studying the origin and adaptive evolution of crabapples and the molecular basis of the accumulation of flavonoids and anthocyanins, facilitating molecular breeding of Malus plants.

Impact of Light and Dark Treatment on Phenylpropanoid Pathway Genes, Primary and Secondary Metabolites in Agastache rugosa Transgenic Hairy Root Cultures by Overexpressing Arabidopsis Transcription Factor AtMYB12

Agastache rugosa, otherwise called Korean mint, has a wide range of medicinal benefits. In addition, it is a rich source of several medicinally valuable compounds such as acacetin, tilianin, and some phenolic compounds. The present study aimed to investigate how the Tartary buckwheat transcription factor AtMYB12 increased the primary and secondary metabolites in Korean mint hairy roots cultured under light and dark conditions. A total of 50 metabolites were detected by using high-performance liquid chromatography (HPLC) and gas chromatography-time-of-flight mass spectrometry (GC-TOFMS). The result showed that the AtMYB12 transcription factor upregulated the phenylpropanoid biosynthesis pathway genes, which leads to the highest accumulation of primary and secondary metabolites in the AtMYB12-overexpressing hairy root lines (transgenic) than that of the GUS-overexpressing hairy root line (control) when grown under the light and dark conditions. However, when the transgenic hairy root lines were grown under dark conditions, the phenolic and flavone content was not significantly different from that of the control hairy root lines. Similarly, the heat map and hierarchical clustering analysis (HCA) result showed that most of the metabolites were significantly abundant in the transgenic hairy root cultures grown under light conditions. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) showed that the identified metabolites were separated far based on the primary and secondary metabolite contents present in the control and transgenic hairy root lines grown under light and dark conditions. Metabolic pathway analysis of the detected metabolites showed 54 pathways were identified, among these 30 were found to be affected. From these results, the AtMYB12 transcription factor activity might be light-responsive in the transgenic hairy root cultures, triggering the activation of the primary and secondary metabolic pathways in Korean mint.

Integrated Metabolomic and Transcriptomic Analysis Reveals Differential Flavonoid Accumulation and Its Underlying Mechanism in Fruits of Distinct Canarium album Cultivars

Canarium album fruit has great potential to be consumed as a raw material not only for food but also medicine. The diverse active metabolites composition and content of C. album fruits greatly affect their pharmacological effects. However, up to now, there has been no report on the global metabolome differences among fruits from distinct C. album cultivars. In our present study, by using non-targeted metabolomics techniques, we identified 87 DAMs (differentially accumulated metabolites) including 17 types of flavonoids from fruits of four different C. album cultivars. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that the flavone and flavonol biosynthesis- and flavonoid biosynthesis-related DAMs were major factors determining their metabolome differences. Comparative transcriptomic analysis revealed that 15 KEGG pathways were significantly enriched by genes of the identified 3655 DEGs (differentially expressed genes) among different C. album cultivars. Consistent with the metabolome data, flavonoid biosynthesis-related DEGs, including eight key structural genes (such as FLS, CCoAOMT, CHI, C4H, DFR, LAR, and C3′H, etc.) and several regulatory transcription factor (TF) genes (including 32 MYBs and 34 bHLHs, etc.), were found to be significantly enriched (p < 0.01). Our study indicated that the differential expression of flavonoid biosynthesis-related genes and accumulation of flavonoids played dominant roles in the various metabolome compositions of fruits from different C. album cultivars.

Heterologous Expression of Three Transcription Factors Differently Regulated Astragalosides Metabolic Biosynthesis in Astragalus membranaceus Hairy Roots

Astragalus membranaceus has been used as a highly popular Chinese herbal medicine for centuries. Triterpenoids, namely astragalosides I, II, III, and IV, represent the main active compounds in this plant species. Transcription factors have a powerful effect on metabolite biosynthesis in plants. We investigated the effect of the Arabidopsis MYB12, production of anthocyanin pigment 1 (PAP1), and maize leaf color (LC) transcription factors in regulating the synthesis of astragaloside metabolites in A. membranaceus. Overexpression of these transcription factors in hairy roots differentially up-regulated these active compounds. Specifically, the overexpression of LC resulted in the accumulation of astragalosides I–IV. The content of astragalosides I and IV were, in particular, more highly accumulated. Overexpression of MYB12 increased the accumulation of astragaloside I in transgenic hairy roots, followed by astragaloside IV, and overexpression of PAP1 resulted in the increased synthesis of astragalosides I and IV. In addition, we found that overexpression of PAP1 together with LC increased astragaloside III levels. At the transcriptional level, several key genes of the mevalonate biosynthetic pathway, especially HMGR1, HMGR2, and HMGR3, were up-regulated differentially in response to these transcription factors, resulting in astragaloside synthesis in the hairy roots of A. membranaceus. Overall, our results indicated that heterologous expression of Arabidopsis MYB12, PAP1, and maize LC differentially affected triterpenoids biosynthesis, leading to the increased biosynthesis of active compounds in A. membranaceus.

Glucose Supply Induces PsMYB2-Mediated Anthocyanin Accumulation in Paeonia suffruticosa 'Tai Yang' Cut Flower

Tree peony (Paeonia suffruticosa) is a well-known Chinese ornamental plant with showy flower color. However, the color fading problem during vase time seriously blocks its development in the cut flower market. In this study, we found that exogenous glucose supply improved the color quality of P. suffruticosa 'Tai Yang' cut flowers with increased total soluble sugar and anthocyanin contents of petals. Besides, the promotion effect of glucose was better than the osmotic control of 3-O-methylglucose (3OMG) treatment and the glucose analog mannose treatment. The structural genes, including PsF3H, PsF3'H, PsDFR, PsAOMT, and PsUF5GT, were remarkably upregulated under glucose treatment. Meanwhile, the regulatory genes, including PsbHLH1, PsbHLH3, PsMYB2, PsWD40-1, and PsWD40-2, also showed a strong response to glucose treatment. Among these five regulatory genes, PsMYB2 showed less response to 3OMG treatment but was highly expressed under glucose and mannose treatments, indicating that PsMYB2 may have an important role in the glucose signal pathway. Ectopic overexpression of PsMYB2 in Nicotiana tabacum resulted in a strong pigmentation in petals and stamens of tobacco flowers accompanied with multiple anthocyanin biosynthetic genes upregulated. More importantly, the overexpression of PsMYB2 enhanced the ability of glucose-induced anthocyanin accumulation in Arabidopsis thaliana seedlings since PsMYB2-overexpressing Arabidopsis showed higher expression levels of AtPAL1, AtCHS, AtF3H, AtF3'H, AtDFR, and AtLDOX than those of wild type under glucose treatment. In summary, we suggested that glucose supply promoted petal coloration of P. suffruticosa 'Tai Yang' cut flower through the signal pathway, and PsMYB2 was a key component in this process. Our research made a further understanding of the mechanism that glucose-induced anthocyanin biosynthesis of P. suffruticosa cut flowers during postharvest development, laying a foundation for color retention technology development of cut flowers.

Tartary Buckwheat R2R3-MYB Gene FtMYB3 Negatively Regulates Anthocyanin and Proanthocyanin Biosynthesis

Anthocyanins and proanthocyanidins (PAs) are vital secondary metabolites in Tartary buckwheat because of their antioxidant capacities and radical scavenging functions. It has been demonstrated that R2R3-MYB transcription factors (TFs) are essential regulators of anthocyanin and PA biosynthesis in many plants. However, their regulatory mechanisms in Tartary buckwheat remain to be clarified. Here, we confirmed the role of FtMYB3 in anthocyanin and PA biosynthesis. FtMYB3, which belongs to the subgroup 4 R2R3 family was predominantly expressed in roots. The transcriptional expression of FtMYB3 increased significantly under hormone treatment with SA and MeJA and abiotic stresses including drought, salt, and cold at the seedling stage. Functional analyses showed that FtMYB3 negatively regulated anthocyanin and PA biosynthesis, primarily via downregulating the expression of the DFR, ANS, BAN, and TT13 in transgenic Arabidopsis thaliana, which may depend on the interaction between FtMYB3 and FtbHLH/FtWD40. Altogether, this study reveals that FtMYB3 is a negative regulatory transcription factor for anthocyanin and PA biosynthesis in Tartary buckwheat.

Transcription factor McWRKY71 induced by ozone stress regulates anthocyanin and proanthocyanidin biosynthesis in Malus crabapple

In plants, anthocyanins and proanthocyanidins (PAs) play important roles in plant resistance to abiotic stress. In this study, ozone (O₃) treatments caused the up-regulation of Malus crabapple structural genes McANS, McCHI, McANR and McF3H, which promoted anthocyanin and PA accumulation. We identified the WRKY transcription factor (TF) McWRKY71 by screening differentially expressed genes (DEGs) that were highly expressed in response to O₃ stress from an RNA sequencing (RNA-seq) analysis. Overexpressing McWRKY71 increased the resistance of 'Orin' apple calli to O₃ stress and promoted the accumulation of anthocyanins and PAs, which facilitated reactive oxygen species scavenging to further enhance O₃ tolerance. Biochemical and molecular analyses showed that McWRKY71 interacted with McMYB12 and directly bound the McANR promoter to participate in the regulation of PA biosynthesis. These findings provide new insights into the WRKY TFs mechanisms that regulate the biosynthesis of secondary metabolites, which respond to O₃ stress, in Malus crabapple.

ROS1 promotes low temperature-induced anthocyanin accumulation in apple by demethylating the promoter of anthocyanin-associated genes

Low temperature can affect the growth and development of plants through changes in DNA demethylation patterns. Another known effect of low temperature is the accumulation of anthocyanin pigments. However, it is not known whether the two phenomena are linked, specifically, whether DNA demethylation participates in anthocyanin accumulation in response to low-temperature stress. The ROS1 gene is involved in plant DNA demethylation and influences methylation levels in response to low temperature stress. In this study, using RNA sequencing, we detected that the transcription levels of MdROS1 correlate with the anthocyanin content, as well as with those of anthocyanin biosynthesis-related genes in apple (Malus domestica), at low temperatures. Genomic bisulfite sequencing showed that the methylation levels of the promoters of the anthocyanin related genes MdCHS, MdCHI, MdF3'H, MdANS, MdUFGT, and MdMYB10 decreased in apple leaves after low-temperature treatment. Similar expression and methylation results were also found in apple fruit. Transiently silencing MdROS1 in the leaves and fruit of apple cultivars inhibited the accumulation of anthocyanins and led to decreased expression of anthocyanin biosynthetic genes, and the opposite results were detected in MdROS1-overexpressing leaves and fruit. A promoter binding assay showed that the conserved RRD-DME domains of MdROS1 directly bind to the promoters of MdF3'H and MdUFGT. Taken together, these results suggest that ROS1 affects the anthocyanin biosynthetic pathway by decreasing the methylation level of anthocyanin-related gene promoters, thereby increasing their expression and increasing anthocyanin accumulation.

Recent advances of chitosan-based nanoparticles for biomedical and biotechnological applications

Chitosan is a natural alkaline polysaccharide, which widely exists in marine crustaceans such as shrimp and crab, has been shown to have various biological activities. It has attracted considerable attention in biomedicine and nanomaterials fields because of its excellent properties, such as biocompatibility, biodegradability, non-toxicity and easy access. In addition, because of active hydroxyl and amino groups in chitosan molecules, different functional groups can be introduced into chitosan molecules by molecular modification or chemical modification, which extends their applications. Nanoparticles with small size and large surface area can be used as diagnostic and therapeutic tools in the biomedical field, which make it easier to understand, detect and treat human diseases. The nanomaterials based on chitosan have important applications in biomedicine, industry, pharmacy, agriculture, and other fields. This review highlights the recent advances on chitosan-based nanoparticles for antibacterial property, drug and gene delivery, cancer and hyperthermia therapy, cell imaging, restorative dentistry, wound healing, tissue engineering and other biomedical fields. The nanotechnology fields involving biosensors, water treatment, food industry and agriculture are also briefly reviewed.

Codon usage bias predicts the functional MYB10 gene in Populus

Analysis of codon usage bias (CUB) in different species can reveal the patterns of genetic information transfer across those species. To better understand the characteristics of MYB10-a key regulator of anthocyanin biosynthesis-and identify the true (functional) MYB10 gene among the two candidates in Populus, we analysed the coding sequences of MYB10 genes in 10 different species using Codon W, CHIPS, CUSP, and CAI. Majority of the optimal amino acid codons of MYB10 genes ended with A/U, and GGA, UCA, GCA, AGA, and CCA were over-represented in all plant species studied. Among the two most promising MYB10 gene candidates in Populus, Potri.17G125700 shared a higher similarity of codon usage with MYB10 genes from other plant species, suggesting that it encodes the functional MYB10 in Populus. We verified this speculation by cloning both candidate MYB10 genes from Populus into vectors to produce transiently transformed seedlings. Colour phenotypes and anthocyanin content of the transiently transformed seedlings indicated that Potri.17G125700 encodes the true MYB10 transcription factor, which positively regulates anthocyanin accumulation in Populus. Furthermore, CUB analysis was used to select the most promising MYB12 candidate in Malus sp. (crabapple). Our results demonstrate the effectiveness of CUB analysis as a promising method to identify the functional gene from a set of candidates in long-living plants with complex genetics.

Comparative transcriptome analysis of tubers, stems, and flowers of Gastrodia elata Blume reveals potential genes involved in the biosynthesis of phenolics

Orchidaceae, well known for its fascinating flowers, is one of the largest and most diverse families of flowering plants. There are many kinds of plants in this family; these are distributed practically globally and have high ornamental and medicinal values. Gastrodia elata Blume, a traditional Chinese medicinal herb, is a rootless and leafless achlorophyllous orchid. Phenolic compounds are considered to be the major bioactive constituents in G. elata, with antioxidant, antiangiogenic, neuroprotective, antidepressant, anxiolytic, and sedative activities. In this study, we determined the contents of six main phenolic components in tubers, stems and flowers from G. elata. Meanwhile, the transcriptomes of the tuber, stem and flower tissues of G. elata were obtained using the BGISEQ-500 platform. A total of 58.29 Gb of data and 113,067 unigenes were obtained, of which 74,820 unigenes were functionally annotated against seven public databases. Differentially expressed genes between tuber, stem and flower tissues were identified. A total of 76 DEGs encoding eight key enzymes were identified as candidate genes involved in the biosynthesis of phenolics in G. elata. For further validation, the expression levels of unigenes were measured using quantitative real-time PCR. Our results greatly enrich the transcriptomic data of G. elata and provide valuable information for the identification of candidate genes involved in the biosynthesis of secondary metabolites.

The R2R3-MYB transcription factor MtMYB134 orchestrates flavonol biosynthesis in Medicago truncatula

Our results provide insights into the flavonol biosynthesis regulation of M. truncatula. The R2R3-MYB transcription factor MtMYB134 emerged as tool to improve the flavonol biosynthesis. Flavonols are plant specialized metabolites with vital roles in plant development and defense and are known as diet compound beneficial to human health. In leguminous plants, the regulatory proteins involved in flavonol biosynthesis are not well characterized. Using a homology-based approach, three R2R3-MYB transcription factor encoding genes have been identified in the Medicago truncatula reference genome sequence. The gene encoding a protein with highest similarity to known flavonol regulators, MtMYB134, was chosen for further experiments and was characterized as a functional flavonol regulator from M. truncatula. MtMYB134 expression levels are correlated with the expression of MtFLS2, encoding a key enzyme of flavonol biosynthesis, and with flavonol metabolite content. MtMYB134 was shown to activate the promoters of the A. thaliana flavonol biosynthesis genes AtCHS and AtFLS1 in Arabidopsis protoplasts in a transactivation assay and to interact with the Medicago promoters of MtCHS2 and MtFLS2 in yeast 1-hybrid assays. To ascertain the functional aspect of the identified transcription factor, we developed a sextuple mutant, which is defective in anthocyanin and flavonol biosynthesis. Ectopic expression of MtMYB134 in a multiple myb A. thaliana mutant restored flavonol biosynthesis. Furthermore, overexpression of MtMYB134 in hairy roots of M. truncatula enhanced the biosynthesis of various flavonol derivatives. Taken together, our results provide insight into the understanding of flavonol biosynthesis regulation in M. truncatula and provides MtMYB134 as tool for genetic manipulation to improve flavonol synthesis.

Combining QTL Mapping and Transcriptomics to Decipher the Genetic Architecture of Phenolic Compounds Metabolism in the Conifer White Spruce

Conifer forests worldwide are becoming increasingly vulnerable to the effects of climate change. Although the production of phenolic compounds (PCs) has been shown to be modulated by biotic and abiotic stresses, the genetic basis underlying the variation in their constitutive production level remains poorly documented in conifers. We used QTL mapping and RNA-Seq to explore the complex polygenic network underlying the constitutive production of PCs in a white spruce (Picea glauca) full-sib family for 2 years. QTL detection was performed for nine PCs and differentially expressed genes (DEGs) were identified between individuals with high and low PC contents for five PCs exhibiting stable QTLs across time. A total of 17 QTLs were detected for eight metabolites, including one major QTL explaining up to 91.3% of the neolignan-2 variance. The RNA-Seq analysis highlighted 50 DEGs associated with phenylpropanoid biosynthesis, several key transcription factors, and a subset of 137 genes showing opposite expression patterns in individuals with high levels of the flavonoids gallocatechin and taxifolin glucoside. A total of 19 DEGs co-localized with QTLs. Our findings represent a significant step toward resolving the genomic architecture of PC production in spruce and facilitate the functional characterization of genes and transcriptional networks responsible for differences in constitutive production of PCs in conifers.

Piriformospora indica based elicitation for overproduction of phenolic compounds by hairy root cultures of Ficus carica

Ficus carica L. is an important source of phenolic and flavonoid compounds with valuable pharmaceutical application across various diseases. The current study was carried out to investigate the influence of Piriformospora indica elicitation on growth, production of phenolic compounds, antioxidant capacity, and expression level of flavonoid biosynthetic pathway genes in hairy root (HR) cultures of F. carica. The maximum improvement in accumulation of phenolic compounds was observed when HR culture of Ficus carica L. was exposed to 2% culture filtrate of P. indica for 72 h: gallic acid (80.5- fold), caffeic acid (26.2-fold), coumaric acid (4.5-fold), and cinnamic acid (60.1-fold), apigenin (27.6-fold) and rutin (5.7-fold). While the highest levels of chlorogenic acid (4.9-fold) and quercetin flavonoid (8.8-fold) were obtained after 48 h elicitation with culture filtrate and cell extract of P. indica at 6% (v/v), respectively. The analysis of biosynthetic genes revealed that the exposure to fungal elicitors resulted in up-regulation of phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT) and MYB3 transcription factor. This study shows the potential of P. indica as an efficacious elicitor for enhancing the secondary metabolites production by F. carica HRs.

Isolation and molecular characterization of NtMYB4a, a putative transcription activation factor involved in anthocyanin synthesis in tobacco

The MYB transcription factors are involved in the regulation of plant secondary metabolism, cell development and morphogenesis, and stress response. Here, a full-length, 816-bp NtMYB4a cDNA, which encodes a protein comprising 271 amino acids, was isolated from tobacco leaves. Phylogenetic analysis revealed that NtMYB4a is most similar to Nicotiana. attenuata MYB4, followed by Eriobotrya japonica MYB4, and NtMYB4a clustered with transcriptional activators rather than repressors. Subcellular localization assays showed that NtMYB4 localized in the nucleus, membrane, and cytoplasm. Expression analyses revealed differential expression of NtMYB4a among different tissues and organs and between different developmental stages, with most expression occurring in the stems and leaves during the full-bloom stage. Moreover, NtMYB4a expression was induced by cold, NaCl, PEG, abscisic acid, methyl jasmonate, and dark stressors, and the expression patterns and maximum expression levels varied with the type of stress. Overexpression of NtMYB4a upregulated NtPAL, Nt4CL, NtCHS, NtCHI, NtF3H, NtDFR, NtANS, and NtUFGT, which resulted in increased anthocyanin content in the tobacco corolla and darker colors. However, CRISPR/Cas9-mediated knockout of NtMYB4a downregulated NtPAL, NtC4H, Nt4CL, NtCHS, NtCHI, NtF3H, NtANS, and NtUFGT, which resulted in reduced anthocyanin content, and lighter corolla colors. These results indicated that NtMYB4a positively regulates anthocyanin biosynthesis and is involved in abiotic stress responses in tobacco plants.

LbNR-Derived Nitric Oxide Delays Lycium Fruit Coloration by Transcriptionally Modifying Flavonoid Biosynthetic Pathway

Anthocyanin-derived fleshy fruit pigmentation has become an excellent system for studying the regulatory network underlying fruit ripening and quality. The transcriptional control of anthocyanin biosynthesis by MYB-bHLH-WDR complexes has been well established, but the intermediate signals through which the environmental or developmental cues regulate these transcription factors remain poorly understood. Here we found that nitric oxide (NO) production during Lycium fruit ripening decreased progressively presenting a negative relationship with anthocyanins. After cloning of the nitric reductase (NR) gene from Lycium barbarum (LbNR) plants, we demonstrated that LbNR-derived NO partially inhibited anthocyanin biosynthesis but enhanced proanthocyanidin (PA) accumulation, and delayed fruit coloration. Application of the NO donor, sodium nitroprusside (SNP), produced a similar effect. The endogenous or exogenous NO downregulated the transcripts both of the regulatory genes and the structural genes that related to anthocyanin biosynthesis, while upregulated both of those genes that related to PA biosynthesis. Given there is a significant negative relationship between the levels of anthocyanins and PAs during Lycium fruit ripening, NO not only inhibited anthocyanin de novo biosynthesis but redirected the flavonoid biosynthetic pathway from anthocyanins to PA production. Two types of LrMYB transcription factors of opposite nature, namely anthocyanin-specific and PA-specific, which belong to the R2R3-MYB subfamily and 1R-MYB subfamily, respectively, were identified from L. ruthenicum fruits. It was further found that NO acts by antagonizing the ABA signaling, a phytohormone we have previously shown playing a positive role in Lycium fruit coloration. Our results provided particularly novel information about NO-ABA-anthocyanin interplay during Lycium fruit development and ripening, which may fill a gap between the developmental cues and the transcriptional regulation of anthocyanin biosynthesis.

Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21

Schizochytrium sp. is the best natural resource for omega-3 long-chain polyunsaturated fatty acids. We report a high-quality genome sequence of Schizochytrium limacinum SR21, which has a 63 Mb genome size, with a contig N50 of 2.67 Mb and 6,838 protein-coding genes. Phylogenomic and comparative genomic analyses revealed that DHA-producing Schizochytrium and Aurantiochytrium strains were highly similar and possessed similar genes. Analysis of the fatty acid synthase (FAS) for LC-PUFAs production results in the annotation of all genes in map00062 and map01212. A gene cluster and 10 ORFs related to PKS pathway were found in the genome. 1,402 differentially expressed genes (DEGs) of the treated groups (0.5 g/L yeast extract) were identified by comparing with the control groups (1.0 g/L yeast extract) at 36 h. A weighted gene coexpression network analysis revealed that 2 of 7 modules correlated highly with the fatty acid and DHA contents. The DEGs and transcription factors were significantly correlated with fatty acid biosynthesis, including MYB, Zinc Finger and ACOX. The results showed that these hub genes are regulated by genes involved in fatty acid biosynthesis pathways. The results providing an important reference for further research on promoting fatty acid and DHA accumulation in S. limacinum SR21.

A novel NAC transcription factor, MdNAC42, regulates anthocyanin accumulation in red-fleshed apple by interacting with MdMYB10

Anthocyanin pigmentation is an important consumption trait of apple (Malus domestica Borkh.). In this study, we focused on the identification of NAC (NAM, ATAF1/2 and CUC2) proteins involved in the regulation of anthocyanin accumulation in apple flesh. A group of MdNACs was selected for comparison of expression patterns between the white-fleshed cultivar 'Granny Smith' and red-fleshed 'Redlove'. Among them, MdNAC42 was screened, which exhibited a higher expression level in red-fleshed than in white-fleshed fruit, and has a positive correlation with anthocyanin content as fruits ripened. Moreover, overexpression of MdNAC42 in apple calli resulted in the up-regulation of flavonoid pathway genes, including MdCHS, MdCHI, MdF3H, MdDFR, MdANS and MdUFGT, thereby increasing the accumulation of anthocyanins, which confirmed the roles of MdNAC42 in anthocyanin biosynthesis. Notably, MdNAC42 was demonstrated to have an obvious interaction with MdMYB10 either in vitro or in vivo by yeast two-hybrid combined with bimolecular fluorescence complementation, further suggesting that MdNAC42 is an important part of the regulatory network controlling the anthocyanin pigmentation of red-fleshed apples. To the best of our knowledge, this is the first report identifying the MdNAC gene as related to anthocyanin accumulation in red-fleshed apples. This study provides valuable information for improving the regulatory model of anthocyanin biosynthesis in apple fruit.

MdMYB8 is associated with flavonol biosynthesis via the activation of the MdFLS promoter in the fruits of Malus crabapple

Flavonols are polyphenolic compounds that play important roles in plant stress resistance and development. They are also valuable components of the human diet. The Malus crabapple cultivar 'Flame' provides an excellent model for studying flavonol biosynthesis due to the high flavonol content of its fruit peel. To obtain a more detailed understanding of the flavonol regulatory network involved in fruit development, the transcriptomes of the fruit of the Malus cv. 'Flame' from five continuous developmental stages were analyzed using RNA sequencing. A flavonol-related gene module was identified through weighted gene coexpression network analysis (WGCNA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that phytohormones are involved in regulating flavonol biosynthesis during fruit development. A putative transcription factor, MdMYB8, was selected for further study through hub gene correlation network analysis and yeast one-hybrid assays. Stable overexpression or RNAi knockdown of MdMYB8 in transgenic 'Orin' apple calli resulted in a higher or lower flavonol content, respectively, suggesting that MdMYB8 is a regulator of flavonol biosynthesis. This transcriptome analysis provides valuable data for future studies of flavonol synthesis and regulation.

Transcriptome Analysis Identifies Two Ethylene Response Factors That Regulate Proanthocyanidin Biosynthesis During Malus Crabapple Fruit Development

Proanthocyanidins (PAs) are a class of flavonoid compounds in plants that play many important roles in pest and disease resistance and are beneficial components of the human diet. The crabapple (Malus) provides an excellent model to study PA biosynthesis and metabolism; therefore, to gain insights into the PA regulatory network in Malus plants, we performed RNA-seq profiling of fruits of the 'Flame' cultivar at five sequential developmental stages. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that differentially expressed genes (DEGs) related to the functional category 'plant hormone signal transduction' were significantly enriched during fruit development. Further analysis showed that ethylene signal transduction pathway genes or response genes, such as ERS (ethylene response sensor), EIN3 (ETHYLENE INSENSITIVE 3) and ERFs (ethylene response factors), may play an important role in the regulatory network of PA biosynthesis. Additionally, 12 DEGs, including 10 ERFs, 1 MYB, and 1 bHLH transcription factor, associated with PA biosynthesis were identified using WGCNA. The expression patterns of these genes correlated with PA accumulation trends and transcriptome data from qRT-PCR analysis. The expression of RAP2-4 (RELATED TO APETALA 2-4) and RAV1 (related to ABI3/VP1), which belong to the ERF transcription factor family, showed the greatest correlations with PAs accumulation among the 12 identified TFs. Agrobacterium mediated-transient overexpression of the RAP2-4 led to an increase in PA abundance in crabapple leaves and apple fruits, and the opposite results were observed in RAV1-overexpressed crabapple leaves and apple fruits. Moreover, a yeast one-hybrid assay showed that RAP2-4 and RAV1 specifically bound the promoters of the PA biosynthetic genes McLAR1 and McANR2, respectively. These results indicate that RAP2-4 act as an inducer and RAV1 act as a repressor of PA biosynthesis by regulating the expression of the PA biosynthetic genes McLAR1 and McANR2. Taken together, we identified two potential regulators of PA biosynthesis and provide new insights into the ethylene-PA regulatory network.

RrMYB5- and RrMYB10-regulated flavonoid biosynthesis plays a pivotal role in feedback loop responding to wounding and oxidation in Rosa rugosa

Flavonoids play critical roles in plant responses to various stresses. Few studies have been reported on what the mechanism of activating flavonoid biosynthesis in plant responses to wounding and oxidation is. In this study, flavonoid metabolites and many MYB transcript factors from Rosa rugosa were verified to be induced by wounding and oxidation. RrMYB5 and RrMYB10, which belong to PA1- and TT2-type MYB TFs, respectively, showed extremely high induction. Overexpression of RrMYB5 and RrMYB10 resulted in an increased accumulation of proanthocyanidins in R. rugosa and tobacco by promoting the expression of flavonoid structural genes. Transcriptomic analysis of the transgenic plants showed that most genes, involved in wounding and oxidation response and ABA signalling modulation, were up-regulated by the overexpression of RrMYB10, which was very much similar to that observed in RrANR and RrDFR overexpression transgenics. RrMYB5 and RrMYB10 physically interacted and mutually activated each other's expressions. They solely or synergistically activated the different sets of flavonoid pathway genes in a bHLH TF EGL3-independent manner. Eventually, the accumulation of proanthocyanidins enhanced plant tolerance to wounding and oxidative stresses. Therefore, RrMYB5 and RrMYB10 regulated flavonoid synthesis in feedback loop responding to wounding and oxidation in R. rugosa. Our study provides new insights into the regulatory mechanisms of flavonoid biosynthesis by MYB TFs and their essential physiological functions in plant responses to wounding and oxidative stresses.

Identification of leucoanthocyanidin reductase and anthocyanidin reductase genes involved in proanthocyanidin biosynthesis in Malus crabapple plants

Proanthocyanidins (PAs) from plants are a nutritionally valuable component of the human diet and play important roles in defense against pests and diseases. PAs are products of the flavonoid pathway, which also leads to the production of anthocyanins and flavonols. The enzymes leucoanthocyanidin reductase (LAR) and anthocyanidin reductase (ANR) are involved in PA biosynthesis. The PA biosynthetic pathway has been characterized in several plant species, but the relationship between its expression and PA accumulation in Malus crabapple remains unclear. Here, we cloned the LAR genes MrLAR1, 2, and the ANR genes MrANR1, 2, from the red leaved Malus crabapple cultivar 'Royalty'. The contents of PAs and the expression levels of the LAR and ANR genes were investigated in different organs of the two crabapple cultivars. The transcript levels of two LAR genes and two ANR genes correlated with the contents of the catechin and epicatechin, which are proanthocyanidin precursors. Over-expression of the MrLAR1, 2 and MrANR1, 2 in tobacco (Nicotiana tabacum) promoted the accumulation of PAs, while transient silencing of their expression in crabapple resulted in reduced PA levels. In addition, a negative correlation between quercetin, anthocyanin, and PA biosynthesis was also found during crabapple leaf and fruit peel development. We also found that MrLAR1 and 2 may contribute to epicatechin biosynthesis. In summary, the LAR and ANR genes are critical factors in PA biosynthesis, and there is competition between the quercetin, anthocyanin, and PA biosynthetic pathways during leaf and fruit peel development in Malus crabapple.

Apigenin produced by maize flavone synthase I and II protects plants against UV-B-induced damage

Flavones, one of the largest groups of flavonoids, have beneficial effects on human health and are considered of high nutritional value. Previously, we demonstrated that maize type I flavone synthase (ZmFNSI) is one of the enzymes responsible for the synthesis of O-glycosyl flavones in floral tissues. However, in related species such as rice and sorghum, type II FNS enzymes also contribute to flavone biosynthesis. In this work, we provide evidence that maize has both one FNSI and one FNSII flavone synthases. Arabidopsis transgenic plants expressing each FNS enzyme were generated to validate the role of flavones in protecting plants against UV-B radiation. Here, we demostrate that ZmCYP93G7 (FNSII) has flavone synthase activity and is able to complement the Arabidopsis dmr6 mutant, restoring the susceptibility to Pseudomonas syringae. ZmFNSII expression is controlled by the C1/PL1 + R/B anthocyanin transcriptional complexes, and both ZmFNSI and ZmFNSII are regulated by UV-B. Arabidopsis transgenic plants expressing ZmFNSI or ZmFNSII that accumulate apigenin exhibit less UV-B-induced damage than wild-type plants. Together, we show that maize has two FNS-type enzymes that participate in the synthesis of apigenin, conferring protection against UV-B radiation.

GmMYB176 Regulates Multiple Steps in Isoflavonoid Biosynthesis in Soybean

Isoflavonoids are a group of plant natural compounds synthesized almost exclusively by legumes, and are abundant in soybean seeds and roots. They play important roles in plant-microbial interactions and the induction of nod gene expression in Rhizobia that form nitrogen-fixing nodules on soybean roots. Isoflavonoids also contribute to the positive health effects associated with soybean consumption by humans and animals. An R1 MYB transcription factor GmMYB176 regulates isoflavonoid biosynthesis by activating chalcone synthase (CHS) 8 gene expression in soybean. Using a combination of transcriptomic and metabolomic analyses of GmMYB176-RNAi silenced (GmMYB176-Si), GmMYB176-overexpressed (GmMYB176-OE), and control soybean hairy roots, we identified a total of 33 differentially expressed genes (DEGs) and 995 differentially produced metabolite features (DPMF) in GmMYB176-Si hairy roots, and 5727 DEGs and 149 DPMFs in GmMYB176-OE hairy roots. By a targeted approach, 25 isoflavonoid biosynthetic genes and 6 metabolites were identified as differentially regulated in GmMYB176-OE and GmMYB176-Si soybean hairy roots. Taken together, our results demonstrate the complexity of isoflavonoid biosynthesis in soybean roots and suggest that a coordinated expression of pathway genes, substrate flux and product threshold level may contribute to the dynamic of the pathway regulation.

AaMYB3 interacts with AabHLH1 to regulate proanthocyanidin accumulation in Anthurium andraeanum (Hort.)-another strategy to modulate pigmentation

Proanthocyanidins (PAs), also known as "condensed tannins", are colorless metabolites produced through the flavonoid pathway that are involved in stress resistance in plants. Because PAs are involved in the anthocyanin biosynthetic pathway, they play a role in the modification of pigmentation conferred by anthocyanins in ornamental organs. In this study, we isolated the gene and functionally characterized an R2R3-MYB transcription factor (TF), AaMYB3, and a basic helix-loop-helix TF, AabHLH1, from Anthurium andraeanum (Hort.), a typical tropical flower. AaMYB3 is primarily expressed in the spathe and negatively correlates with anthocyanin accumulation. A complementation test in an Arabidopsis tt8 mutant showed that AabHLH1 successfully restores the PA-deficient seed coat phenotype. The ectopic overexpression of AaMYB3 alone or its coexpression with AabHLH1 in transgenic tobacco resulted in light pink or even pale-pink corolla limbs by reducing their anthocyanin levels and greatly enhancing their accumulation of PAs. This overexpression of the anthurium TF genes upregulated the late anthocyanin enzyme-encoding genes (NtDFR and NtANS) and the key PA genes (NtLAR and NtANR) in transgenic tobacco. The interaction between AaMYB3 and the AabHLH1 protein was confirmed using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. In the developing red spathes of the cultivars "Vitara" and "Tropical", the expression of AaMYB3 was closely linked to PA accumulation, and AaMYB3 was coexpressed with AaCHS, AaF3H, AaDFR, AaANS, AaLAR, and AaANR. The expression pattern of AabHLH1 was similar to that of AaF3'H. Our results suggest that AaMYB3 and AabHLH1 are involved in the regulation of PA biosynthesis in anthurium and could potentially be used to metabolically engineer PA biosynthesis in plants.

Seasonal Variability of the Phytochemical Composition of New Red-Fleshed Apple Varieties Compared with Traditional and New White-Fleshed Varieties

The main objective of this study was to evaluate the impact of the season on the apple phytochemical composition (phenolic compounds, triterpenes, and organic and ascorbic acids). For this proposal, four red-fleshed and five white-fleshed apple varieties from two consecutive seasons (2015 and 2016) were studied. A significant interaction with the season in some compounds was observed. The total phenolic content in the apple flesh from 2015 was higher than that from 2016 probably related with the lower rainfall during the harvest period in 2015 that could have favored hydric stress in the apple trees. The impact of the season on the apple skin was different. The 2016 season was characterized by higher maximum and minimum temperatures resulting in a higher content of flavonols, triterpenes, and organic acids. Anthocyanin concentration in both the flesh and skin of the red-fleshed apples showed no clear relationship to the season, and each variety showed an individual pattern.

Characteristics of dihydroflavonol 4-reductase gene promoters from different leaf colored Malus crabapple cultivars

Anthocyanins are secondary metabolites in land plants that contribute to the colors of leaves and flowers, and are nutritionally valuable components of the human diet. The DFR gene plays an important role in the anthocyanin biosynthetic pathway. In this study, we investigated the regulation of DFR expression and in different Malus crabapple cultivars that show distinct patterns of leaf coloration, and how it influences leaf anthocyanin accumulation and coloration. Specifically, we studied the ever-red leaved cultivar 'Royalty', the ever-green leaved cultivar 'Flame' and the spring-red leaved cultivar 'Radiant'. RT-PCR analysis showed that the expression of McDFR1 correlated with the expression of a MYB transcription factor, McMYB10, and with anthocyanin accumulation. We isolated five McDFR1 promoter fragments from the three cultivars and identified four different fragments (F1-4) that were present either in several cultivars, or only in one. Yeast one-hybrid and electrophoretic mobility shift assay analyses showed that McMYB10 could bind to all the McDFR1 promoters, except McDFR1-Ra2. The F1, F2 and F3 fragments did not affect McMYB10 binding to the McDFR1 promoters; however, we found evidence that the F4 fragment suppressed binding, and that the MYBGAHV amino-acid sequence maybe an important cis-element for McMYB10 protein binding. This information has potential value for strategies to modify plant color through genetic transformation.