Molecular components associated with the regulation of flavonoid biosynthesis

Comparative transcriptome analyses of different orthosiphon aristatus tissues reveal differentially expressed genes associated with flavonoid biosynthesis

Orthosiphon aristatus (O. aristatus) has been used as a popular traditional folk medicine for the treatment of kidney disease. Recent studies have shown that O. aristatus root contains more flavonoids and has higher antioxidant capacity compared to its medicinal parts. However, there is limited knowledge on the mechanisms behind the synthetic biology of flavonoid in all tissues of O. aristatus. Here, we performed high-performance liquid chromatography (HPLC) analysis and comparative transcriptome analyses of flavonoids in all tissues. The content of 4 major flavonoids is significantly higher in roots and leaves compared to stems in O. aristatus. Out of a total of 138,294 Unigenes, the KEGG pathway analysis identified 66 Unigenes encoding 8 key metabolic enzymes involved in the biosynthetic pathway of flavonoid compounds. Additionally, 5,154 on average DEGs involved in flavonoid biosynthesis could be categorised into 58 transcription factor (TF) families. Among the identified DEGs, a total of 5,897 were common to all tissues, with 212 DEGs strongly associated with flavonoid accumulation in root. Several of these key enzyme genes were further validated by quantitative real-time polymerase chain reaction (qRT-PCR). Our research provides novel insights into flavonoids synthetic biology, and highlights O. aristatus root may serve as a valuable resource for medicinal use.

Chickpea defense against dual stresses of salt and Fusarium wilt is enhanced through selected bHLH transcription factors carrying the bHLH-MYC_N domain

The plant transcriptome varies between combined stresses and single stresses, and is regulated differentially by transcription factors. Therefore, understanding the complexities of plant interactions with pathogens in stressed soils is always a challenge. In chickpea, 197 CabHLH genes were newly identified. Expression of 28 defense-associated CabHLHs [individual and combined stresses of Fusarium oxysporum f. sp. ciceris (Foc) and salt (NaCl) in three chickpea cultivars (JG-315: wilt resistant, JG-36: wilt tolerant, and JG-62: wilt susceptible) in Trichoderma asperellum T42 primed and non-primed conditions] revealed upregulation of most CabHLHs at 12 h post-stress in individual stresses but decreased significantly in the combined stress (Foc and salt). However, T42 priming stimulated the transcript accumulation of most CabHLHs even earlier (6 h). Three genes (CabHLH119, 158, and 184 carrying an additional domain bHLH-MYC_N) and two additional genes (CabHLH69 and 172) belonging to the subfamilies IIIde and IIIf were upregulated significantly in all three cultivars under individual and combined stresses, and upregulated further when primed with T42. Expression of the three bHLH-MYC_N domain containing genes, and defense activities (PAL, PO activities, phenylpropanoid accumulation) in the combined stress correlated very strongly. Protein-protein interactome studies further strengthened the claim that the three bHLH-MYC_N domain carrying CabHLHs, is likely to regulate the defense signaling in chickpea under stress as they could form complexes either directly or indirectly with cis-elements of promoters of some important defense genes. The results thus showed the significance of the IIIde and IIIf subfamily genes, particularly those carrying the bHLH-MYC_N domain, in mitigating combined stresses.

Integrated metabolomic and transcriptomic analysis revealed the transition of functional components in edible flower buds of Hemerocallis citrina Baroni

The edible flower buds of Hemerocallis citrina Baroni are used both as a vegetable and functional food. It has various health benefits due to the diversity of natural products. However, the establishment of functional components in the edible flower bud remains to be studied. We conducted a high-resolution metabolomic analysis of flower buds at three developmental stages, 1-2 cm, 4-6 cm, and edible (10-15 cm). Our analysis revealed 157 differential accumulated metabolites, including flavonoids (49), fatty acids (17) and terpenoids (13) while most of them decreased during flower bud development. Among them, 2 flavonoids, 2 long-chain fatty acids and 1 triterpene saponin are highly accumulated in edible flower buds. Furthermore, the expression levels of catalytic genes mirrored the changes in metabolite levels detected. These results track the dynamics of functional component accumulation during edible flower bud development, laying the theoretical basis for nutrition formation in H. citrina.

Ectopic expression of a truncated NLR gene from wild Arachis enhances resistance to Fusarium oxysporum

Fusarium oxysporum causes devastating vascular wilt diseases in numerous crop species, resulting in substantial yield losses. The Arabidopsis thaliana-F. oxysporum f.sp. conglutinans (FOC) model system enables the identification of meaningful genotype-phenotype correlations and was applied in this study to evaluate the effects of overexpressing an NLR gene (AsTIR19) from Arachis stenosperma against pathogen infection. AsTIR19 overexpression (OE) lines exhibited enhanced resistance to FOC without any discernible phenotype penalties. To elucidate the underlying resistance mechanisms mediated by AsTIR19 overexpression, we conducted whole transcriptome sequencing of an AsTIR19-OE line and non-transgenic wild-type (WT) plants inoculated and non-inoculated with FOC using Illumina HiSeq4000. Comparative analysis revealed 778 differentially expressed genes (DEGs) attributed to transgene overexpression, while fungal inoculation induced 434 DEGs in the OE line, with many falling into defense-related Gene Ontology (GO) categories. GO and KEGG enrichment analysis showed that DEGs were enriched in the phenylpropanoid and flavonoid pathways in the OE plants. This comprehensive transcriptomic analysis underscores how AsTIR19 overexpression reprograms transcriptional networks, modulating the expression of stress-responsive genes across diverse metabolic pathways. These findings provide valuable insights into the molecular mechanisms underlying the role of this NLR gene under stress conditions, highlighting its potential to enhance resistance to Fusarium oxysporum.

Effect of Slow-Release Urea on Yield and Quality of Euryale ferox

Slow-release urea, as an environmentally friendly fertiliser, can provide a continuous and uniform supply of nutrients needed by the crop, reduce the amount and frequency of fertiliser application, and promote the uptake and utilisation of nitrogen in crops. The production of E. ferox is often dominated by the application of quick-acting fertilisers, resulting in serious problems of over-fertilisation, inappropriate periods of fertilisation, eutrophication of soil and water due to fertilisation, and difficulties in applying fertilisers. Therefore, in this study, different amounts (CK, T1, T2, T3, T4, T5) of SRU (Slow-release Urea) were first applied, and T3 (18.8 kg·667 m-2) was found to significantly improve both yield and quality. Further, it was found that under different SRU (CK, S1, S2, S3, S4) application period treatments, application of 18.8 kg·667 m-2 at AFP20 (S2) period significantly increased the yield and quality of E. ferox. In the seed kernels of E. ferox, the total yield, soluble sugar content, total starch, and flavonoid content increased significantly by 10.35%, 36.40%, 5.91%, and 22.80%, respectively, compared with CK. In addition, the expression of key sugar transporter genes (EfSWEETs), flavonoid synthesis-related genes (EfPAL, EfDFR, etc.), and starch synthesis-related enzyme activities (SBE, SSS, GBSS) were significantly increased. By exploring the quantity of application and application period of SRU, this study was carried out to investigate the in-depth effect of SRU on the growth and development of E. ferox and to provide technical references for the increase in E. ferox yield, the improvement in E. ferox quality, and the simplification of fertiliser application.

UV-induced reactive oxygen species and transcriptional control of 3-deoxyanthocyanidin biosynthesis in black sorghum pericarp

Black pericarp sorghum has notable value due to the biosynthesis of 3-deoxyanthocyanidins (3-DOAs), a rare class of bioactive polyphenols valued as antioxidant food additives and as bioactive compounds with cytotoxicity to human cancer cells. A metabolic and transcriptomic study was conducted to ascertain the cellular events leading to the activation of 3-DOA biosynthesis in black sorghum pericarp. Prolonged exposure of pericarp during grain maturation to high-fluence ultraviolet (UV) light resulted in elevated levels of reactive oxygen species (ROS) and the activation of 3-DOA biosynthesis in pericarp tissues. In conjunction with 3-DOA biosynthesis was the transcriptional activation of specific family members of early and late flavonoid biosynthesis pathway genes as well as the downstream activation of defense-related pathways. Promoter analysis of genes highly correlated with 3-DOA biosynthesis in black pericarp were enriched in MYB and HHO5/ARR-B motifs. Light microscopy studies of black pericarp tissues suggest that 3-DOAs are predominantly localized in the epicarp and are associated with the cell wall. A working model of UV-induced 3-DOA biosynthesis in black pericarp is proposed that shares features of plant immunity associated with pathogen attack or mechanical wounding. The present model depicts ROS accumulation, the transcriptional activation of receptor kinases and transcription factors (TFs) including NAC, WRKY, bHLH, AP2, and C2H2 Zinc finger domain. This study identified key biosynthetic and regulatory genes of 3-DOA accumulation in black pericarp and provided a deeper understanding of the gene networks and cellular events controlling this tissue-and genotype-specific trait.

Genome-wide analysis of Citrus medica ABC transporters reveals the regulation of fruit development by CmABCB19 and CmABCC10

ATP-binding cassette (ABC) transporters are vital for plant growth and development as they facilitate the transport of essential molecules. Despite the family's significance, limited information exists about its functional distinctions in Citrus medica. Our study identified 119 genes encoding ABC transporter proteins in the C. medica genome. Through an evolutionary tree and qPCR analysis, two ABC genes, CmABCB19 and CmABCC10, were implicated in C. medica fruit development, showing upregulation in normal fruits compared to malformed fruits. CmABCB19 was found to localize to the plasma membrane of Nicotiana tabacum, exhibiting indole-3-acetic acid (IAA) efflux activity in the yeast mutant strain yap1. CmABCC10, a tonoplast-localized transporter, exhibited efflux of diosmin, nobiletin, and naringin, with rutin influx in strain ycf1. Transgenic expression of CmABCB19 and CmABCC10 in Arabidopsis thaliana induced alterations in auxin and flavonoid content, impacting silique and seed size. This effect was attributed to the modulation of structural genes in the auxin biosynthesis (YUC5/9, CYP79B2, CYP83B1, SUR1) and flavonoid biosynthesis (4CL2/3, CHS, CHI, FLS1/3) pathways. In summary, the functional characterization of CmABCB19 and CmABCC10 illuminates auxin and flavonoid transport, offering insights into their interplay with biosynthetic pathways and providing a foundation for understanding the transporter's role in fruit development.

The influence of spatial distribution and transcriptional regulation of secondary metabolites on the bioactivities of Adenophora triphylla (Japanese lady bell)

The distribution of secondary metabolites in plant tissues plays a crucial role in determining their pharmacological properties. In this study, we investigated the dynamics of the bioactive compounds in Adenophora triphylla, a medicinal herb with diverse therapeutic applications. The anti-inflammatory properties of the EtOAc fraction from the aerial part extract (A_ EtF) exhibited an IC50 value of 27.2 ± 2.3 μg/mL, significantly surpassing that of the EtOAc fraction from the root extract (R_EtF) with an IC50 of 38.9 ± 2.9 μg/mL. Similarly, the anti-melanogenic activity of A_EtF (IC50 = 68.9 ± 2.3 μg/mL) outperformed that of R_EtF (IC50 = 90.0 ± 5.5 μg/mL). Analysis of the distinct chemical profiles of these tissues using UPLC-ESI-Q-TOF-MS revealed that the distribution of secondary metabolites contributes to the observed variations in pharmacological properties between the aerial parts and roots. Transcriptome analysis further elucidated spatially regulated genes associated with secondary metabolism, highlighting the role of AbtYABBYs as potential regulators of phenylpropanoid biosynthesis. To validate their function, these genes were transiently expressed in tobacco leaves via agro-infiltration, confirming their role in modulating polyphenolic compound biosynthesis. Our findings underscore the importance of understanding spatial gene expression patterns for harnessing the complete pharmacological potential of medicinal plants. This study provides valuable insights into the spatial regulation of secondary metabolism and lays the groundwork for targeted manipulation of plant bioactivity for therapeutic and industrial applications.

Flavonoid Synthesis Pathway Response to Low-Temperature Stress in a Desert Medicinal Plant, Agriophyllum Squarrosum (Sandrice)

Background/Objectives:Agriophyllum squarrosum (L.) Moq. (A. squarrosum), also known as sandrice, is an important medicinal plant widely distributed in dunes across all the deserts of China. Common garden trials have shown content variations in flavonoids among the ecotypes of sandrice, which correlated with temperature heterogeneity in situ. However, there have not been any environmental control experiments to further elucidate whether the accumulation of flavonoids was triggered by cold stress; Methods: This study conducted a four-day ambient 4 °C low-temperature treatment on three ecotypes along with an in situ annual mean temperature gradient (Dulan (DL), Aerxiang (AEX), and Dengkou (DK)); Results: Target metabolomics showed that 12 out of 14 flavonoids in sandrice were driven by cold stress. Among them, several flavonoids were significantly up-regulated, such as naringenin and naringenin chalcone in all three ecotypes; isorhamnetin, quercetin, dihydroquercetin, and kaempferol in DL and AEX; and astragalin in DK. They were accompanied by 19 structural genes of flavonoid synthesis and 33 transcription factors were markedly triggered by cold stress in sandrice. The upstream genes, AsqAEX006535-CHS, AsqAEX016074-C4H, and AsqAEX004011-4CL, were highly correlated with the enrichment of naringenin, which could be fine-tuned by AsqAEX015868-bHLH62, AsqAEX001711-MYB12, and AsqAEX002220-MYB1R1; Conclusions: This study sheds light on how desert plants like sandrice adapt to cold stress by relying on a unique flavonoid biosynthesis mechanism that regulating the accumulation of naringenin. It also supports the precise development of sandrice for the medicinal industry. Specifically, quercetin and isorhamnetin should be targeted for development in DL and AEX, while astragalin should be precisely developed in DK.

Integrative metabolome and transcriptome analysis characterized methyl jasmonate-elicited flavonoid metabolites of Blumea balsamifera

As a commonly used medicinal plant, the flavonoid metabolites of Blumea balsamifera and their association with genes are still elusive. In this study, the total flavonoid content (TFC), flavonoid metabolites and biosynthetic gene expression patterns of B. balsamifera after application of exogenous methyl jasmonate (MeJA) were scrutinized. The different concentrations of exogenous MeJA increased the TFC of B. balsamifera leaves after 48 h of exposure, and there was a positive correlation between TFC and the elicitor concentration. A total of 48 flavonoid metabolites, falling into 10 structural classes, were identified, among which flavones and flavanones were predominant. After screening candidate genes by transcriptome mining, the comprehensive analysis of gene expression level and TFC suggested that FLS and MYB may be key genes that regulate the TFC in B. balsamifera leaves under exogenous MeJA treatment. This study lays a foundation for elucidating flavonoids of B. balsamifera, and navigates the breeding of flavonoid-rich B. balsamifera varieties.

HY5 and PIF antagonistically regulate HMGR expression and sterol biosynthesis in Arabidopsis thaliana

Secondary metabolites play multiple crucial roles in plants by modulating various regulatory networks. The biosynthesis of these compounds is unique to each species and is intricately controlled by a range of developmental and environmental factors. While light's role in certain secondary metabolites is evident, its impact on sterol biosynthesis remains unclear. Previous studies indicate that ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor, is pivotal in skotomorphogenesis to photomorphogenesis transition. Additionally, PHYTOCHROME INTERACTING FACTORs (PIFs), bHLH transcription factors, act as negative regulators. To unveil the light-dependent regulation of the mevalonic acid (MVA) pathway, a precursor for sterol biosynthesis, mutants of light signaling components, specifically hy5-215 and the pifq quadruple mutant (pif 1,3,4, and 5), were analyzed in Arabidopsis thaliana. Gene expression analysis in wild-type and mutants implicates HY5 and PIFs in regulating sterol biosynthesis genes. DNA-protein interaction analysis confirms their interaction with key genes like AtHMGR2 in the rate-limiting pathway. Results strongly suggest HY5 and PIFs' pivotal role in light-dependent MVA pathway regulation, including the sterol biosynthetic branch, in Arabidopsis, highlighting a diverse array of light signaling components finely tuning crucial growth pathways.

Integrated metabolomic and transcriptomic analysis reveals biosynthesis mechanism of flavone and caffeoylquinic acid in chrysanthemum

BACKGROUND

Chrysanthemum morifolium 'HangBaiJu', a popular medicinal and edible plant, exerts its biological activities primarily through the presence of flavones and caffeoylquinic acids (CQAs). However, the regulatory mechanism of flavone and CQA biosynthesis in the chrysanthemum capitulum remains unclear.

RESULTS

In this study, the content of flavones and CQAs during the development of chrysanthemum capitulum was determined by HPLC, revealing an accumulation pattern with higher levels at S1 and S2 and a gradual decrease at S3 to S5. Transcriptomic analysis revealed that CmPAL1/2, CmCHS1/2, CmFNS, CmHQT, and CmHCT were key structural genes in flavones and CQAs biosynthesis. Furthermore, weighted gene co-expression correlation network analysis (WGCNA), k-means clustering, correlation analysis and protein interaction prediction were carried out in this study to identify transcription factors (TFs) associated with flavone and CQA biosynthesis, including MYB, bHLH, AP2/ERF, and MADS-box families. The TFs CmERF/PTI6 and CmCMD77 were proposed to act as upstream regulators of CmMYB3 and CmbHLH143, while CmMYB3 and CmbHLH143 might form a complex to directly regulate the structural genes CmPAL1/2, CmCHS1/2, CmFNS, CmHQT, and CmHCT, thereby controlling flavone and CQA biosynthesis.

CONCLUSIONS

Overall, these findings provide initial insights into the TF regulatory network underlying flavones and CQAs accumulation in the chrysanthemum capitulum, which laid a theoretical foundation for the quality improvement of C. morifolium 'HangBaiJu' and the high-quality development of the industry.

Identification of MYB Transcription Factor, a Regulator Related to Hydrolysable Tannin Synthesis in Canarium album L., and Functional Analysis of CaMYBR04

Hydrolysed tannins (HTs) are polyphenols, which are related to the astringency, flavour, colour, stability, medicinal value and other characteristics of many fruits and vegetables. The biosynthetic mechanism of the majority of HTs remains unknown, and many biosynthetic pathways of HTs are speculative conclusions that have not been confirmed. The fruit of Canarium album L. (Chinese olive), which is notable for its pharmacological and edible properties, is rich in HTs. The fruit has a distinctive bitter and astringent taste when initially consumed, which mellows to a sweet sensation upon chewing. HTs serve as the primary material basis for the formation of the Chinese olive fruit's astringent quality and pharmacological effects. In this study, the fruit of C. album Changying was utilised as the research material. The objective of this study was to provide a theoretical basis for the quality control of Chinese olive fruit and the application and development of its medicinal value. In addition, the study aimed to identify and screen related MYB transcription factors involved in the synthesis of HTs in the fruit and to clarify the mechanism of MYBs in the process of synthesis and regulation of HTs in Chinese olive fruit. The principal findings were as follows. A total of 83 differentially expressed Chinese olive MYB transcription factors (CaMYBs) were identified, including 54 1R-MYBs (MYB-related), 25 2R-MYBs (R2R3-MYBs), 3 3R-MYBs, and 1 4R-MYB. Through trend analysis and correlation analysis, it was found that CaMYBR04 (Isoform0032534) exhibited a significantly higher expression (FPKM) than the other CaMYBs. The full-length cDNA sequence of CaMYBR04 was cloned and transformed into strawberry. The results demonstrated that CaMYBR04 significantly enhanced the fruit's hydrolysable tannin content. Consequently, this study elucidated the function of CaMYBR04, a regulator of the Chinese olive fruit hydrolysable tannin synthesis pathway, and established a theoretical foundation for the synthesis and regulation of fruit HTs.

Jasmonate enhances cold acclimation in jojoba by promoting flavonol synthesis

Jojoba is an industrial oil crop planted in tropical arid areas, and its low-temperature sensitivity prevents its introduction into temperate areas. Studying the molecular mechanisms associated with cold acclimation in jojoba is advantageous for developing breeds with enhanced cold tolerance. In this study, metabolomic analysis revealed that various flavonols accumulate in jojoba during cold acclimation. Time-course transcriptomic analysis and weighted correlation network analysis (WGCNA) demonstrated that flavonol biosynthesis and jasmonates (JAs) signaling pathways played crucial roles in cold acclimation. Combining the biochemical and genetic analyses showed that ScMYB12 directly activated flavonol synthase gene (ScFLS). The interaction between ScMYB12 and transparent testa 8 (ScTT8) promoted the expression of ScFLS, but the negative regulator ScJAZ13 in the JA signaling pathway interacted with ScTT8 to attenuate the transcriptional activity of the ScTT8 and ScMYB12 complex, leading to the downregulation of ScFLS. Cold acclimation stimulated the production of JA in jojoba leaves, promoted the degradation of ScJAZ13, and activated the transcriptional activity of ScTT8 and ScMYB12 complexes, leading to the accumulation of flavonols. Our findings reveal the molecular mechanism of JA-mediated flavonol biosynthesis during cold acclimation in jojoba and highlight the JA pathway as a promising means for enhancing cold tolerance in breeding efforts.

CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum

MAIN CONCLUSION

Our findings shed light on the regulation of anthocyanin and proanthocyanidin biosynthesis in chickpea seed coats. Expression of R2R3-MYB transcription factors CaLAP1 and CaLAP2 enhanced the anthocyanins and proanthocyanidins content in chickpea. The seed coat color is a major economic trait in leguminous crop chickpea (Cicer arietinum). Anthocyanins and proanthocyanidins (PAs) are two classes of flavonoids that mainly contribute to the flower, seed coat and color of Desi chickpea cultivars. Throughout the land plant lineage, the accumulation of anthocyanins and PAs is regulated by MYB and bHLH transcription factors (TFs), which form an MBW (MYB, bHLH, and WD40) complex. Here, we report two R2R3-MYB TFs in chickpea belonging to the anthocyanin-specific subgroup-6, CaLAP1 (Legume Anthocyanin Production 1), and CaLAP2 (Legume Anthocyanin Production 2), which are mainly expressed in the flowers and developmental stages of the seeds. CaLAP1 and CaLAP2 interact with TT8-like CabHLH1 and WD40, forming the MBW complex, and bind to the promoter sequences of anthocyanin- and PA biosynthetic genes CaCHS6, CaDFR2, CaANS, and CaANR, leading to anthocyanins and PA accumulation in the seed coat of chickpea. Moreover, these CaLAPs partially complement the anthocyanin-deficient phenotype in the Arabidopsis thaliana sextuple mutant seedlings. Overexpression of CaLAPs in chickpea resulted in significantly higher expression of anthocyanin and PA biosynthetic genes leading to a darker seed coat color with higher accumulation of anthocyanin and PA. Our findings show that CaLAPs positively modulate anthocyanin and PA content in seed coats, which might influence plant development and resistance to various biotic and abiotic stresses.

Foliar application of iron impacts flavonoid glycosylation and promotes flavonoid metabolism in coloured rice

Coloured rice is known as a healthcare food owing its rich flavonoid content. To better understand the effects of iron on the flavonoid metabolism of coloured rice grains, different concentrations of FeSO4 were foliar sprayed on to red rice Yuhongdao 5815 (RR) and black rice Nanheinuo (BR). The results revealed the association of iron with the increased accumulation of anthocyanins in BR and proanthocyanins in RR along with enhancements in their antioxidant capacities and total flavonoid contents. Metabolomic analysis revealed that the differential metabolites between the iron treated coloured rice and the control primarily occurred because of the O-linked glycosylation of aglycones, which are involved in the flavonoid pathway. RR exhibited a significantly higher number of differential metabolites compared with BR. Thus, foliar FeSO4 application affects the O-linked glycosylation and positively regulates flavonoid metabolism.

Combined Metabolomics and Transcriptomics Analysis of the Distribution of Flavonoids in the Fibrous Root and Taproot of Polygonatum kingianum Coll.et Hemsl

Polygonati rhizoma, known for its distinct yellow rhizomes, is a common therapeutic and culinary plant in Far East Asia. The hue of medicinal plants is closely tied to the flavonoid biosynthesis and content levels. In this research, the fibrous root and taproot of Polygonatum kingianum Coll.et Hemsl. were studied to explore the secondary metabolite expression and flavonoid biosynthesis mechanisms using transcriptomics and metabolomics. Metabolic analysis identified that the differentially accumulated metabolites (DAMs) in the fibrous root and taproot were predominantly flavonoids, steroids, alkaloids, and phenolic acids. Overall, 200 flavonoids were identified in P. kingianum Coll.et Hemsl., with 170 exhibiting variances between the fibrous root and taproot. The transcriptome analysis revealed that a total of 289 unigenes encoding 32 enzymes were annotated into four flavonoid biosynthesis pathways, which include phenylpropanoid biosynthesis pathway, flavonoid biosynthesis pathway, isoflavonoid biosynthesis pathway, and flavone and flavonol biosynthesis pathway. The integration of transcriptomic and metabolomic data elucidated that the 76 differentially expressed genes (DEGs) encoding 13 enzyme genes (HCT, CCOMT, C4H, C3'H, CHI, PGT1, FLS, F3'H, CHS, ANR, DFR, F3'5'H, and LAR) and 15 DAMs preferred to be regulated in the flavonoid biosynthesis pathway. The expression of 10 DEGs was validated by qRT-PCR, agreeing with the same results by RNA-Seq. These findings shed light into the biosynthesis of secondary metabolites in P. kingianum Coll.et Hemsl., offering valuable information for the sustainable utilization and enhancement of this plant species.

Exploring regulatory network of icariin synthesis in Herba Epimedii through integrated omics analysis

Herba Epimedii's leaves are highly valued in traditional Chinese medicine for their substantial concentration of flavonoids, which play a crucial role in manifesting the plant's therapeutic properties. This study investigated the metabolomic, transcriptomic and proteomic profiles of leaves from two Herba Epimedii cultivars, Epipremnum sagittatum (J) and Epipremnum pubescens (R), at three different developmental stages. Metabolite identification and analysis revealed a total of 1,412 and 1,421 metabolites with known structures were found. Flavonoids made up of 33%, including 10 significant accumulated icariin analogues. Transcriptomic analysis unveiled totally 41,644 differentially expressed genes (DEGs) containing five encoded genes participated in icariin biosynthesis pathways. Totally, 9,745 differentially expressed proteins (DEPs) were found, including Cluster-47248.2.p1 (UDP-glucuronosy/UDP-glucosyltransferase), Cluster-30441.2.p1 (O-glucosyltransferase), and Cluster-28344.9.p1 (anthocyanidin 3-O-glucoside 2 "-O-glucosyltransferase-like) through proteomics analysis which are involved to icariin biosynthesis. Protein-protein interaction (PPI) assay exhibited, totally 12 proteins showing a strong relationship of false discovery rate (FDR) <0.05 with these three proteins containing 2 leucine-rich repeat receptor kinase-like protein SRF7, and 5 methyl jasmonate esterase 1. Multi-omics connection networks uncovered 237 DEGs and 72 DEPs exhibited significant associations with the 10 icariin analogues. Overall, our integrated omics approach provides comprehensive insights into the regulatory network underlying icariin synthesis in Herba Epimedii, offering valuable resources for further research and development in medicinal plant cultivation and pharmaceutical applications.

Exploring the dynamic adaptive responses of Epimedium pubescens to phosphorus deficiency by Integrated transcriptome and miRNA analysis

Phosphorus, a crucial macronutrient essential for plant growth and development. Due to widespread phosphorus deficiency in soils, phosphorus deficiency stress has become one of the major abiotic stresses that plants encounter. Despite the evolution of adaptive mechanisms in plants to address phosphorus deficiency, the specific strategies employed by species such as Epimedium pubescens remain elusive. Therefore, this study observed the changes in the growth, physiological reponses, and active components accumulation in E. pubescensunder phosphorus deficiency treatment, and integrated transcriptome and miRNA analysis, so as to offer comprehensive insights into the adaptive mechanisms employed by E. pubescens in response to phosphorus deficiency across various stages of phosphorus treatment. Remarkably, our findings indicate that phosphorus deficiency induces root growth stimulation in E. pubescens, while concurrently inhibiting the growth of leaves, which are of medicinal value. Surprisingly, this stressful condition results in an augmented accumulation of active components in the leaves. During the early stages (30 days), leaves respond by upregulating genes associated with carbon metabolism, flavonoid biosynthesis, and hormone signaling. This adaptive response facilitates energy production, ROS scavenging, and morphological adjustments to cope with short-term phosphorus deficiency and sustain its growth. As time progresses (90 days), the expression of genes related to phosphorus cycling and recycling in leaves is upregulated, and transcriptional and post-transcriptional regulation (miRNA regulation and protein modification) is enhanced. Simultaneously, plant growth is further suppressed, and it gradually begins to discard and decompose leaves to resist the challenges of long-term phosphorus deficiency stress and sustain survival. In conclusion, our study deeply and comprehensively reveals adaptive strategies utilized by E. pubescens in response to phosphorus deficiency, demonstrating its resilience and thriving potential under stressful conditions. Furthermore, it provides valuable information on potential target genes for the cultivation of E. pubescens genotypes tolerant to low phosphorus.

The MYB family and their response to abiotic stress in ginger (Zingiber officinale Roscoe)

BACKGROUND

Zingiber officinale Roscoe, colloquially known as ginger, is a crop of significant medicinal and culinary value that frequently encounters adversity stemming from inhospitable environmental conditions. The MYB transcription factors have garnered recognition for their pivotal role in orchestrating a multitude of plant biological pathways. Nevertheless, the enumeration and characterization of the MYBs within Z. officinale Roscoe remains unknown. This study embarks on a genome-wide scrutiny of the MYB gene lineage in ginger, with the aim of cataloging all ZoMYB genes implicated in the biosynthesis of gingerols and curcuminoids, and elucidating their potential regulatory mechanisms in counteracting abiotic stress, thereby influencing ginger growth and development.

RESULTS

In this study, we identified an MYB gene family comprising 231 members in ginger genome. This ensemble comprises 74 singular-repeat MYBs (1R-MYB), 156 double-repeat MYBs (R2R3-MYB), and a solitary triple-repeat MYB (R1R2R3-MYB). Moreover, a comprehensive analysis encompassing the sequence features, conserved protein motifs, phylogenetic relationships, chromosome location, and gene duplication events of the ZoMYBs was conducted. We classified ZoMYBs into 37 groups, congruent with the number of conserved domains and gene structure analysis. Additionally, the expression profiles of ZoMYBs during development and under various stresses, including ABA, cold, drought, heat, and salt, were investigated in ginger utilizing both RNA-seq data and qRT-PCR analysis.

CONCLUSION

This work provides a comprehensive understanding of the MYB family in ginger and lays the foundation for the future investigation of the potential functions of ZoMYB genes in ginger growth, development and abiotic stress tolerance of ginger.

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.

Molecular mechanism of miRNA mediated biosynthesis of secondary metabolites in medicinal plants

Plant secondary metabolites are important raw materials for the pharmaceutical industry, and their biosynthetic processes are subject to diverse and precise regulation by miRNA. The identification of miRNA molecules in medicinal plants and exploration of their mechanisms not only contribute to a deeper understanding of the molecular genetic mechanisms of plant growth, development and resistance to stress, but also provide a theoretical basis for elucidating the pharmacological effects of authentic medicinal materials and constructing bioreactors for the synthesis of medicinal secondary metabolite components. This paper summarizes the research reports on the discovery of miRNA in medicinal plants and their regulatory mechanisms on the synthesis of secondary metabolites by searching the relevant literature in public databases. It summarizes the currently discovered miRNA and their functions in medicinal plants, and summarizes the molecular mechanisms regulating the synthesis and degradation of secondary metabolites. Furthermore, it provides a prospect for the research and development of medicinal plant miRNA. The compiled information contributes to a comprehensive understanding of the research progress on miRNA in medicinal plants and provides a reference for the industrial development of related secondary metabolite biosynthesis.

Fruit development and ripening orchestrating the biosynthesis and regulation of Lycium barbarum polysaccharides in goji berry

Lycium barbarum polysaccharides (LBPs) are the primary bioactive components in fruits of L. barbarum, commonly known as goji berry. Despite significant progress in understanding the chemical structures and health benefits of LBPs, the biosynthesis and regulation of LBPs in goji berry remains largely unknown. In this study, physiological indicators, including LBPs, were monitored in goji berry during fruit development and ripening (FDR), suggesting that pectin might be the major component of LBPs with increased content reaching 235.8 mg/g DW. Proteomic and transcriptomic analysis show that 6410 differentially expressed genes (DEGs) and 2052 differentially expressed proteins (DEPs) were identified with overrepresentation of flavonoids and polysaccharides-related gene ontology (GO) terms and KEGG pathways. Weighted gene co-expression network analysis (WGCNA) showed that LBPs coexpress with genes involved in pectin biosynthesis (LbGALS3, LbGATL5, LbQUA1, LbGAUT1/4/7, LbRGGAT1, LbRRT1/7, and LbRHM2), modification (LbSBT1.7), and regulation (LbAP2, LbGL2 LbTLP2, LbERF4, and LbTTG2), as well as with novel transcription factors (LbSPL9 and LbRIN homologs) and glycosyltransferases. Transgenic hairy roots overexpressing LbRIN validated that LbRIN modulate the expression of WGCNA-predicted regulators, including LbERF4, LbTTG2, and LbSPL9. These findings suggest that the biosynthesis and regulation of LBPs is conserved partially to those in Arabidopsis pectin. Taken together, this study provides valuable insights into the biosynthesis and regulation of LBPs, which can facilitate future studies on synthetic biology applications and genetic improvement of LBPs.

Comparative Transcriptomics and Metabolomics Analyses of Avicennia marina and Kandelia obovata under Chilling Stress during Seedling Stage

One of the most productive ecosystems in the world, mangroves are susceptible to cold stress. However, there is currently insufficient knowledge of the adaptation mechanisms of mangrove plants in response to chilling stress. This study conducted a comparative analysis of transcriptomics and metabolomics to investigate the adaptive responses of Kandelia obovata (chilling-tolerant) and Avicennia marina (chilling-sensitive) to 5 °C. The transcriptomics results revealed that differentially expressed genes (DEGs) were mostly enriched in signal transduction, photosynthesis-related pathways, and phenylpropanoid biosynthesis. The expression pattern of genes involved in photosynthesis-related pathways in A. marina presented a downregulation of most DEGs, which correlated with the decrease in total chlorophyll content. In the susceptible A. marina, all DEGs encoding mitogen-activated protein kinase were upregulated. Phenylpropanoid-related genes were observed to be highly induced in K. obovata. Additionally, several metabolites, such as 4-aminobutyric acid, exhibited higher levels in K. obovata than in A. marina, suggesting that chilling-tolerant varieties regulated more metabolites in response to chilling. The investigation defined the inherent distinctions between K. obovata and A. marina in terms of signal transduction gene expression, as well as phenylpropanoid and flavonoid biosynthesis, during exposure to low temperatures.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Potential Regulation of Flavonoids in the Production of Embryogenic Cultures during Early Somatic Embryogenesis of Longan (Dimocarpus longan Lour.)

Embryogenic cultures of longan (Dimocarpus longan Lour.) contain various metabolites with pharmacological properties that may function in the regulation of somatic embryogenesis (SE). In this study, based on widely targeted metabolomics, 501 metabolites were obtained from the embryogenic calli, incomplete compact proembryogenic cultures, and globular embryos during early SE of longan, among which 41 flavonoids were differentially accumulated during the SE. Using RNA sequencing, 36 flavonoid-biosynthesis-related genes and 43 MYB and 52 bHLH transcription factors were identified as differentially expressed genes. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the flavonoid metabolism-related pathways were significantly enriched during the early SE. These results suggested that the changes in flavonoid levels in the embryogenic cultures of longan were mediated by MYBs and bHLHs via regulating flavonoid-biosynthesis-related genes, thus potentially regulating early SE. The identified metabolites in the embryogenic cultures of longan can be used to develop pharmaceutical ingredients.

Serendipita indica Promotes the Growth of Tartary Buckwheat by Stimulating Hormone Synthesis, Metabolite Production, and Increasing Systemic Resistance

The main objective of this study was to investigate the influence of Serendipita indica on the growth of Tartary buckwheat plants. This study highlighted that the roots of Tartary buckwheat can be colonized by S. indica and that this fungal endophyte improved plants height, fresh weight, dry weight, and grain yield. In the meantime, the colonization of S. indica in Tartary buckwheat leaves resulted in elevated levels of photosynthesis, plant hormone content, antioxidant enzyme activity, proline content, chlorophyll content, soluble sugars, and protein content. Additionally, the introduction of S. indica to Tartary buckwheat roots led to a substantial rise in the levels of flavonoids and phenols found in the leaves and seeds of Tartary buckwheat. In addition, S. indica colonization reduced the content of malondialdehyde and hydrogen peroxide when compared to non-colonized plants. Importantly, the drought tolerance of Tartary buckwheat plants is increased, which benefits from physiology and bio-chemical changes in plants after S. indica colonized. In conclusion, we have shown that S. indica can improve systematic resistance and promote the growth of Tartary buckwheat by enhancing the photosynthetic capacity of Tartary buckwheat, inducing the production of IAA, increasing the content of secondary metabolites such as total phenols and total flavonoids, and improving the antioxidant enzyme activity of the plant.

Integrated Transcriptomic and Metabolomic Analysis Reveals the Mechanism of Gibberellic acid Regulates the Growth and Flavonoid Synthesis in Phellodendron chinense Schneid Seedlings

The phytohormone gibberellic acids (GAs) play a crucial role in the processes of growth, organ development, and secondary metabolism. However, the mechanism of exogenous GA3 regulating the growth and flavonoid synthesis in Phellodendron chinense Schneid (P. chinense Schneid) seedlings remains unclear. In this study, the physicochemical properties, gene expression level, and secondary metabolite of P. chinense Schneid seedlings under GA3 treatment were investigated. The results showed that GA3 significantly improved the plant height, ground diameter, fresh weight, chlorophyll content, soluble substance content, superoxide dismutase, and peroxidase activities. This was accompanied by elevated relative expression levels of Pc(S)-GA2ox, Pc(S)-DELLA, Pc(S)-SAUR50, Pc(S)-PsaD, Pc(S)-Psb 27, Pc(S)-PGK, Pc(S)-CER3, and Pc(S)-FBA unigenes. Conversely, a notable reduction was observed in the carotenoid content, catalase activity and the relative expression abundances of Pc(S)-KAO, Pc(S)-GID1/2, and Pc(S)-GH 3.6 unigenes in leaves of P. chinense Schneid seedlings (p < 0.05). Furthermore, GA3 evidently decreased the contents of pinocembrin, pinobanksin, isosakuranetin, naringin, naringenin, (-)-epicatechin, tricetin, luteolin, and vitexin belonged to flavonoid in stem bark of P. chinense Schneid seedlings (p < 0.05). These results indicated that exogenous GA3 promoted growth through improving chlorophyll content and gene expression in photosynthesis and phytohormone signal pathway and inhibited flavonoid synthesis in P. chinense Schneid seedlings.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

ATP-binding cassette protein ABCC8 promotes anthocyanin accumulation in strawberry fruits

Anthocyanins are important health-promoting flavonoid compounds that substantially contribute to fruit quality. Anthocyanin biosynthesis and most regulatory mechanisms are relatively well understood. However, the functions of anthocyanin transport genes in strawberry fruit remain unclear. In this study, a gene encoding an ATP-binding cassette (ABC) protein of type C, ABCC8, was isolated from strawberry fruits. qRT-PCR analysis demonstrated that the transcript levels of FvABCC8 were the highest and were strongly correlated with anthocyanin accumulation during strawberry fruit ripening. Transient overexpression and RNAi of FvABCC8 led to an increase and decrease in anthocyanin content in strawberry fruits, respectively. Moreover, the ABCC8 promoter was activated by MYB and bHLH transcription factors MYB10, bHLH33, and MYC1. Sucrose enhanced anthocyanin accumulation in FvABCC8-overexpressing Arabidopsis, particularly at higher concentrations. FvABCC8-overexpressing lines were less sensitive to ABA during seed germination and seedling development. These results suggest that strawberry vacuolar anthocyanin transport may be mediated by the ABCC transporter ABCC8, the expression of which may be regulated by transcription factors MYB10, bHLH33, and MYC1.

SnRK1 inhibits anthocyanin biosynthesis through both transcriptional regulation and direct phosphorylation and dissociation of the MYB/bHLH/TTG1 MBW complex

Plants have evolved an extensive specialized secondary metabolism. The colorful flavonoid anthocyanins, for example, not only stimulate flower pollination and seed dispersal, but also protect different tissues against high light, UV and oxidative stress. Their biosynthesis is highly regulated by environmental and developmental cues and induced by high sucrose levels. Expression of the biosynthetic enzymes involved is controlled by a transcriptional MBW complex, comprising (R2R3) MYB- and bHLH-type transcription factors and the WD40 repeat protein TTG1. Anthocyanin biosynthesis is not only useful, but also carbon- and energy-intensive and non-vital. Consistently, the SnRK1 protein kinase, a metabolic sensor activated in carbon- and energy-depleting stress conditions, represses anthocyanin biosynthesis. Here we show that Arabidopsis SnRK1 represses MBW complex activity both at the transcriptional and post-translational level. In addition to repressing expression of the key transcription factor MYB75/PAP1, SnRK1 activity triggers MBW complex dissociation, associated with loss of target promoter binding, MYB75 protein degradation and nuclear export of TTG1. We also provide evidence for direct interaction with and phosphorylation of multiple MBW complex proteins. These results indicate that repression of expensive anthocyanin biosynthesis is an important strategy to save energy and redirect carbon flow to more essential processes for survival in metabolic stress conditions.

Time-series transcriptome provides insights into the gene regulation network involved in the icariin-flavonoid metabolism during the leaf development of Epimedium pubescens

Herba Epimedii (Epimedium) leaves are rich in prenylated flavonol glycosides (PFGs) with high medicinal value. However, the dynamics and regulatory network of PFG biosynthesis remain largely unclear. Here, we combined metabolite profiling (targeted to PFGs) and a high-temporal-resolution transcriptome to elucidate PFGs' regulatory network in Epimedium pubescens and identified key candidate structural genes and transcription factors (TFs) involved in PFG accumulation. Chemical profile analysis revealed that PFG content was quite different between buds and leaves and displayed a continuous decline with leaf development. The structural genes are the determinant reasons, and they are strictly regulated by TFs under temporal cues. We further constructed seven time-ordered gene co-expression networks (TO-GCNs) of PFG biosynthesis genes (including EpPAL2, EpC4H, EpCHS2, EpCHI2, EpF3H, EpFLS3, and EpPT8), and three flavonol biosynthesis routines were then predicted. The TFs involved in TO-GCNs were further confirmed by WGCNA analysis. Fourteen hub genes, comprising 5 MYBs, 1 bHLH, 1 WD40, 2 bZIPs, 1 BES1, 1 C2H2, 1 Trihelix, 1 HD-ZIP, and 1 GATA were identified as candidate key TFs. The results were further validated by TF binding site (TFBS) analysis and qRT-PCR. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of PFGs biosynthesis, enriching the gene resources, which will guide further research on PFG accumulation in Epimedium.

The role of flavonols in insect resistance and stress response

Plants are sessile organisms and must adapt to various environmental changes, especially from stress conditions. Synthesis of secondary metabolites by the plant is one of the adaptive mechanisms against stress to provide resistance. Among several secondary metabolites, flavonols, a subgroup of flavonoids, are one of the most widely distributed in the plant kingdom. These molecules work as antioxidants, reduce reactive oxygen species (ROS) in plants, and cause detrimental effects on insect growth on feeding. Despite the great interest in flavonol function leading to insect tolerance and stress response, the detailed mechanisms related to these specific functions have yet to be studied. In this review, we have summarized the role of flavonols in plant defense against insects and different abiotic stresses and possible mechanisms involved in these functions.

Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry (Vaccinium spp.)

As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.

FtbZIP85 Is Involved in the Accumulation of Proanthocyanidin by Regulating the Transcription of FtDFR in Tartary Buckwheat

As a drought-tolerant crop, Tartary buckwheat survives under adverse environmental conditions, including drought stress. Proanthocyanidins (PAs) and anthocyanins are flavonoid compounds, and they participate in the regulation of resistance to both biotic and abiotic stresses by triggering genes' biosynthesis of flavonoids. In this study, a basic leucine zipper, basic leucine zipper 85 (FtbZIP85), which was predominantly expressed in seeds, was isolated from Tartary buckwheat. Our study shows that the expressions of FtDFR, FtbZIP85 and FtSnRK2.6 were tissue-specific and located in both the nucleus and the cytosol. FtbZIP85 could positively regulate PA biosynthesis by binding to the ABA-responsive element (ABRE) in the promoter of dihydroflavonol 4-reductase (FtDFR), which is a key enzyme in the phenylpropanoid biosynthetic pathway. Additionally, FtbZIP85 was also involved in the regulation of PA biosynthesis via interactions with FtSnRK2.6 but not with FtSnRK2.2/2.3. This study reveals that FtbZIP85 is a positive regulator of PA biosynthesis in TB.

Integrative Analysis of Metabolome and Transcriptome Reveals Molecular Insight into Metabolomic Variations during Hawthorn Fruit Development

Hawthorn (Crataegus pinnatifida var. major), a cultivated fruit tree, is native and unique to China. Its fruits have high nutritional, health, and medicinal values. However, the development and ripening process of hawthorns is accompanied by dramatic changes in flavor, aroma, and bioactive phytochemicals, which are the fundamental factors that contribute to the potential health benefits and establishment of fruit quality. Therefore, an exploration of the dynamic changes in metabolites and their regulatory networks during the development of hawthorn fruits can elucidate the formation mechanisms of active substances in hawthorn fruits. In this study, we used a broad targeted metabolomics approach to identify and analyze the dynamics of metabolites in hawthorn fruits at five developmental stages. The results revealed 998 primary and secondary metabolites that were classified into 15 categories. The accumulation levels of most sugars increased during fruit development and then accelerated at the fruit ripening stage. The accumulation levels of a few organic acids (e.g., citric acid, isocitric acid, and quinic acid) continuously increased. Many organic acids exhibited significant decreasing trends. Among the 561 secondary metabolites detected, 189 were phenolic acids and 199 were flavonoids. The levels of many flavonoids were significantly reduced at later stages of fruit development; in contrast, the levels of two anthocyanins significantly increased during fruit ripening. Correlation analysis revealed that there is a certain correlation within and between primary as well as secondary metabolites during fruit development. Furthermore, the integration of metabolomic and transcriptomic data in this study revealed that changes in the expression of some differentially expressed genes (DEGs) were associated with the accumulation of metabolites such as sugars, organic acids, and flavonoids, e.g., the upregulated expression levels of CS (citrate synthase) genes were consistent with the continued accumulation of citric acid. Overall, this study demonstrates the metabolic changes that occur during the development of hawthorn fruit, explores the molecular mechanisms that underlie metabolite changes during fruit development, and lays a strong theoretical foundation for the improvement of hawthorn fruit quality and the development of functional components.

Transcriptome analysis reveals the crucial function of hyperoside in inhibiting anthocyanin accumulation in grape (Vitis vinifera L.) fruits by inducing VvMYB62

INTRODUCTION

The formation of color in plants is significantly dependent on anthocyaninpigments. Grape species vary in color due to the differences in anthocyanin accumulation. It is widely recognized that both biotic and abiotic conditions may have an impact on anthocyanin synthesis in plants. The underlying molecular mechanisms by which external application of hyperoside impacts anthocyanin formation in grapes, however, have received little attention.

METHODS

In the current study,the transcriptome of Gemstone seedless grape was examined using high-throughput RNA sequencing at various developmental stages reply to both control and hyperoside treatments.

RESULTS

The results of this study suggested that the major genes controlling anthocyanin accumulation in response to the externalinjection of hyperoside could be VvMYB62, VvPAL, VvCHS, and VvF3'5'H.Quantitative reverse transcription PCR (RT-qPCR) results were used to confirm the changes in the expression levels of the genes encoding the anthocyanin biosynthesis pathway under the control and hyperoside treatments. Using a transient transformation system, it was discovered that VvMYB62 was shown to regulate the anthocyanin accumulation at both the transcriptional and posttranslational levels and could be influenced by the external administration of hyperoside. In grape embryogenic calli, hyperoside could specifically suppress theexpression of VvMYB62 and anthocyanin accumulation. In this instance, the VvMYB62 characterisation brought attention to the significance of exogenous hyperoside-induced anthocyanin accumulation. Therefore, the results demonstrated that VvMYB62 could be hindered in the process of grape during anthocyanin accumulation caused by hyperoside.

DISCUSSION

These findings offer excellent candidate genes in the future breeding of novel grape varieties in addition to serving as a crucial reference for understanding the underlying molecular processes of hyperoside suppression of anthocyanin formation in plants.

Red and blue light-specific metabolic changes in soybean seedlings

Red and blue artificial light sources are commonly used as photosynthetic lighting in smart farm facilities, and they can affect the metabolisms of various primary and secondary metabolites. Although the soybean plant contains major flavonoids such as isoflavone and flavonol, using light factors to produce specific flavonoids from this plant remains difficult because the regulation of light-responded flavonoids is poorly understood. In this study, metabolic profiling of soybean seedlings in response to red and blue lights was evaluated, and the isoflavone-flavonol regulatory mechanism under different light irradiation periods was elucidated. Profiling of metabolites, including flavonoids, phenolic acids, amino acids, organic acids, free sugars, alcohol sugars, and sugar acids, revealed that specific flavonol, isoflavone, and phenolic acid showed irradiation time-dependent accumulation. Therefore, the metabolic gene expression level and accumulation of isoflavone and flavonol were further investigated. The light irradiation period regulated kaempferol glycoside, the predominant flavonol in soybeans, with longer light irradiation resulting in higher kaempferol glycoside content, regardless of photosynthetic lights. Notably, blue light stimulated kaempferol-3-O-(2,6-dirhamnosyl)-galactoside accumulation more than red light. Meanwhile, isoflavones were controlled differently based on isoflavone types. Malonyl daidzin and malonyl genistin, the predominant isoflavones in soybeans, were significantly increased by short-term red light irradiation (12 and 36 h) with higher expressions of flavonoid biosynthetic genes, which contributed to the increased total isoflavone level. Although most isoflavones increased in response to red and blue lights, daidzein increased in response only to red light. In addition, prolonged red light irradiation downregulated the accumulation of glycitin types, suggesting that isoflavone's structural specificity results in different accumulation in response to light. Overall, these findings suggest that the application of specific wavelength and irradiation periods of light factors enables the regulation and acquisition of specialized metabolites from soybean seedlings.

Effects of plant growth regulators on the contents of rutin, hyperoside and quercetin in Hypericum attenuatum Choisy

To explore the accumulation of rutin, hyperoside and quercetin in Hypericum attenuatum Choisy under treatment with different plant growth regulators, 100 mg/L, 200 mg/L and 300 mg/L cycocel, 100 mg/L, 200 mg/L and 300 mg/L mepiquat chloride and 1 mg/L, 2 mg/L and 3 mg/L naphthalene acetic acid were foliage sprayed on Hypericum attenuatum Choisy plants at the early growth stage. We sampled and determined the important flavonoid contents at the flowering stage. The results showed that the three plant growth regulators had different effects on the accumulation of rutin, hyperoside and quercetin in the leaves, stems and flowers of Hypericum attenuatum Choisy at the flowering stage. After spraying 1 mg/L naphthalene acetic acid at the early growth stage, the rutin contents in the leaves, stems and flowers increased by approximately 60.33%, 223.85% and 192.02%, respectively (P < 0.05). Spraying 100 mg/L mepiquat chloride increased the hyperoside contents in the leaves and flowers by approximately 7.77% and 12.87%, respectively (P < 0.05). Spraying 2 mg/L naphthalene acetic acid significantly increased the quercetin contents in the flowers and leaves by approximately 95.62% and 47.85%, respectively (P < 0.05). Therefore, at the early growth stage, spraying 1 mg/L naphthalene acetic acid significantly increased rutin content, spraying 100 mg/L mepiquat chloride significantly increased hyperoside content, and spraying 2 mg/L naphthalene acetic acid significantly increased quercetin content in Hypericum attenuatum Choisy. In conclusion, the accumulation of flavonoids in Hypericum attenuatum Choisy was regulated by plant growth regulators.

Comparative transcriptomic and metabolomic analyses reveal the delaying effect of naringin on postharvest decay in citrus fruit

INTRODUCTION

Naringin exhibits antioxidant capacity and can partially inhibit pathogens in many horticultural products, such as citrus fruit; however, the effects of naringin on the storage quality and mechanisms that regulate senescence in citrus fruit have not been comprehensively analyzed.

METHODS AND RESULTS

In this study, exogenous naringin treatment was found to significantly delay citrus fruit disease, decreasing the H₂O₂ content, increasing the antioxidant capacity and maintaining the quality of the fruit. Metabolomic analysis of citrus peel indicated the vast majority (325) of metabolites belonging to flavonoids. Moreover, the auraptene, butin, naringenin, and luteolin derivative levels within the phenylpropanoid pathway were significantly higher in the naringin-treated fruit than in the control fruit. Transcriptomic analysis also revealed that twelve genes in the phenylpropanoid and flavonoid biosynthesis pathways were significantly upregulated. Further analysis with a co-expression network revealed significant correlation between these differential genes and metabolites. Additionally, MYC and WRKY, screened from the MAPK signaling pathway, may contribute to naringin-induced disease resistance.

CONCLUSION

In conclusion, naringin treatment can efficiently delay decay and maintain the quality of citrus fruit, mainly by promoting metabolites accumulation, and upregulating differentially expressed genes in phenylpropanoid and flavonoid biosynthesis pathway. This study provides a better understanding of the regulatory mechanisms through which naringin delays citrus fruit decay and maintains fruit quality.

Transcriptomic profiling analysis to identify genes associated with PA biosynthesis and insolubilization in the late stage of fruit development in C-PCNA persimmon

PA-enhanced content causes astringency in persimmon fruit. PCNA persimmons can lose their astringency naturally and they become edible when still on the tree, which allows for conserves of physical and financial resources. C-PCNA persimmon originates in China. Its deastringency trait primarily depends on decreased PA biosynthesis and PA insolubilization at the late stage of fruit development. Although some genes and transcription factors that may be involved in the deastringency of C-PCNA persimmon have been reported, the expression patterns of these genes during the key deastringency stage are reported less. To investigate the variation in PA contents and the expression patterns of deastringency-related genes during typical C-PCNA persimmon 'Xiaoguo-tianshi' fruit development and ripening, PA content and transcriptional profiling were carried out at five late stages from 70 to 160 DAF. The combinational analysis phenotype, PA content, and DEG enrichment revealed that 120-140 DAF and 140-160 DAF were the critical phases for PA biosynthesis reduction and PA insolubilization, respectively. The expression of PA biosynthesis-associated genes indicated that the downregulation of the ANR gene at 140-160 DAF may be associated with PA biosynthesis and is decreased by inhibiting its precursor cis-flavan-3-ols. We also found that a decrease in acetaldehyde metabolism-associated ALDH genes and an increase in ADH and PDC genes might result in C-PCNA persimmon PA insolubilization. In addition, a few MYB-bHLH-WD40 (MBW) homologous transcription factors in persimmon might play important roles in persimmon PA accumulation. Furthermore, combined coexpression network analysis and phylogenetic analysis of MBW suggested that three putative transcription factors WD40 (evm.TU.contig1.155), MYB (evm.TU.contig8910.486) and bHLH (evm.TU.contig1398.203), might connect and co-regulate both PA biosynthesis and its insolubilization in C-PCNA persimmon. The present study elucidated transcriptional insights into PA biosynthesis and insolubilization during the late development stages based on the C-PCNA D. kaki genome (unpublished). Thus, we focused on PA content variation and the expression patterns of genes involved in PA biosynthesis and insolubilization. Our work has provided additional evidence on previous knowledge and a basis for further exploration of the natural deastringency of C-PCNA persimmon.

Two homeologous MATE transporter genes, NtMATE21 and NtMATE22, are involved in the modulation of plant growth and flavonol transport in Nicotiana tabacum

The multidrug and toxic compound extrusion (MATE) protein family has been implicated in the transport of a diverse range of molecules, including specialized metabolites. In tobacco (Nicotiana tabacum), only a limited number of MATE transporters have been functionally characterized, and no MATE transporter has been studied in the context of flavonoid transport in this plant species so far. In the present study, we characterize two homeologous tobacco MATE genes, NtMATE21 and NtMATE22, and demonstrate their role in flavonol transport and in plant growth and development. The expression of these two genes was reported to be up-regulated in trichomes as compared with the trichome-free leaf. The transcript levels of NtMATE21 and NtMATE22 were found to be higher in flavonol overproducing tobacco transgenic lines as compared with wild type tobacco. The two transporters were demonstrated to be localized to the plasma membrane. Genetic manipulation of NtMATE21 and NtMATE22 led to altered growth phenotypes and modulated flavonol contents in N. tabacum. The β-glucuronidase and green fluorescent protein fusion transgenic lines of promoter regions suggested that NtMATE21 and NtMATE22 are exclusively expressed in the trichome heads in the leaf tissue and petals. Moreover, in a transient transactivation assay, NtMYB12, a flavonol-specific MYB transcription factor, was found to transactivate the expression of NtMATE21 and NtMATE22 genes. Together, our results strongly suggest the involvement of NtMATE21 and NtMATE22 in flavonol transport as well as in the regulation of plant growth and development.

Increasing the activities of protective enzymes is an important strategy to improve resistance in cucumber to powdery mildew disease and melon aphid under different infection/infestation patterns

Powdery mildew, caused by Sphaerotheca fuliginea (Schlecht.) Poll., and melon aphids (Aphis gossypii Glover) are a typical disease and insect pest, respectively, that affect cucumber production. Powdery mildew and melon aphid often occur together in greenhouse production, resulting in a reduction in cucumber yield. At present there are no reports on the physiological and biochemical effects of the combined disease and pest infection/infestation on cucumber. This study explored how cucumbers can regulate photosynthesis, protective enzyme activity, and basic metabolism to resist the fungal disease and aphids. After powdery mildew infection, the chlorophyll and free proline contents in cucumber leaves decreased, while the activities of POD (peroxidase) and SOD (superoxide dismutase) and the soluble protein and MDA (malondialdehyde) contents increased. Cucumber plants resist aphid attack by increasing the rates of photosynthesis and basal metabolism, and also by increasing the activities of protective enzymes. The combination of powdery mildew infection and aphid infestation reduced photosynthesis and basal metabolism in cucumber plants, although the activities of several protective enzymes increased. Aphid attack after powdery mildew infection or powdery mildew infection after aphid attack had the opposite effect on photosynthesis, protective enzyme activity, and basal metabolism regulation. Azoxystrobin and imidacloprid increased the contents of chlorophyll, free proline, and soluble protein, increased SOD activity, and decreased the MDA content in cucumber leaves. However, these compounds had the opposite effect on the soluble sugar content and POD and CAT (catalase) activities. The mixed ratio of the two single agents could improve the resistance of cucumber to the combined infection of powdery mildew and aphids. These results show that cucumber can enhance its pest/pathogen resistance by changing physiological metabolism when exposed to a complex infection system of pathogenic microorganisms and insect pests.

Function deficiency of GhOMT1 causes anthocyanidins over-accumulation and diversifies fibre colours in cotton (Gossypium hirsutum)

Naturally coloured cotton (NCC) fibres need little or no dyeing process in textile industry to low-carbon emission and are environment-friendly. Proanthocyanidins (PAs) and their derivatives were considered as the main components causing fibre coloration and made NCCs very popular and healthy, but the monotonous fibre colours greatly limit the wide application of NCCs. Here a G. hirsutum empurpled mutant (HS2) caused by T-DNA insertion is found to enhance the anthocyanidins biosynthesis and accumulate anthocyanidins in the whole plant. HPLC and LC/MS-ESI analysis confirmed the anthocyanidins methylation and peonidin, petunidin and malvidin formation are blocked. The deficiency of GhOMT1 in HS2 was associated with the activation of the anthocyanidin biosynthesis and the altered components of anthocyanidins. The transcripts of key genes in anthocyanidin biosynthesis pathway are significantly up-regulated in HS2, while transcripts of the genes for transport and decoration were at similar levels as in WT. To investigate the potential mechanism of GhOMT1 deficiency in cotton fibre coloration, HS2 mutant was crossed with NCCs. Surprisingly, offsprings of HS2 and NCCs enhanced PAs biosynthesis and increased PAs levels in their fibres from the accumulated anthocyanidins through up-regulated GhANR and GhLAR. As expected, multiple novel lines with improved fibre colours including orange red and navy blue were produced in their generations. Based on this work, a new strategy for breeding diversified NCCs was brought out by promoting PA biosynthesis. This work will help shed light on mechanisms of PA biosynthesis and bring out potential molecular breeding strategy to increase PA levels in NCCs.

EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus

Erigeron breviscapus, a traditional Chinese medicinal plant, is enriched in flavonoids that are beneficial to human health. While we know that R2R3-MYB transcription factors (TFs) are crucial to flavonoid pathway, the transcriptional regulation of flavonoid biosynthesis in E. breviscapus has not been fully elucidated. Here, EbMYBP1, a R2R3-MYB transcription factor, was uncovered as a regulator involved in the regulation of flavonoid accumulation. Transcriptome and metabolome analysis revealed that a large group of genes related to flavonoid biosynthesis were significantly changed, accompanied by significantly increased concentrations of the flavonoid in EbMYBP1-OE transgenic tobacco compared with the wild-type (WT). In vitro and in vivo investigations showed that EbMYBP1 participated in flavonoid biosynthesis, acting as a nucleus-localized transcriptional activator and activating the transcription of flavonoid-associated genes like FLS, F3H, CHS, and CHI by directly binding to their promoters. Collectively, these new findings are advancing our understanding of the transcriptional regulation that modulates the flavonoid biosynthesis.