Phenylpropanoid Biosynthesis Research Articles

Machine learning-based metabolomics analysis reveals the early biomarkers for Diplodia stem-end rot in grapefruit caused by Lasiodiplodia theobromae

Lasiodiplodia theobromae is a key postharvest pathogen causing Diplodia stem-end rot (SER) disease in grapefruit. While the disease remains quiescent before harvest, its symptoms become evident during the postharvest period. This dormant behavior poses a challenge in managing fruits after harvest. To effectively detect asymptomatic fruit and detect SER disease at an early stage, it's crucial to identify early-stage biomarkers that can serve as disease indicators. In this study, a machine learning-based metabolomics analysis was utilized to identify characteristic metabolites and to elucidate the underlying biosynthetic mechanisms. Six machine learning algorithms were used, and Gradient boosting (GBT) exhibited the highest accuracy identifying early biomarkers such as shikimate, succinic acid, quinic acid, coumaric acid, tyrosine, phenylalanine, and tryptophan. Moreover, dynamic time warping (DTW), was used to investigate the trend of metabolites across timepoints. Our result revealed that the metabolic analysis enabled differentiating infected from non-infected fruits within 1 day, even though symptoms appeared after 7 days of inoculation. Pathway enrichment analysis indicated that three pathways (biosynthesis of plant hormones, phenylpropanoid biosynthesis, and glutamate metabolism) were strongly involved in the defense mechanism. Metabolite mapping analysis showed the behavior of each compound against the pathogen. With these novel strategies, our findings suggest a prediction model for identifying asymptomatic grapefruit affected by Diplodia SER.

Rice-Magnaporthe oryzae interactions in resistant and susceptible rice cultivars under panicle blast infection based on defense-related enzyme activities and metabolomics.

Rice blast, caused by rice blast fungus (Magnaporthe oryzae), is a global threat to food security, with up to 50% yield losses. Panicle blast is a severe form of rice blast, and disease responses vary between cultivars with different genotypes. Reactive oxygen species (ROS)-mediated signaling reactions and the phenylpropanoid pathway are important defense mechanisms involved in recognizing and resisting against fungal infection. To understand rice-M. oryzae interactions in resistant and susceptible cultivars, we determined dynamic changes in the activities of five defense-related enzymes in resistant cultivar jingsui 18 and susceptible cultivar jinyuan 899 infected with M. oryzae from 4 to 25 days after infection. We then performed untargeted metabolomics analyses to profile the metabolomes of the cultivars under infected and non-infected conditions. Dynamic changes in the activities of five defense-related enzymes were closely related to panicle blast resistance in rice. Metabolome data analysis identified 634 differentially accumulated metabolites (DAMs) between resistant and susceptible cultivars following infection, potentially explaining differences in disease response between varieties. The most enriched DAMs were associated with lipids and lipid-like molecules, phenylpropanoids and polyketides, organoheterocyclic compounds, organic acids and derivatives, and lignans, neolignans, and related compounds. Multiple metabolic pathways are involved in resistance to panicle blast in rice, including biosynthesis of other secondary metabolites, amino acid metabolism, lipid metabolism, phenylpropanoid biosynthesis, arachidonic acid metabolism, arginine biosynthesis, tyrosine metabolism, tryptophan metabolism, tyrosine and tryptophan biosynthesis, lysine biosynthesis, and oxidative phosphorylation.

Unveiling the role of vermicompost in modulating phenylpropanoid metabolism in basil (Ocimum basilicum L.): A single-cell type PGT approach

This research delves into phenylpropanoid metabolism, focusing on phenylpropene biosynthesis in the methyleugenol chemotype of basil (Ocimum basilicum L.). We isolated peltate glandular trichomes (PGTs) from basil leaves to eliminate primary metabolic influences, offering a unique perspective into these complex processes. Vermicompost, chosen for its eco-friendly composition and superiority in invigorating phenylpropanoid metabolism. In this study, we investigated the impacts of solid and tea-form vermicompost applications at 0%, 10%, and 25% doses on the methyleugenol chemotype of basil, focusing on the expression levels of PAL, 4CL, EGS, EOMT, and CVOMT genes and phenylpropene accumulation in the peltate glandular trichomes. Results showed that 10% solid vermicompost (SV) application increased 4CL expression level at 236%, while 25% SV application further enhanced EOMT and CVOMT expressions to towering values by 7,494-fold and 19,643-fold, respectively. SV applications did not significantly impact eugenol accumulation but suppressed chavicol biosynthesis. Methyleugenol and methylchavicol accumulation rose in a dose-dependent manner, with significant increases observed in the 25% SV application. A positive correlation was found between CVOMT expression and accumulation rates of methyleugenol and methylchavicol phenylpropenes following SV applications. Conversely, vermicompost tea (VT) applications led to mixed gene expression patterns and reduced eugenol and methyleugenol ratios in peltate glandular trichomes compared to control. In summary, the notably high gene expressions observed in the results of our preliminary study offer a new perspective in the field of phenylpropanoid metabolism. This underscores the value of utilizing single-cell type PGTs for examining secondary metabolic pathways in plants and demonstrates the impact of vermicompost on phenylpropene production.

Integrated metabolome and transcriptome analyses reveal the molecular mechanism underlying dynamic metabolic processes during taproot development of Panax notoginseng

BackgroundPanax notoginseng (Burk) F. H. Chen is one of the most famous Chinese traditional medicinal plants. The taproot is the main organ producing triterpenoid saponins, and its development is directly linked to the quality and yield of the harvested P. notoginseng. However, the mechanisms underlying the dynamic metabolic changes occurring during taproot development of P. notoginseng are unknown.ResultsWe carried out metabolomic and transcriptomic analyses to investigate metabolites and gene expression during the development of P. notoginseng taproots. The differentially accumulated metabolites included amino acids and derivatives, nucleotides and derivatives, and lipids in 1-year-old taproots, flavonoids and terpenoids in 2- and 3-year-old taproots, and phenolic acids in 3-year-old taproots. The differentially expressed genes (DEGs) are related to phenylpropanoid biosynthesis, metabolic pathway and biosynthesis of secondary metabolites at all three developmental stages. Integrative analysis revealed that the phenylpropanoid biosynthesis pathway was involved in not only the development of but also metabolic changes in P. notoginseng taproots. Moreover, significant accumulation of triterpenoid saponins in 2- and 3-year-old taproots was highly correlated with the up-regulated expression of cytochrome P450s and uridine diphosphate-dependent glycosyltransferases genes. Additionally, a gene encoding RNase-like major storage protein was identified to play a dual role in the development of P. notoginseng taproots and their triterpenoid saponins synthesis.ConclusionsThese results elucidate the molecular mechanism underlying the accumulation of and change relationship between primary and secondary metabolites in P. notoginseng taproots, and provide a basis for the quality control and genetic improvement of P. notoginseng.

Transcriptome Profiling Reveals Molecular Responses to Salt Stress in Common Vetch (Vicia sativa L.).

Common vetch (Vicia sativa L.) is an important annual diploid leguminous forage. In the present study, transcriptomic profiling in common vetch in response to salt stress was conducted using a salt-tolerant line (460) and a salt-sensitive line (429). The common responses in common vetch and the specific responses associated with salt tolerance in 460 were analyzed. Several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including plant hormone and MAPK (mitogen-activated protein kinase) signaling, galactose metabolism, and phenylpropanoid phenylpropane biosynthesis, were enriched in both lines, though some differentially expressed genes (DEGs) showed distinct expression patterns. The roots in 460 showed higher levels of lignin than in 429. α-linolenic acid metabolism, carotenoid biosynthesis, the photosynthesis-antenna pathway, and starch and sucrose metabolism pathways were specifically enriched in salt-tolerant line 460, with higher levels of accumulated soluble sugars in the leaves. In addition, higher transcript levels of genes involved in ion homeostasis and reactive oxygen species (ROS) scavenging were observed in 460 than in 429 in response to salt stress. The transcriptomic analysis in common vetch in response to salt stress provides useful clues for further investigations on salt tolerance mechanism in the future.

Pod-shattering characteristic differences between shattering-resistant and shattering-susceptible common vetch accessions are associated with lignin biosynthesis

The common vetch (Vicia sativa L.) is a self-pollinated annual forage legume that is widely distributed worldwide. It has wide adaptability and high nutritional value and is commonly used as an important protein source for livestock feed. However, pod shattering seriously limits the yield of common vetch. To clarify the mechanism of pod shattering in common vetch, the pod walls of three shattering-resistant (SR) accessions (B65, B135, and B392) and three shattering-susceptible (SS) accessions (L33, L170, and L461) were selected for transcriptome sequencing. A total of 17190 differentially expressed genes (DEGs) were identified in the pod wall of B135 and L461 common vetch at 5, 10, 15, 20, and 25 days after anthesis. KEGG analysis showed that “phenylpropanoid biosynthesis” was the most significantly enriched pathway, and 40 structural genes associated with lignin biosynthesis were identified and differentially expressed in B135 and L461 common vetch. We analysed the DEGs in the pod wall of three SR and three SS accessions at 15 days after anthesis, and most of the DEGs were consistent with the significant enrichment pathways identified in B135 and L461 common vetch. The total lignin content of SR accessions was significantly lower than the SS accessions. The present study lays a foundation for understanding the molecular regulatory mechanism of pod shattering related to lignin biosynthesis in common vetch and provides reference functional genes for breeders to further cultivate shattering-resistant common vetch varieties.

Transcriptome analysis reveals key genes and pathways for prickle development in Zanthoxylumarmatum

Zanthoxylum armatum is an economically important tree species. However, well-developed prickles on its stems and leaves pose serious challenges in terms of management and harvesting. To investigate the molecular mechanism underlying prickle development, we sequenced different stages of prickle morphological development and transcriptomes of different tissues in the root tips (Gen), leaf buds (Ya), and fruits of Z. armatum. The results revealed that proteins related to cell division and genes related to the growth hormone signaling pathway were highly expressed in the prickle just protrusion (PC1). In addition, a high expression of lignin biosynthesis genes was observed during the developmental onset of lignification (PC2) and prickle lignification (PC3). These findings indicate that phenylpropanoid biosynthesis and plant hormone signal transduction are key pathways for the completion of lignification development in the prickle. During prickle development, ZaMYB2 and ZaWRKY3 were significantly upregulated in PC2 and PC3, suggesting their possible involvement in prickle development. Transcriptome and qRT-PCR analyses revealed differential gene expression of zaPAL3, za4CLL1, zaCOMT1, ZaWRKY3, and ZaCCD31 in the Gen, Ya, newly formed fruit (ZaF1), newly oil-spotted fruits (ZaF2), PC1, PC2, and PC3 of Zarmatum. zaCCD31 was highly expressed in leaf buds, whereas Za4CLL1 was highly expressed in root tips. During the lignification of prickles, the relative expression of genes including zaMYB2 increased gradually; however, the relative expression of zaCCD31 decreased during this process. Therefore, we inferred that these genes might be closely related to prickle development. Notably, zaMYB2 was expressed at higher levels in PC2 and PC3 than in PC1 and was not expressed in Gen, Ya, ZaF1, and ZaF2. Therefore, zaMYB2 is a key gene involved in prickle development of Z. armatum that exhibited tissue-specific expression. This study establishes a foundation for future analyses of the molecular mechanism underlying prickle development in Z. armatum.

Metabolomic and transcriptomic analysis of bitter compounds in Dendrocalamopsis oldhamii shoots

Dendrocalamopsis oldhamii is an important shoot-edible bamboo with a favourable taste and rich nutritional composition. In this study, we aimed to uncover the intricate process behind bitterness formation in Dendrocalamopsis oldhamii shoots, which significantly impacts their nutritional quality and economic worth upon being unearthed. Employing a combination of metabolomic and transcriptomic analyses, we scrutinized both underground (DoS) and unearthed (DoB) shoots. The metabolomic assessment unveiled 1017 secondary metabolites, with 151 potentially linked to bitterness based on BitterDB and literature references. Through integrated metabolomic and transcriptomic investigations, we delineated the biosynthetic pathways responsible for bitter compounds in bamboo shoots, encompassing "phenylpropanoid biosynthesis," "glycolysis/gluconeogenesis," circadian rhythm, and amino acid metabolism pathways. Moreover, we singled out four bitter compounds—3-caffeoylquinic acid, arbutin, phenylalanine, and tryptophan—from the regulatory pathways for targeted metabolic verification. Notably, arbutin exhibited a remarkable 242.52% increase from DoS to DoB, underscoring its pivotal role as a bitter metabolite in unearthed bamboo shoots. Our findings offer crucial insights into the mechanisms underpinning bamboo shoot bitterness, thereby facilitating the cultivation of superior-quality bamboo shoots.

Integrated transcriptome and proteome analyses reveal potential mechanisms in Stipa breviflora underlying adaptation to grazing

AbstractBackgroundLong‐term overgrazing has led to severe degradation of grasslands, posing a significant threat to the sustainable use of grassland resources.MethodsBased on the investigation of changes in functional traits and photosynthetic physiology of Stipa breviflora under no grazing, moderate grazing, and heavy grazing treatments, the changes in expression patterns of genes and proteins associated with different grazing intensities were assessed through integrative transcriptomic and proteomic analyses.ResultsDifferentially expressed genes and proteins were identified under different grazing intensities. They were mainly related to RNA processing, carbon metabolism, and secondary metabolite biosynthesis. These findings suggest that long‐term grazing leads to molecular phenotypic plasticity, affecting various biological processes and metabolic pathways in S. breviflora. Correlation analysis revealed low correlation between the transcriptome and the proteome, indicating a large‐scale regulation of gene expression at the posttranscriptional and translational levels during the response of S. breviflora to grazing. The expression profiles of key genes and proteins involved in photosynthesis and phenylpropanoid metabolism pathways suggested their synergistic response to grazing in S. breviflora.ConclusionsOur study provides insight into the adaptation mechanisms of S. breviflora to grazing and provides a scientific basis for the development of more efficient grassland protection and utilization practices.

Expression Analysis of Phenylpropanoid Pathway Genes and Phenylpropanoid Accumulation in Different Organs of Chelidonium majus L.

Objective This study set out to examine the phenylpropanoid pathway gene expression and phenolic compound accumulation in different organs of Chelidonium majus (C. majus). Methods Total RNA was extracted and expression of phenylpropanoid biosynthesis genes was assessed using quantitative real-time polymerase chain reaction in different organs of C. majus. In addition, the phenylpropanoid compounds were analyzed from different organs of C. majus by using high-performance liquid chromatography. Results The results demonstrate the variance in the expression levels of phenylpropanoid pathway genes in the flowers, leaves, stems, and roots of C. majus. CmPAL and CmC4H were expressed at their greatest levels in the stem, while CmCHS and CmCHI were strongly expressed in the leaf, and CmF3H, CmFLS, Cm4CL, and CmDFR were more abundant in the flower. The total phenolic contents in the different organs also varied significantly. The highest value was recorded in the flowers (2152.89 ± 78.71 μg/g dry wt.), which was 54.26 times higher than the lowest values obtained from roots (39.68 ± 0.05 μg/g dry wt.). Except for roots, rutin showed the highest level in all other organs. According to a heat map, the majority of the phenolic compounds were highest in the flower. By using variable importance in projection analysis, the most significant metabolite was found to be chlorogenic acid, which had a positive association with all phenolic chemicals, but it showed a negative correlation with trans-cinnamic acid. Except for trans-cinnamic acid, all other phenolic compounds likewise showed positive correlation with other phenolic compounds. Conclusions This work offers pertinent data on the expression analysis of genes involved in the phenylpropanoid biosynthetic pathway and the presence of phenolic compounds in C. majus. These findings will be helpful for the researcher to understand the relationship between the expression level of phenylpropanoid pathway genes and phenylpropanoid compound accumulation in C. majus.

Analysis of physiological response and differential protein expression of Paramichelia baillonii saplings under phosphorus deficiency.

Paramichelia baillonii is a rare and fast-growing tree species in subtropical China. The acidic red soil in southern China severely limits its growth as it lacks sufficient available phosphorus (P), resulting in declining soil fertility and nutrient availability. The effect of P deficiency on P. Baillonii growth, root attributes, and physiological response has not yet been reported. Understanding the adaptability of P. baillonii to low-P conditions can improve afforestation and soil management in southern China. Therefore, we conducted a pot experiment on 2-year-old saplings and treated them with different P levels. Results showed that P deficiency (0-5 mg L-1 ) decreased growth attributes, root morphological traits, and nutrient uptake of P. baillonii saplings compared to control (CK). Similarly, reduction in chlorophyll a, b, total chlorophyll, net photosynthetic rate (Pn), transpiration rate (Tr), and Gs were seen in low P treatment saplings compared to CK. Whereas superoxide dismutase, peroxidase, malondialdehyde, acid phosphatase activity, and soluble protein content increased with increasing P-deficiency up to 5 mg L-1 , and soluble sugar showed oppsite trend. Moreover, the proteomics analysis identified 2721 proteins, 196 showing differential expression, with 90 up- and 106 down-regulated. Importantly, the metabolic activities increased in the pentose phosphate pathway, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and phenylpropanoid biosynthesis pathways to sustain regular plant growth under P deficiency. This study delves into the dynamic morpho-physiological and proteomic changes in response to P deficiency. Overall, growth and nutrient uptake were reduced, countered by adaptive biochemical and proteomic shifts, including heightened antioxidant activities and modifications in metabolic pathways, highlighting the resilient strategies of P. baillonii saplings under P deficiency.

RNA-seq-based comparative transcriptome analysis reveals the role of CsPrx73 in waterlogging-triggered adventitious root formation in cucumber.

Abiotic stressors like waterlogging are detrimental to cucumber development and growth. However, comprehension of the highly complex molecular mechanism underlying waterlogging can provide an opportunity to enhance cucumber tolerance under waterlogging stress. We examined the hypocotyl and stage-specific transcriptomes of the waterlogging-tolerant YZ026A and the waterlogging-sensitive YZ106A, which had different adventitious rooting ability under waterlogging. YZ026A performed better under waterlogging stress by altering its antioxidative machinery and demonstrated a greater superoxide ion (O 2-) scavenging ability. KEGG pathway enrichment analysis showed that a high number of differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis. By pairwise comparison and weighted gene co-expression network analysis analysis, 2616 DEGs were obtained which were categorized into 11 gene co-expression modules. Amongst the 11 modules, black was identified as the common module and yielded a novel key regulatory gene, CsPrx73. Transgenic cucumber plants overexpressing CsPrx73 enhance adventitious root (AR) formation under waterlogging conditions and increase reactive oxygen species (ROS) scavenging. Silencing of CsPrx73 expression by virus-induced gene silencing adversely affects AR formation under the waterlogging condition. Our results also indicated that CsERF7-3, a waterlogging-responsive ERF transcription factor, can directly bind to the ATCTA-box motif in the CsPrx73 promoter to initiate its expression. Overexpression of CsERF7-3 enhanced CsPrx73 expression and AR formation. On the contrary, CsERF7-3-silenced plants decreased CsPrx73 expression and rooting ability. In conclusion , our study demonstrates a novel CsERF7-3-CsPrx73 module that allows cucumbers to adapt more efficiently to waterlogging stress by promoting AR production and ROS scavenging.

Overexpression of GiLEA5-2.1, a late embryogenesis abundant gene LEA3 from Glycyrrhiza inflata Bat., enhances the drought and salt stress tolerance of transgenic tobacco (Nicotiana benthamiana)

Abiotic stress, including drought and salt, reduces the yield of all major crop plants globally. Exploring the stress tolerance factors and mechanisms of dominant species is still an urgent task that is crucial for food and feed production. Glycyrrhiza inflata Bat., which is a halophytic plant, is economically important due to its medicinal, feeding, and ecological value. The plant is widely distributed in the salinized land of Northwest China. The plant demonstrates a robust capacity to withstand drought and salt stress, rendering it an excellent candidate for investigating the molecular mechanism behind drought and salt stress tolerance. Late embryogenesis abundant (LEA) proteins have been ascribed as significant stress tolerance factors attributed to their crucial role in improving the resilience against drought and salt stress. However, research on the salt tolerance mechanism of G. inflata is rare and limited to the physiological level. Furthermore, the role of the genes in G. inflata during abiotic stress conditions remains unclear. In this research, comprehensive knowledge of how G. inflata responds to salt stress was attained by investigating RNA-seq transcriptomes from the root of seedlings treated with 200 mM NaCl for three different time points (0 h, 3 h, and 48 h). Compared to the control, the roots exhibited a significant up-regulation in MDA and proline content as well as SOD and POD activity. The RNA-seq analysis revealed that there were 1938 DEGs that were common across various time points. GO and KEGG indicated that during salt stress, DEGs were found to be abundant in starch and sucrose metabolism, phenylpropanoid biosynthesis, glycolysis/gluconeogenesis, flavonoid biosynthesis, and the ABA signaling pathway. The correlation analysis suggested that Glyur000227s00015126.1 (GiLEA5–2.1) might be a candidate gene modulating the protection of G. inflata roots from salt stress. Apparently, the expression of GiLEA5–2.1 was triggered by drought and salt treatments. To investigate the role of GiLEA5–2.1 in drought and salt stress, plants overexpressed-GiLEA5–2.1 were generated. Overexpression of GiLEA5–2.1 in tobacco (N. benthamiana) could improve resistance against drought and salinity. Under drought and salty conditions, plants that overexpressed GiLEA5–2.1 exhibited enhanced activity of antioxidant enzymes and higher proline levels, along with decreased MDA content. Functional analyses demonstrate that GiLEA5–2.1 has a positive role in drought and salt treatments, it significantly increased the ability of tobacco to withstand drought and salt stress.

DkWRKY transcription factors enhance persimmon resistance to Colletotrichum horii by promoting lignin accumulation through DkCAD1 promotor interaction

Persimmon anthracnose, a severe disease caused by the hemibiotrophic fungus Colletotrichum horii, poses a substantial threat to China’s persimmon industry. Previous research showed that ‘Kangbing Jianshi’ cultivar exhibits strong resistance to anthracnose. Notably, ‘Kangbing Jianshi’ branches exhibit greater lignification compared with the susceptible ‘Fuping Jianshi’ cultivar. In this study, higher lignin content was observed in ‘Kangbing Jianshi’ compared with ‘Fuping Jianshi’, and this difference was associated with disease resistance. Transcriptome and metabolome analyses revealed that the majority of differentially expressed genes and differentially accumulated metabolites were primarily enriched in the phenylpropanoid biosynthesis and lignin synthesis pathways. Furthermore, significant upregulation of DkCAD1, a pivotal gene involved in lignin metabolism, was observed in the resistant cultivar when inoculated with C. horii. Transient overexpression of DkCAD1 substantially increased lignin content and improved resistance to C. horii in a susceptible cultivar. Furthermore, through yeast one-hybrid (Y1H) assays, we identified two WRKY transcription factors, DkWRKY8 and DkWRKY10, which interacts with the DkCAD1 promoter and induces its activity. Overexpression of DkWRKY8 and DkWRKY10 not only increased leaf lignin content but also enhanced persimmon tolerance to C. horii. Moreover, the expression levels of DkCAD1, DkWRKY8, and DkWRKY10 were significantly increased in response to salicylic acid and jasmonic acid in the resistant cultivar. These findings enhance our understanding of the molecular functions of DkWRKY8, DkWRKY10, and DkCAD1 in persimmons, as well as their involvement in molecular breeding processes in persimmons.

Calcium deficiency leads to fruit blackheart formation by disrupting glycometabolism and phenylpropanoid metabolism in wax gourd

Wax gourd (Benincasa hispida (Thunb.) Cogn) is a vegetable crop with a long storage period; however, blackheart disorder seriously compromises its storability and economic value. This study delves into the spatial-temporal process of blackheart disorder in wax gourd fruit at the physiological, transcriptional, and metabolic levels. The findings revealed decreased concentrations of total calcium (Ca), Ca-pectinate, and chelate-soluble pectin (CSP), and increased levels of total phenolics, flavonoids, and lignin during the development of blackheart disorder. These changes in physiological indicators in blackheart fruit were regulated by the expression of relevant genes, the accumulation of key metabolites, and increased enzyme activities in the glycometabolism and phenylpropane metabolism pathways. Moreover, transcriptome analysis revealed significant suppression in the expression of Ca channel and transport-related genes in blackheart fruit. Finally, there was a pronounced correlation between CSP, Ca-pectinate, phenolic acid, flavonoids, and monosaccharides. Weighted gene co-expression network analysis identified several transcription factors related to blackheart development were identified. Importantly, it has been discovered for the first time that the development of blackheart disorder in wax gourd results from pectin degradation and metabolic disturbance caused by Ca deficiency. These findings lay a theoretical foundation for devising strategies to manage and control blackheart in wax gourds.

Integrated metabolomics and transcriptomics analysis highlight key pathways involved in the somatic embryogenesis of Darjeeling tea.

Darjeeling tea is a globally renowned beverage, which faces numerous obstacles in sexual reproduction, such as self-incompatibility, poor seed germination, and viability, as well as issues with vegetative propagation. Somatic embryogenesis (SE) is a valuable method for rapid clonal propagation of Darjeeling tea. However, the metabolic regulatory mechanisms underlying SE in Darjeeling tea remain largely unknown. To address this, we conducted an integrated metabolomics and transcriptomics analysis of embryogenic callus (EC), globular embryo (GE), and heart-shaped embryo (HE). The integrated analyses showed that various genes and metabolites involved in the phenylpropanoid pathway, auxin biosynthesis pathway, gibberellin, brassinosteroid and amino acids biosynthesis pathways were differentially enriched in EC, GE, and HE. Our results revealed that despite highly up-regulated auxin biosynthesis genes YUC1, TAR1 and AAO1 in EC, endogenous indole-3-acetic acid (IAA) was significantly lower in EC than GE and HE. However, bioactive Gibberellin A4 displayed higher accumulation in EC. We also found higher BABY BOOM (BBM) and Leafy cotyledon1 (LEC1) gene expression in GE along with high accumulation of castasterone, a brassinosteroid. Total flavonoids and phenolics levels were elevated in GE and HE compared to EC, especially the phenolic compound chlorogenic acid was highly accumulated in GE. Integrated metabolome and transcriptome analysis revealed enriched metabolic pathways, including auxin biosynthesis and signal transduction, brassinosteroid, gibberellin, phenylpropanoid biosynthesis, amino acids metabolism, and transcription factors (TFs) during SE in Darjeeling tea. Notably, EC displayed lower endogenous IAA levels, conducive to maintaining differentiation, while higher IAA concentration in GE and HE was crucial for preserving embryo identity. Additionally, a negative correlation between bioactive gibberellin A4 (GA4) and IAA was observed, impacting callus growth in EC. The high accumulation of chlorogenic acid, a phenolic compound, might contribute to the low success rate in GE and HE formation in Darjeeling tea. TFs such as BBM1, LEC1, FUS3, LEA, WOX3, and WOX11 appeared to regulate gene expression, influencing SE in Darjeeling tea.

Rice responds to Spodoptera frugiperda infestation via epigenetic regulation of H3K9ac in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways.

This study provided important insights into the complex epigenetic regulatory of H3K9ac-modified genes involved in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways of rice in response to Spodoptera frugiperda infestation. Physiological and molecular mechanisms underlying plant responses to insect herbivores have been well studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of hidden genes remain largely unknown. Histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plants that can activate gene transcription. In this study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using CUT&Tag-seq and RNA-seq. There were 3269 and 4609 up-regulated genes identified in plants infested by FAW larvae for 3h and 12h, respectively, which were mainly enriched in alpha-linolenic acid and phenylpropanoid pathways according to transcriptomic analysis. In addition, CUT&Tag-seq analysis revealed increased H3K9ac in FAW-infested plants, and there were 422 and 543 up-regulated genes enriched with H3K9ac observed at 3h and 12h after FAW feeding, respectively. Genes with increased H3K9ac were mainly enriched in the transcription start site (TSS), suggesting that H3K9ac is related to gene transcription. Integrative analysis of both RNA-seq and CUT&Tag-seq data showed that up-expressed genes with H3K9ac enrichment were mainly involved in the jasmonic acid (JA) and phenylpropanoid pathways. Particularly, two spermidine hydroxycinnamoyl transferase genes SHT1 and SHT2 involved in phenolamide biosynthesis were highly modified by H3K9ac in FAW-infested plants. Furthermore, the Ossht1 and Ossht2 transgenic lines exhibited decreased resistance against FAW larvae. Our findings suggest that rice responds to insect herbivory via H3K9ac epigenetic regulation in the JA signaling and phenolamide biosynthesis pathways.

Foliar application of nettle and Japanese knotweed extracts on Vitis vinifera: impact on phenylpropanoid biosynthesis and antioxidant activity during veraison and harvest of cv. Touriga Franca.

Plant-based extracts have been recently used as sustainable tools to improve biotic and abiotic stress tolerance and increase grape (Vitis vinifera L.) quality. However, knowledge about the effect of these extracts on secondary metabolism compounds, that are fundamental for grape and wine quality, is still scarce. In this study, a trial was installed in an experimental vineyard with the variety Touriga Franca located at University of Trás-os-Montes e Alto Douro, Baixo Corgo sub-region of the Douro Demarcated Region, Portugal in two growing seasons: 2019 and 2020. The aim was to evaluate the effect of foliar application of nettle (Urtica spp.) extract (NE) and Japanese knotweed (Reynoutria japonica) extract (JKE) on grapevines leaves and berries bioactive compounds contents and antioxidant activity, at veraison and harvest. The application of NE increased the total carotenoids in leaves and the total phenolics content and the antioxidant activity (ferric reducing antioxidant power, FRAP) in berries while JKE increased flavonoids content in leaves and the antioxidant activity (2,2-diphenyl-1-picrylhydrazyl, DPPH) in berries. These extracts seem to have a stimulatory effect on grapevine, enhancing bioactive compounds contents and antioxidant capacity and, consequently, the physiological performance of the plant and the quality of the berries. © 2024 Society of Chemical Industry.

Integrated transcriptomic and metabolomic analyses elucidate the mechanism of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress

Seed propagation is the main method of mulberry expansion in China, an important economic forest species. However, seed germination is the most sensitive stage to various abiotic stresses, especially salinity stress. To reveal the molecular regulatory mechanism of mulberry seed germination under salt stress, flavonoid metabolomics and transcriptomics analyses were performed on mulberry seeds germinated under 50 and 100 mmol/L NaCl stress. Analysis of the flavonoid metabolome revealed that a total of 145 differential flavonoid metabolites (DFMs) were classified into 9 groups, 40 flavonols, 32 flavones, 16 chalcones and 14 flavanones. Among them, 61.4% (89) of the DFMs accumulated continuously with increasing salt concentration, reaching the highest level at a 100 mmol/L salt concentration; these DFMs included quercetin-3-O-glucoside (isoquercitrin), kaempferol (3,5,7,4'-tetrahydroxyflavone), quercetin-7-O-glucoside, taxifolin (dihydroquercetin) and apigenin (4',5,7-trihydroxyflavone), indicating that these flavonoids may be key metabolites involved in the response to salt stress. Transcriptional analysis identified a total of 3055 differentially expressed genes (DEGs), most of which were enriched in flavonoid biosynthesis (ko00941), phenylpropanoid biosynthesis (ko00940) and biosynthesis of secondary metabolites (ko01110). Combined analysis of flavonoid metabolomic and transcriptomic data indicated that phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), flavonol synthase (FLS), bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR) and anthocyanidin reductase (ANR) were the key genes involved in flavonoid accumulation during mulberry seed germination under 50 and 100 mmol/L NaCl stress. In addition, three transcription factors, MYB, bHLH and NAC, were involved in the regulation of flavonoid accumulation under salt stress. The results of quantitative real-time PCR (qRT‒PCR) validation showed that the expression levels of 11 DEGs, including 7 genes involved in flavonoid biosynthesis, under different salt concentrations were consistent with the transcriptomic data, and parallel reaction monitoring (PRM) results showed that the expression levels of 6 key enzymes (proteins) involved in flavonoid synthesis were consistent with the accumulation of flavonoids. This study provides a new perspective for investigating the regulatory role of flavonoid biosynthesis in the regulation of mulberry seed germination under salt stress at different concentrations.

Transcriptomic Insights and Cytochrome P450 Gene Analysis in Kadsura coccinea for Lignan Biosynthesis.

Kadsura coccinea is a medicinal plant from the Schisandraceae family that is native to China and has great pharmacological potential due to its lignans. However, there are significant knowledge gaps regarding the genetic and molecular mechanisms of lignans. We used transcriptome sequencing technology to analyze root, stem, and leaf samples, focusing on the identification and phylogenetic analysis of Cytochrome P450 (CYP) genes. High-quality data containing 158,385 transcripts and 68,978 unigenes were obtained. In addition, 36,293 unigenes in at least one database, and 23,335 across five databases (Nr, KEGG, KOG, TrEMBL, and SwissProt) were successfully annotated. The KEGG pathway classification and annotation of these unigenes identified 10,825 categorized into major metabolic pathways, notably phenylpropanoid biosynthesis, which is essential for lignan synthesis. A key focus was the identification and phylogenetic analysis of 233 Cytochrome P450 (CYP) genes, revealing their distribution across 38 families in eight clans, with roots showing specific CYP gene expression patterns indicative of their role in lignan biosynthesis. Sequence alignment identified 22 homologous single genes of these CYPs, with 6 homologous genes of CYP719As and 1 of CYP81Qs highly expressed in roots. Our study significantly advances the understanding of the biosynthesis of dibenzocyclooctadiene lignans, offering valuable insights for future pharmacological research and development.