Anthocyanin Metabolism Research Articles

Sustained carbon import supports sugar accumulation and anthocyanin biosynthesis during fruit development and ripening in blueberry (Vaccinium ashei)

Fruit ripening is a highly coordinated process involving molecular and biochemical changes that collectively determine fruit quality. The underlying metabolic programs and their transitions leading to fruit ripening remain largely under-characterized in blueberry (Vaccinium sp.), which exhibits atypical climacteric behavior. In this study, we focused on sugar, acid and anthocyanin metabolism in two rabbiteye blueberry cultivars, Premier and Powderblue, during fruit development and ripening. Concentrations of the three major sugars, sucrose (Suc), glucose (Glc), and fructose (Fru) increased steadily during fruit development leading up to ripening, and increased dramatically by around 2-fold in ‘Premier’ and 2- to 3-fold in ‘Powderblue’ during the final stage of fruit ripening. Starch concentration was very low throughout fruit development in both cultivars indicating that it does not serve the role of a major transitory carbon (C) storage form in blueberry fruit. Together, these patterns indicate continued import of C, likely in the form of Suc, throughout blueberry fruit development. Concentrations of the predominant acids, malate and quinate, decreased during ripening, and may contribute to increased shikimate biosynthesis which, in-turn, allows for downstream phenylpropanoid metabolism leading to anthocyanin synthesis. Consistently, anthocyanin concentrations were highest in fully ripened blue fruit. Weighted gene co-expression network analysis (WGCNA) was performed using a ‘Powderblue’ fruit ripening transcriptome and targeted fruit metabolite concentration data. A ‘dark turquoise’ module positively correlated with sugars and anthocyanins, and negatively correlated with acids (malate, quinate), was identified. Gene Ontology (GO) enrichment analysis of this module identified transcripts related to sugar, acid, and phenylpropanoid metabolism pathways. Among these, increased transcript abundance of a VACUOLAR INVERTASE during ripening was consistent with sugar storage in the vacuole. In general, transcript abundance of the glycolysis pathway genes was upregulated during ripening. The transcript abundance of PHOSPHOENOLPYRUVATE (PEP) CARBOXYKINASE increased during fruit ripening and was negatively correlated with malate concentration, suggesting increased malate conversion to PEP, which supports anthocyanin production during fruit ripening. This was further supported by the co-upregulation of several anthocyanin biosynthesis-related genes. Together, this study provides insights into important metabolic programs, and their underlying gene expression patterns during fruit development and ripening in blueberry.

Transcriptomic and Metabolic Analysis Reveals Genes and Pathways Associated with Flesh Pigmentation in Potato (Solanum tuberosum) Tubers.

Anthocyanins, flavonoid pigments, are responsible for the purple and red hues in potato tubers. This study analyzed tubers from four potato cultivars-red RR, purple HJG, yellow QS9, and white JZS8-to elucidate the genetic mechanisms underlying tuber pigmentation. Our transcriptomic analysis identified over 2400 differentially expressed genes between these varieties. Notably, genes within the flavonoid biosynthesis pathway were enriched in HJG and RR compared to the non-pigmented JZS8, correlating with their higher levels of anthocyanin precursors and related substances. Hierarchical clustering revealed inverse expression patterns for the key genes involved in anthocyanin metabolism between pigmented and non-pigmented varieties. Among these, several MYB transcription factors displayed strong co-expression with anthocyanin biosynthetic genes, suggesting a regulatory role. Specifically, the expression of 16 MYB genes was validated using qRT-PCR to be markedly higher in pigmented HJG and RR versus JZS8, suggesting that these MYB genes might be involved in tuber pigmentation. This study comprehensively analyzed the transcriptome of diverse potato cultivars, highlighting specific genes and metabolic pathways involved in tuber pigmentation. These findings provide potential molecular targets for breeding programs focused on enhancing tuber color.

Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening.

Long non-coding RNAs (lncRNAs), a class of important regulatory factors for many biological processes in plants, have received much attention in recent years. To explore the molecular roles of lncRNAs in sweet cherry fruit ripening, we conducted widely targeted metabolome, transcriptome and lncRNA analyses of sweet cherry fruit at three ripening stages (yellow stage, pink stage, and dark red stage). The results show that the ripening of sweet cherry fruit involves substantial metabolic changes, and the rapid accumulation of anthocyanins (cyanidin 3-rutinoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside) is the main cause of fruit coloration. These ripening-related alterations in the metabolic profile are driven by specific enzyme genes related to the synthesis and decomposition of abscisic acid (ABA), cell wall disintegration, and anthocyanin biosynthesis, as well as transcription factor genes, such as MYBs, bHLHs, and WD40s. LncRNAs can target these ripening-related genes to form regulatory modules, incorporated into the sweet cherry fruit ripening regulatory network. Our study reveals that the lncRNA-mRNA module is an important component of the sweet cherry fruit ripening regulatory network. During sweet cherry fruit ripening, the differential expression of lncRNAs will meditate the spatio-temporal specific expression of ripening-related target genes (encoding enzymes and transcription factors related to ABA metabolism, cell wall metabolism and anthocyanin metabolism), thus driving fruit ripening.

Chlorophyllase (PsCLH1) and light-harvesting chlorophyll a/b binding protein 1 (PsLhcb1) and PsLhcb5 maintain petal greenness in Paeonia suffruticosa ‘Lv Mu Yin Yu’

IntroductionGreen flowers are not an adaptive trait in natural plants due to the challenge for pollinators to discriminate from leaves, but they are valuable in horticulture. The molecular mechanisms of green petals remain unclear. Tree peony (Paeonia suffruticosa) is a globally cultivated ornamental plant and considered the ‘King of Flowers’ in China. The P. suffruticosa ‘Lv Mu Yin Yu (LMYY)’ cultivar with green petals could be utilized as a representative model for understanding petal-specific chlorophyll (Chl) accumulation and color formation. ObjectivesIdentify the key genes related to Chl metabolism and understand the molecular mechanism of petal color changes. MethodsThe petal color parameter was analyzed at five developmental stages using a Chroma Spectrophotometer, and Chl and anthocyanin accumulation patterns were examined. Based on comparative transcriptomes, differentially expressed genes (DEGs) were identified, among which three were functionally characterized through overexpression in tobacco plants or silencing in ‘LMYY’ petals. ResultsDuring flower development and blooming, flower color changed from green to pale pink, consistent with the Chl and anthocyanin levels. The level of Chl demonstrated a similar pattern with petal epidermal cell striation density. The DEGs responsible for Chl and anthocyanin metabolism were characterized through a comparative transcriptome analysis of flower petals over three critical developmental stages. The key chlorophyllase (PsCLH1) and light-harvesting chlorophyll a/b binding protein 1 (PsLhcb1) and PsLhcb5 influenced the Chl accumulation and the greenness of ‘LMYY’ petals. ConclusionPsCLH1, PsLhcb1, and PsLhcb5 were critical in accumulating the Chl and maintaining the petal greenness. Flower color changes from green to pale pink were regulated by the homeostasis of Chl degradation and anthocyanin biosynthesis. This study offers insights into underlying molecular mechanisms in the green petal and a strategy for germplasm innovation.

Exogenous inoculation of Pediococcus pentosaceus SSC12 positively regulates anthocyanin biosynthesis to alleviate browning of postharvest litchi (Litchi chinensis Sonn.)

Litchi is prone to pericarp browning after-harvest, which seriously affects the quality of litchi and causes huge loss. Pericarp browning is closely related to anthocyanin metabolism. Lactic acid bacteria (LAB), a kind of probiotics, is used for food preservation. The aim of this study was to investigate whether and how inoculation of LAB strain Pediococcus pentosaceus SSC12 of litchi fruit affect the pericarp browning and anthocyanin metabolism in postharvest through transcriptome and metabolome analyses. This is the first work showing that strain SSC12 suppressed development of browning and maintained the coloration of litchi pericarp at 10 ± 1 °C. Strain SSC12 upregulated 8 key differentially expressed genes (DEGs) associated with anthocyanin biosynthesis and transport, while downregulated 3 key DEGs involved in anthocyanin degradation in anthocyanin synthesis pathway. Strain SSC12 caused increase in 9 different anthocyanin-related metabolites levels and phenylalanine ammonia lyase activity, disease in peroxidase, laccase and polyphenol oxidase activities. Taken together, strain SSC12 suppressed browning of litchi via elevateing anthocyanin synthesis and transport and inhibiting anthocyanin degradation. These findings suggested that strain SSC12 might serve as a potential probiotic strains to alternative for chemical reagents in postharvest fruit preservation and contribute to the exploration of newgreen approachs for postharvest losses.

Promoting Anthocyanin Biosynthesis in Purple Lettuce through Sucrose Supplementation under Nitrogen Limitation

Although nitrogen deficiency and sucrose are linked to anthocyanin synthesis, the potential role of sucrose in regulating anthocyanin biosynthesis under low nitrogen conditions (LN) in purple lettuce (Lactuca sativa L.) remains unclear. We found that adding exogenous sucrose enhanced anthocyanin biosynthesis but significantly inhibited lettuce growth at high concentrations. Optimal results were obtained using 1 mmol/L sucrose in a low-nitrogen nutrient solution (LN + T1). Chlorophyll fluorescence imaging indicated that the addition of exogenous sucrose induced mild stress. Meanwhile, the activities of antioxidant enzymes (SOD, CAT, and POD) and antioxidant capacity were both enhanced. The mild stress activated the antioxidant system, thereby promoting the accumulation of anthocyanins induced by exogenous sucrose. LN + T1 (low nitrogen nutrient solution supplemented with 1 mmol/L sucrose) up-regulated enzyme genes in the biosynthetic pathway of anthocyanins, including phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), dihydroflavonol reductase (DFR), flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H), flavone synthase II (FNSII), and anthocyanidin synthase (ANS). Additionally, various transcription factors such as AP2/ERF, MYB, bHLH, C2H2, NAC, C2C2, HB, MADS, bZIP, and WRKY were found to be up-regulated. This study elucidates the regulatory mechanism of anthocyanin metabolism in response to the addition of exogenous sucrose under low nitrogen conditions and provides a nutrient solution formula to enhance anthocyanin content in modern, high-quality agricultural cultivation.

Differential analysis of metabolites from mulberry (Morus abla L. cv. Longsang 1) juices fermented with Pichia kudriavzevii and Weissella confusa alone or in combination

Mulberry is rich in bioactive substances, which might undergo biotransformation through microbial fermentation, and therefore show great prospect in improving the bioavailability of these substances. We studied the differential metabolites in mulberry juices fermented by Pichia kudriavzevii S1 and Weissella confusa L1 alone or in combination. The sensory analysis using electronic nose and electronic tongue showed that fermentation caused higher response value of aromatic components, reduced bitterness and bitter aftertaste of the juices. The differential metabolites of juices identified by non-targeted metabolomics showed that the contents of total anthocyanins, total flavonoids and total polyphenols in juices fermented by W. confusa and P. kudriavzevii increased by 13.34%, 43.75% and 9.40%, respectively. A total of 10 categories involving 111 kinds of key metabolites were identified in four different treatment groups. These metabolites were mostly involved in amino acid, flavonoid and anthocyanin metabolism pathways. This study might offer new pathways for improving the functional features of mulberry juices through microbial fermentation.

Integrated Transcriptome and Metabolome to Elucidate the Mechanism of Aluminum-Induced Blue-Turning of Hydrangea Sepals

Hydrangea macrophylla is an ornamental plant with varied calyx colors. Interestingly, from red, to purple, to blue, the colors of all Hydrangea macrophylla are formed by unique delphinidin-3-O-glucoside and aluminum ions (Al3+) and 5-O-p-coumaroylquinic acid. The sepals of ‘Blue Mama’ changed from pink to blue, and the contents of delphinidin-3-O-glucoside and aluminum ions increased under 3 g/L aluminum sulfate treatment. However, the mechanism of the effect of aluminum ions on the synthesis and metabolism of anthocyanins in Hydrangea macrophylla is still unclear. In this project, transcriptome sequencing and anthocyanin metabolome analysis were performed on the sepals of ‘Blue Mama’ during flower development at the bud stage (S1), discoloration stage (S2) and full-bloom stage (S3) under aluminum treatment. It was found that delphinidin, delphinidin-3-O-glucoside and delphinidin-3-O-galactoside were the main differential metabolites. The structural genes CHS, F3H, ANS, DFR and BZI in the anthocyanin synthesis pathway were up-regulated with the deepening in sepal color. There was no significant difference between the aluminum treatment and the non-aluminum treatment groups. However, seven transcription factors were up-regulated and expressed to regulate anthocyanin synthesis genes CHS, F3H, BZI and 4CL, promoting the sepals to turn blue. The KEGG enrichment pathway analysis of differentially expressed genes showed that the glutathione metabolism and the ABC transporter pathway were closely related to anthocyanin synthesis and aluminum-ion transport. GST (Hma1.2p1_0158F.1_g069560.gene) may be involved in the vacuolar transport of anthocyanins. The expression of anthocyanin transporter genes ABCC1 (Hma1.2p1_0021F.1_g014400.gene), ABCC2 (Hma1.2p1_0491F.1_g164450.gene) and aluminum transporter gene ALS3 (Hma1.2p1_0111F.1_g053440.gene) were significantly up-regulated in the aluminum treatment group, which may be an important reason for promoting the transport of anthocyanin and aluminum ions to vacuoles and making the sepals blue. These results preliminarily clarified the mechanism of aluminum ion in the synthesis and transport of anthocyanin in Hydrangea macrophylla, laying a foundation for the further study of the formation mechanism of ‘blue complex’ in Hydrangea macrophylla.

Tracing the color: quantitative trait loci analysis reveals new insights into red-flesh pigmentation in apple (Malus domestica).

Red-flesh color development in apple fruit is known to depend upon a particular allele of the MdMYB10 gene. While the anthocyanin metabolic pathway is well characterized, current genetic models do not explain the observed variations in red-flesh pigmentation intensity. Previous studies focused on total anthocyanin content as a phenotypic trait to characterize overall flesh color. While this approach led to a global understanding of the genetic mechanisms involved in color expression, it is essential to adopt a more quantitative approach, by analyzing the variations of other phenolic compound classes, in order to better understand the molecular mechanisms involved in the subtle flesh color variation and distribution. In this study, we performed pedigree-based quantitative trait loci (QTL) mapping, using the FlexQTL™ software, to decipher the genetic determinism of red-flesh color in five F1 inter-connected families segregating for the red-flesh trait. A total of 452 genotypes were evaluated for flesh color and phenolic profiles during 3years (2021-2023). We identified a total of 24 QTLs for flesh color intensity and phenolic compound profiles. Six QTLs were detected for red-flesh color on LG1, LG2, LG8, LG9, LG11, and LG16. Several genes identified in QTL confidence intervals were related to anthocyanin metabolism. Further analyses allowed us to propose a model in which the competition between anthocyanins and flavan-3-ols (monomer and oligomer) end-products is decisive for red-flesh color development. In this model, alleles favorable to high red-flesh color intensity can be inherited from both white-flesh and red-flesh parents.

Unraveling the mechanism of flower color variation in Brassica napus by integrated metabolome and transcriptome analyses.

Brassica napus is one of the most important oil crops in the world. Breeding oilseed rape with colorful flowers can greatly enhance the ornamental value of B. napus and thus improve the economic benefits of planting. As water-soluble flavonoid secondary metabolites, anthocyanins are very important for the synthesis and accumulation of pigments in the petals of plants, giving them a wide range of bright colors. Despite the documentation of over 60 distinct flower shades in B. napus, the intricacies underlying flower color variation remain elusive. Particularly, the mechanisms driving color development across varying flower color backgrounds necessitate further comprehensive investigation. This research undertook a comprehensive exploration through the integration of transcriptome and metabolome analyses to pinpoint pivotal genes and metabolites underpinning an array of flower colors, including beige, beige-red, yellow, orange-red, deep orange-red, white, light-purple, and purple. First, we used a two-way BLAST search to find 275 genes in the reference genome of B. napus Darmor v10 that were involved in making anthocyanins. The subsequent scrutiny of RNA-seq outcomes underscored notable upregulation in the structural genes F3H and UGT, alongside the MYB75, GL3, and TTG1 transcriptional regulators within petals, showing anthocyanin accumulation. By synergizing this data with a weighted gene co-expression network analysis, we identified CHS, F3H, MYB75, MYB12, and MYB111 as the key players driving anthocyanin synthesis in beige-red, orange-red, deep orange-red, light-purple, and purple petals. By integrating transcriptome and weighted gene co-expression network analysis findings with anthocyanin metabolism data, it is hypothesized that the upregulation of MYB75, which, in turn, enhances F3H expression, plays a pivotal role in the development of pigmented oilseed rape flowers. These findings help to understand the transcriptional regulation of anthocyanin biosynthesis in B. napus and provide valuable genetic resources for breeding B. napus varieties with novel flower colors.

Csn-miR156d-CsSPL1 regulates flowering and anthocyanin metabolism.

MiR156 play important roles in regulation of plant growth and development, secondary metabolite synthesis, and other biological processes by targeting the SQUAMOSA promoter binding protein-like (SPL) family. Our previous sequencing data analysis suggested that Csn-miR156d may regulate flowering and anthocyanin accumulation by cleavage and degradation of the expression of the SPL in tea plant, but it remains to be elucidated. In this study, 5'RLM-RACE experiment, tobacco transient transformation, qRT-PCR, and antisense oligonucleotide (asODN) were used to verify that CsSPL1 is the target gene of Csn-miR156d. Stable transformation of Arabidopsis revealed that Csn-miR156d could delay flowering by negatively regulating the transcript levels of FT, AP1, FUL, and SOC1, while overexpression of CsSPL1 showed an opposite effect. Additionally, overexpression of Csn-miR156d in Arabidopsis could enhance the transcription of the anthocyanin biosynthesis-related structural genes DFR, ANS, F3H, UGT78D2, and LDOX, as well as regulatory genes PAP1, MYB113, GL3, MYB11, and MYB12, leading to anthocyanin accumulation. Moreover, asODN experiment revealed that Csn-miR156d could increase the anthocyanin content in tea plant. These results suggest that Csn-miR156d regulates flowering and anthocyanin accumulation in tea plant by suppressing the expression of CsSPL1. Our study provides new insights into the development and anthocyanin accumulation in tea plant and lays a theoretical foundation for further research on the molecular mechanism of miRNAs in regulating tea plant growth and secondary metabolism.

Genome-Wide Identification Analysis of GST Gene Family in Wild Blueberry Vaccinium duclouxii and Their Impact on Anthocyanin Accumulation.

Vaccinium duclouxii, a wild blueberry species native to the mountainous regions of southwestern China, is notable for its exceptionally high anthocyanin content, surpassing that of many cultivated varieties and offering significant research potential. Glutathione S-transferases (GSTs) are versatile enzymes crucial for anthocyanin transport in plants. Yet, the GST gene family had not been previously identified in V. duclouxii. This study utilized a genome-wide approach to identify and characterize the GST gene family in V. duclouxii, revealing 88 GST genes grouped into seven distinct subfamilies. This number is significantly higher than that found in closely related species, with these genes distributed across 12 chromosomes and exhibiting gene clustering. A total of 46 members are classified as tandem duplicates. The gene structure of VdGST is relatively conserved among related species, showing closer phylogenetic relations to V. bracteatum and evidence of purifying selection. Transcriptomic analysis and qRT-PCR indicated that VdGSTU22 and VdGSTU38 were highly expressed in flowers, VdGSTU29 in leaves, and VdGSTF11 showed significant expression in ripe and fully mature fruits, paralleling trends seen with anthocyanin accumulation. Subcellular localization identified VdGSTF11 primarily in the plasma membrane, suggesting a potential role in anthocyanin accumulation in V. duclouxii fruits. This study provides a foundational basis for further molecular-level functional analysis of the transport and accumulation of anthocyanins in V. duclouxii, enhancing our understanding of the molecular mechanisms underlying anthocyanin metabolism in this valuable species.

Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

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.

Impact of dielectric barrier discharge cold plasma on anthocyanin metabolism in blueberries: A targeted metabonomic and transcriptomic analysis

The impact of cold plasma (CP) treatment on anthocyanin accumulation in postharvest blueberries is well-documented. However, the underlying regulatory mechanisms are still not fully understood. To gain further insights, we conducted biochemistry, transcriptomic, and metabolomic analyses. The comparison between control and CP-treated samples revealed 948 differentially expressed genes (DEGs) and 20 differentially accumulated metabolites (DAMs) (Malvidin-3-O-galactoside, Cyanidin-3-O-galactoside, proanthocyanidin B1, peonidin-3-O-galactoside, etc.). A total of 63 DEGs may be involved in anthocyanins biosynthesis, including PAL, C4H, 4CL, CHS, CHI, F3H, F3’H, F3’5’H, FLS, DFR, LDOX, F3GT, UGT, and GST. The co-expression network analysis revealed that UGT plays an important role in the biosynthesis of anthocyanins in CP-treated blueberry at postharvest. These findings indicate that CP treatment promotes the accumulation of anthocyanins by affecting the phenylpropanoid pathways and flavonoid biosynthesis. This research provides fundamental insights into the molecular mechanisms underlying anthocyanin accumulation in blueberries following CP treatment.

Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content.

Understanding the intricate regulatory mechanisms underlying the anthocyanin content (AC) in fruits and vegetables is crucial for advanced biotechnological customization. In this study, we generated high-quality haplotype-resolved genome assemblies for two mulberry cultivars: the high-AC 'Zhongsang5801' (ZS5801) and the low-AC 'Zhenzhubai' (ZZB). Additionally, we conducted a comprehensive analysis of genes associated with AC production. Through genome-wide association studies (GWAS) on 112 mulberry fruits, we identified MaVHAG3, which encodes a vacuolar-type H+-ATPase G3 subunit, as a key gene linked to purple pigmentation. To gain deeper insights into the genetic and molecular processes underlying high AC, we compared the genomes of ZS5801 and ZZB, along with fruit transcriptome data across five developmental stages, and quantified the accumulation of metabolic substances. Compared to ZZB, ZS5801 exhibited significantly more differentially expressed genes (DEGs) related to anthocyanin metabolism and higher levels of anthocyanins and flavonoids. Comparative analyses revealed expansions and contractions in the flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) genes, resulting in altered carbon flow. Co-expression analysis demonstrated that ZS5801 displayed more significant alterations in genes involved in late-stage AC regulation compared to ZZB, particularly during the phase stage. In summary, our findings provide valuable insights into the regulation of mulberry fruit AC, offering genetic resources to enhance cultivars with higher AC traits.

Impact of lipase treatment on cuticle wax structure and anthocyanin metabolism in postharvest blueberries

AbstractIn this paper, we explored the influence of lipase on cuticle wax and anthocyanin metabolism in blueberries. The results demonstrated a progressive alteration in wax crystal structure, transitions from rod‐like to short rod‐like and flaky, and even disappearance of the cuticle wax. Gas chromatography–mass spectrometry analysis revealed a reduction in esters, aldehydes, long‐chain alkanes, and total wax content following lipase treatment of blueberry fruits. Additionally, ultra high performance liquid chromatography–mass spectrometry analysis showed significant decreases in peonidin, petunidin, cyanidin, and delphinidin, accompanied by an increase in malvidin content due to lipase treatment. Subsequent investigations uncovered that lipase treatment inhibited the activities of key anthocyanin synthetic enzymes, namely phenylalanine ammonia‐lyase (PAL), chalcone isomerase (CHI), and dihydroflavonol reductase (DFR). Moreover, lipase treatment downregulated the expression of synthesis‐related genes, including PAL, 4‐coumarate: CoA ligase, chalcone synthase (CHS), CHI, and DFR. In summary, our findings indicate that lipase disrupts the integrity of cuticle wax structure, inhibits anthocyanin synthesis, and reduces anthocyanin content. Accordingly, our studies suggest that inhibiting lipase could offer a novel approach to preserving the freshness and anthocyanin concentration of blueberries.

Metabolomics and transcriptomics reveal molecular mechanisms of anthocyanin accumulation in 'Nanhong' pear (Pyrus ussuriensis) peel at different temperatures

The bright red hue of the 'Nanhong' pear's pericarp is a key sensory attribute, yet its susceptibility to discoloration at harvest poses challenges for maintaining its commercial appeal. This study, employs quality metrics, metabolomics, and transcriptomics to examine fruit quality and anthocyanin metabolism, along with gene expression involved in anthocyanin biosynthesis, under dark conditions at 0 °C, 10 °C, 20 °C, and 30 °C for up to 21 d. Findings indicate that 0 °C is optimal for long-term storage, while 10 °C is preferable for retail display. LC-MS/MS identified 42 anthocyanin metabolites cyanidin-3-O-galactoside (cya-3-O-gal) being the primary pigment in the pericarp. Discoloration was primarily associated with cyanidin-type and peonidin-type anthocyanins. Transcriptome analysis identified a large number of differentially expressed genes (DEGs) in different comparison groups, KEGG pathway analysis highlighted the significant enrichment of DEGs in phenylpropane and flavonoid metabolic pathways. Key genes in the anthocyanin synthesis pathway, including PuPAL, PuCHS, PuCHI, PuF3`H, PuANS, and PuDFR were markedly down-regulated at 20 °C and 30 °C. Transcription factors such as AP2/ERF, WRKY, MYB, NAC, C2H2, bHLH,and bZIP played an influential part in this process. The study also established that fruit senescence and high-temperature stress were the primary causes of pericarp discoloration at these temperatures. Consequently, identifying optimal storage conditions that preserve fruit quality, delay senescence, and sustain anthocyanin accumulation is crucial. In this study, storage at 10 °C demonstrated the most favorable outcomes for maintaining the pericarp's red color during the marketing period.

Comparative Transcriptome Analysis Reveals Changes in Gene Expression Associated with Anthocyanin Metabolism in Begonia semperflorens under Light Conditions

Anthocyanins, recognized as stress indicators, particularly under high-light conditions, play a pivotal role in plant stress responses. The advent of transcriptomics has opened avenues to elucidate the mechanisms underlying high light-induced anthocyanin biosynthesis. This study delved into transcriptomic changes in Begonia semperflorens leaves under varying light intensities: 950–9600 lx (TL_100), 6800–7000 lx (HS_75), and 4300–4500 lx (LS_25). To confirm the expression profiles of the key genes, we chose 12 critical genes associated with anthocyanin production for quantitative reverse transcription PCR (qRT-qPCR) analysis. Following this, we measured the levels of anthocyanins to substantiate the findings from the gene expression analysis. The transcriptome assembly in this study was extensive, yielding 43,038 unigenes that collectively spanned about 49.83 million base pairs, with an average unigene length of 1157 bp and an N50 value of 1685 bp. This assembly facilitated a thorough functional annotation across seven distinct protein databases, leading to the classification of 16,363 unigenes into 58 different families of transcription factors. Our comparative analysis of the transcriptomes highlighted a substantial number of differentially expressed genes (DEGs): 5411 DEGs between HS_75 and TL_100 conditions, with 3078 showing increased expression and 2333 showing decreased expression; 4701 DEGs between LS_25 and TL_100, consisting of 2648 up-regulated and 2053 down-regulated genes; and 6558 DEGs between LS_25 and HS_75, with 3032 genes up-regulated and 3526 down-regulated. These DEGs were significantly involved in critical pathways, such as anthocyanin synthesis, plant hormone signaling, and other regulatory mechanisms. This study suggests that genes, including F3′H, MYB102, and SWEET1, could play vital roles in regulating anthocyanin synthesis in response to various light conditions, potentially impacting the expression levels of other genes, like WRKYs, ATHB12, and those similar to HSP.

GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms.

GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.