Phenylpropanoid Pathway Engineering: An Emerging Approach towards Plant Defense

Metabolic profiling of Citrus maxima L. seedlings in response to cadmium stress using UPLC-QTOF-MS

Cadmium (Cd) pollution significantly reduces agricultural crop yields. In our research, metabolomic changes in Citrus maxima L. subjected to Cd stress were investigated using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) in tandem with multivariate analytical techniques. This integrative method, coupled with physiological evaluations, aimed to elucidate the core adaptive mechanisms to Cd stress. We found that under Cd stress, C. maxima seedlings exhibited elevated levels of reactive oxygen species, malondialdehyde, and electrolyte leakage. Furthermore, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) demonstrated distinct a separation of the metabolome among the different treatment groups under Cd stress, indicating dynamic metabolic changes. Metabolic analysis suggested that genes involved are initially induced by Cd treatment, followed by the activation of the flavonoid biosynthesis pathway. This investigation provides new insights into the complex metabolic responses of C. maxima seedlings to Cd exposure.

Comparative physiological and transcriptomic analyses provide induction resistance mechanisms of Bacillus tequilensis against Colletotrichum fructicola in Camellia oleifera

Bacillus tequilensis DZY 6715 was isolated from healthy leaves in Camellia oleifera, and the strain DZY 6715 significantly inhibited anthracnose disease resulting from Colletotrichum fructicola in C. oleifera, besides, its associated mechanism of disease resistance was explored. B. tequilensis DZY 6715 treatment controlled mycelial growth of C. fructicola in C. oleifera, and significantly decreased C. oleifera anthracnose incidence and disease index compared with the control group. B. tequilensis DZY 6715 has strong biofilm forming ability, and also secretes extracellular β-1, 3-glucanase and chitinase, which could cause cell membranes damage and increased cellular compound leakage. C.oleifera treated with DZY 6715 also effectively enhanced enzyme activities and stimulated the synthesis the substances related to phenylpropane metabolism and reactive oxygen metabolism. Moreover, transcript profiling analysis revealed more differentially expressed genes related to phenylpropanoid pathway metabolism and antioxidant system inducing by DZY 6715 compared with the control in C. oleifera. Thus, it can be concluded that B. tequilensis DZY 6715 is a suitable bio-control agent to control anthracnose disease in C. oleifera.

Comparative transcriptome and metabolome reveal the role of acidic electrolyzed oxidizing water in improving postharvest disease resistance of longan fruit

Acidic electrolyzed oxidizing water (AEOW) was applied to suppress disease development and maintain good quality of fresh fruit. However, the involvement of AEOW in improving disease resistance of fresh longan remains unknown. Here, transcriptomic and metabolic analyses were performed to compare non-treated and AEOW-treated longan during storage. The transcriptome analysis showed AEOW-induced genes associated with phenylpropanoid and flavonoid biosynthesis. The metabolome analysis found the contents of coumarin, phenolic acid, and tannin maintained higher levels in AEOW-treated longan than non-treated longan. Moreover, the weighted correlation network analysis (WGCNA) was performed to identify hub genes, and a gene-metabolite correlation network associated with AEOW-improved disease resistance in longan was constructed by the co-analysis of transcriptomics and metabolomics. These findings identified a series of important genes and metabolites involving in AEOW-induced disease resistance of longan fruit, expanding our knowledges on fruit disease resistance and quality maintenance at the transcript and metabolic levels.

Dual Transcriptomic and Metabolomic Analysis of Elicited Flax Sheds Light on the Kinetics of Immune Defense Activation Against the Biotrophic Pathogen Oidium lini

Flax (Linum usitatissimum) grown under controlled conditions displayed genotype-dependent resistance to powdery mildew (Oidium lini) following COS-OGA (comprising chitosan- and pectin-derived oligomers) elicitor application. The present study reveals a two-step immune response in plants preventively challenged with the elicitor: an initial, rapid response characterized by the transcription of defense genes whose protein products act in contact with or within the cell wall, where biotrophic pathogens initially thrive, followed by a prolonged activation of cell wall peroxidases and accumulation of secondary metabolites. Thus, dozens of genes encoding membrane receptors, pathogenesis-related proteins, and wall peroxidases were initially overexpressed. Repeated COS-OGA treatments had a transient effect on the transcriptome response while cumulatively remodeling the metabolome over time, with a minimum of two applications required for maximal metabolomic shifts. Secondary metabolites, in particular terpenoids and phenylpropanoids, emerged as major components of this secondary defense response alongside pathogenesis-related proteins and wall peroxidases. The sustained accumulation of secondary metabolites, even after cessation of elicitation, contrasted with the short-lived transcriptomic response. Wall peroxidase enzyme activity also exhibited cumulative effects, increasing strongly for weeks after a third elicitor treatment. This underscores the plasticity of the plant immune response in the face of a potential infection, and the need for repeated preventive applications to achieve the full protective potential of the elicitor.

AMF inhibit the production of phenolic acid autotoxins at the seed-filling stage in soybeans with continuous monocropping

BACKGROUND

Soybean is the main oil crop in Northeast China. Continuous monocropping is more commonly used for soybean production due to rising market demand and arable land constraints. However, autotoxic substances, such as phenolic acids, produced by continuously cropped soybean can reduce yield and quality. The mycorrhiza formed of Arbuscular mycorrhizal fungi (AMF) and plant roots regulate the metabolic activities of the host plant and increase its disease resistance. The main purpose of this study was to inhibit the production of phenolic acids and determine the adverse effects on the growth of continuous monocropping soybean by inoculating Funneliformis mosseae (F. mosseae).

RESULTS

Transcriptomics results showed that the production of phenolic acids in continuous monocropping soybean roots was mainly regulated by the expression of the CHS6, PCL1, SAMT, SRG1, and ACO1 genes, and the expression of these genes was significantly downregulated after inoculation with F. mosseae. Metabolomics results showed that continuous monocropping soybean roots inoculated with F. mosseae inhibited phenolic acid production through the phenylpropane biosynthetic, α-linoleic acid, linoleic acid, and other metabolic pathways. Phenolic acids in the phenylpropane metabolic pathway, such as 4-hydroxybenzoic acid, phthalic acid, and vanillic acid, decreased significantly after inoculation with F. mosseae. The combined analysis of the two showed that genes such as YLS9 and ARF3 were positively correlated with 4-hydroxybenzoic acid and so on, while genes such as CHS6 and SRG1 were negatively correlated with butyric acid and so on.

CONCLUSION

F. mosseae regulated the expression of functional genes and related phenolic acid metabolic pathways produced by continuous monocropping soybean roots, inhibiting the production of phenolic acid autotoxic substances in continuous cropped soybean, and slowing down the disturbance of continuous monocropping. This study provides a new solution for continuous monocropping of plants to overcome the autotoxicity barrier and provides a new basis for the development and utilization of AMF as a biological agent.

Nanomaterial-Based Sensors for Coumarin Detection

Sensors are widely used owing to their advantages including excellent sensing performance, user-friendliness, portability, rapid response, high sensitivity, and specificity. Sensor technologies have been expanded rapidly in recent years to offer many applications in medicine, pharmaceuticals, the environment, food safety, and national security. Various nanomaterial-based sensors have been developed for their exciting features, such as a powerful absorption band in the visible region, excellent electrical conductivity, and good mechanical properties. Natural and synthetic coumarin derivatives are attracting attention in the development of functional polymers and polymeric networks for their unique biological, optical, and photochemical properties. They are the most abundant organic molecules in medicine because of their biological and pharmacological impacts. Furthermore, coumarin derivatives can modulate signaling pathways that affect various cellular processes. This review covers the discovery of coumarins and their derivatives, the integration of nanomaterial-based sensors, and recent advances in nanomaterial-based sensing for coumarins. This review also explains how sensors work, their types, their pros and cons, and sensor studies for coumarin detection in recent years.

Spotlight on Secondary Metabolites Produced by an Early-Flowering Apulian Artichoke Ecotype Sanitized from Virus Infection by Meristem-Tip-Culture and Thermotherapy

Globe artichoke (Cynara cardunculus L. subsp. scolymus) is an important crop of the Mediterranean basin characterized by many properties, like hepatoprotective, anticarcinogenic, antioxidant, antibacterial, and beneficial to human health. The high bioactive compounds (BACs) content, as polyphenols, has attracted the research interest in artichoke extracts. We analysed the changes in polyphenol transcriptome profile between sanitized (S) virus-free and non-sanitized (NS) artichoke plants, focusing on genes involved in phenylpropanoid metabolic pathway and flavonoid biosynthesis. A total of 2458 upregulated and 2154 downregulated differentially expressed genes (DEGs) were functionally characterized. Among them, 31 and 35 KEGG orthology entries characterized by upregulated and downregulated DEGs, respectively, were involved in the biosynthesis of other secondary metabolites. A downregulation of PAL, C4H, 4CL, HST/HQT, C3'H, CCoAMT, CCR1, and F5H, was observed in S artichoke compared to NS one, whereas the CSE, CHS, and CHI genes were upregulated in S samples. Transcriptome results were compared to the polyphenols accumulation in S and NS artichoke leaves. A higher content of total polyphenols was observed in older leaves of NS samples, compared to extracts obtained from young leaves or from S plants, and this result was associated with the presence of viral infections in NS plants. In all the conditions tested, the most represented compound was chlorogenic acid, followed by luteolin-7-O-glucoside. The different composition of each extract was evaluated by a polyphenol dose-response treatment on the rodent hepatoma FaO cell line to the accumulation of reactive oxygen species (ROS). A significant reduction in ROS content ranging between -40% and -48% was observed when 10-20 mg/L of polyphenols from NS or S plants were used, characterized by a specific profile of compounds. To reduce MetOH residues in polyphenol extracts, a supercritical fluid CO2 extraction was evaluated to propose a sustainable green extraction.

Transcriptome analysis discloses antioxidant detoxification mechanism of Gracilaria bailinae under different cadmium concentrations and stress durations

To remedy Cd pollution in the ocean, macroalgae are used as a bioremediation tool because of their ability to absorb and accumulate Cd. Gracilaria bailinae has high economic and ecological value and can survive in Cd contaminated waters; however, the underlying molecular mechanisms remain unclear. In this study, physiological and biochemical indexes were analyzed after 1, 3, 5, or 7 days of Cd2+ exposure; further, the transcriptome of G. bailinae was examined after a 7-day exposure to a Cd2+ culture environment with Cd levels of 0 mg L-1 (cd1, control), 1 mg L-1 (cd2, low concentration), and 2.5 mg L-1 (cd3, high concentration). The results showed that in the cd2 group, G. bailinae maintained a stable RGR that did not differ significantly (P > 0.05) from that of the cd1 group. However, the soluble protein and MDA contents, as well as the activities of SOD, CAT and POD, were significantly increased (P< 0.05) compared to the cd1 group. No significant differences (P > 0.05) were found among the different Cd2+ stress durations. In contrast, compared with the cd1 group, the RGR, soluble protein content, SOD, CAT, and POD activities were significantly decreased (P< 0.05), while the MDA content was significantly increased (P< 0.05) in the cd3 group. Furthermore, significant differences (P< 0.05) were observed among the various tested Cd2+ stress durations within the cd3 group. Compared to the cd1 group, a total of 30,072 DEGs and 21,680 were identified in the cd2 and cd3 treatments, respectively. More up-regulated genes were found in cd2 group than in cd3 group. GO enrichment analysis showed that these genes were related to peptidase activity, endopeptidase activity, ion transport, peptide biosynthetic and metabolism. In addition, DEGs related to histidine metabolism and the stilbene, diarylheptane, and gingerol pathways were significantly up-regulated in the cd2 group compared to the cd3 group, which resulted in enhanced activities of antioxidant enzymes and promoted cell wall regeneration. The results of this study reveal the response mechanism of G. bailinae to Cd2+ stress, providing valuable insights for assessing the bioremediation potential of G. bailinae for Cd-contaminated waters.

Flavonoid synthesis is crucial for Trichoderma asperellum-induced systemic resistance to root-knot nematodes in tomato plants

Trichoderma spp. can enhance plant resistance against a wide range of biotic stressors. However, the fundamental mechanisms by which Trichoderma enhances plant resistance against Meloidogyne incognita, known as root-knot nematodes (RKNs), are still unclear. Here, we identified a strain of Trichoderma asperellum (T141) that could effectively suppress RKN infestation in tomato (Solanum lycopersicum L.). Nematode infestation led to an increase in the concentrations of reactive oxygen species (ROS) and malondialdehyde (MDA) in roots but pre-inoculation with T141 significantly decreased oxidative stress. The reduction in ROS and MDA was accompanied by an increase in the activity of antioxidant enzymes and the accumulation of flavonoids and phenols. Moreover, split root test-based analysis showed that T141 inoculation in local roots before RKN inoculation increased the concentration of phytohormone jasmonate (JA) and the transcripts of JA synthesis and signaling-related genes in distant roots. UPLC-MS/MS-based metabolomics analysis identified 1051 differentially accumulated metabolites (DAMs) across 4 pairwise comparisons in root division test, including 81 flavonoids. Notably, 180 DAMs were found in comparison between RKN and T141-RKN, whereas KEGG annotation and enrichment analysis showed that the secondary metabolic pathways, especially the flavonoid biosynthesis, played a key role in the T141-induced systemic resistance to RKNs. The role of up-regulated flavonoids in RKN mortality was further verified by in vitro experiments with the exogenous treatment of kaempferol, hesperidin and rutin on J2-stage RKNs. Our results revealed a critical mechanism by which T141 induced resistance of tomato plants against the RKNs by systemically promoting secondary metabolism in distant roots.

Methyl jasmonate-loaded composite biofilm sustainably alleviates chilling lignification of loquat fruit during postharvest storage

In this work, the MeJA-loaded gelatin/pullulan/chitosan composite biofilm was prepared to inhibit the chilling lignification of the loquat fruit during storage at 0 °C. The firmness and lignin content were decreased by 89 % and 81.77 % after MeJA-loaded biofilm treatment. Malondialdehyde (MDA) production was almost completely suppressed and chilling injury of loquat fruit was significantly reduced. Enzyme activity results show that the biofilm alleviated chilling lignification mainly by inhibiting peroxidase (POD) activity in the phenylpropanoid pathway (PCCs = 0.715, with lignin content). Also, the conventional MeJA vapor treatment only alleviated lignification on day 3, but the biofilm treatment had a better and more sustained effect throughout the whole storage due to its sustained release ability. Besides, the biofilm had good mechanical properties, transparency and water vapor transmission rate. This work indicates that loading preservatives into biofilms has a promising application prospect for inhibiting the postharvest quality deterioration of fruit and vegetables.

Plant-derived and dietary phenolic cinnamic acid derivatives: Anti-inflammatory properties

Cinnamic acids are aromatic acids primarily found in plants and plant-derived food. Phenolic cinnamic acids, with one or more hydroxyl groups in the aromatic ring, often contribute to the biological activities attributed to these compounds. The presence of hydroxyl groups and a carboxyl group makes cinnamic acids very hydrophilic, preventing them from crossing biological membranes and exerting their biological activities. To alleviate this condition, a panel of synthetic modifications have been made leading to a diverse set of phenolic cinnamic structures. In this review, an overview of the natural phenolic cinnamic acid derivatives and their plant sources (more than 200) is described. The synthetic approaches to obtain the referred derivatives (more than 200) namely esters and amides are reviewed. Further, their anti-inflammatory activity (more than 70 compounds) is scrutinized. Finally, future directions will be indicated to translate the research on phenolic cinnamic derivatives into potentially effective anti-inflammatory drugs.

Biosynthesis and metabolic engineering of isoflavonoids in model plants and crops: a review

Isoflavonoids, the major secondary metabolites within the flavonoid biosynthetic pathway, play important roles in plant defense and exhibit free radical scavenging properties in mammals. Recent advancements in understanding the synthesis, transport, and regulation of isoflavonoids have identified their biosynthetic pathways as promising targets for metabolic engineering, offering potential benefits such as enhanced plant resistance, improved biomass, and restoration of soil fertility. This review provides an overview of recent breakthroughs in isoflavonoid biosynthesis, encompassing key enzymes in the biosynthetic pathway, transporters influencing their subcellular localization, molecular mechanisms regulating the metabolic pathway (including transcriptional and post-transcriptional regulation, as well as epigenetic modifications). Metabolic engineering strategies aimed at boosting isoflavonoid content in both leguminous and non-leguminous plants. Additionally, we discuss emerging technologies and resources for precise isoflavonoid regulation. This comprehensive review primarily focuses on model plants and crops, offering insights for more effective and sustainable metabolic engineering approaches to enhance nutritional quality and stress tolerance.

Integrated Transcriptome and Metabolome Analysis Reveals Molecular Mechanisms Underlying Resistance to Phytophthora Root Rot

Soybean production is significantly impacted by Phytophthora root rot (PRR), which is caused by Phytophthora sojae. The nucleotide-binding leucine-rich repeat (NLR) gene family plays a crucial role in plant disease resistance. However, current understanding of the function of soybean NLR genes in resistance to PRR is limited. To address this knowledge gap, transgenic soybean plants overexpressing the NLR gene (Glyma.18g283200) were generated to elucidate the molecular mechanism of resistance. Here, transcript changes and metabolic differences were investigated at three time points (12, 24, and 36 h) after P. sojae infection in hypocotyls of two soybean lines, Dongnong 50 (susceptible line, WT) and Glyma.18g283200 overexpression line (resistant line, OE). Based on the changes in differentially expressed genes (DEGs) in response to P. sojae infection in different lines and at different time points, it was speculated that HOPZ-ACTIVATED RESISTANCE 1 (ZAR1), valine, leucine, and isoleucine degradation, and phytohormone signaling may be involved in the defense response of soybean to P. sojae at the transcriptome level by GO term and KEGG pathway enrichment analysis. Differentially accumulated metabolites (DAMs) analysis revealed that a total of 223 and 210 differential metabolites were identified in the positive ion (POS) and negative ion (NEG) modes, respectively. An integrated pathway-level analysis of transcriptomics (obtained by RNA-seq) and metabolomics data revealed that isoflavone biosynthesis was associated with disease resistance. This work provides valuable insights that can be used in breeding programs aiming to enhance soybean resistance against PRR.

Transcriptome sequencing of medical herb Salvia Rosmarinus (Rosemary) revealed the phenylpropanoid biosynthesis pathway genes and their phylogenetic relationships

BACKGROUND

The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely.

METHODS AND RESULTS

We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis.

CONCLUSION

The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.

Isolation and Characterization of Phenylalanine Ammonia Lyase (PAL) Genes in Ferula pseudalliacea: Insights into the Phenylpropanoid Pathway

Phenylalanine ammonia lyase (PAL) is a key enzyme regulating the biosynthesis of the compounds of the phenylpropanoid pathway. This study aimed to isolate and characterize PAL genes from Ferula pseudalliacea Rech.f. (Apiales: Apiaceae) to better understand the regulation of metabolite production. Three PAL gene isoforms (FpPAL1-3) were identified and cloned using the 3'-RACE technique and confirmed by sequencing. Bioinformatics analysis revealed important structural features, such as phosphorylation sites, physicochemical properties, and evolutionary relationships. Expression analysis by qPCR demonstrated the differential transcription profiles of each FpPAL isoform across roots, stems, leaves, flowers, and seeds. FpPAL1 showed the highest expression in stems, FpPAL2 in roots and flowers, and FpPAL3 in flowers. The presence of three isoforms of PAL in F. pseudalliacea, along with the diversity of PAL genes and their tissue-specific expression profiles, suggests that complex modes of regulation exist for phenylpropanoid biosynthesis in this important medicinal plant. The predicted interaction network revealed associations with key metabolic pathways, emphasizing the multifaceted roles of these PAL genes. In silico biochemical analyses revealed the hydrophilicity of the FpPAL isozyme; however, further analysis of substrate specificity and enzyme kinetics can clarify the specific role of each FpPAL isozyme. These comprehensive results increase the understanding of PAL genes in F. pseudalliacea, helping to characterize their contributions to secondary metabolite biosynthesis.

Transcriptome responses of Arabidopsis to necrotrophic fungus Alternaria brassicae reveal pathways and candidate genes associated with resistance

Alternaria leaf blight (ALB), caused by a necrotrophic fungus Alternaria brassicae is a serious disease of oleiferous Brassicas resulting in significant yield losses worldwide. No robust resistance against A. brassicae has been identified in the Brassicas. Natural accessions of Arabidopsis show a spectrum of responses to A. brassicae ranging from high susceptibility to complete resistance. To understand the molecular mechanisms of resistance/ susceptibility, we analysed the comparative changes in the transcriptome profile of Arabidopsis accessions with contrasting responses- at different time points post-infection. Differential gene expression, GO enrichment, pathway enrichment, and weighted gene co-expression network analysis (WGCNA) revealed reprogramming of phenylpropanoid biosynthetic pathway involving lignin, hydroxycinnamic acids, scopoletin, anthocyanin genes to be highly associated with resistance against A. brassicae. T-DNA insertion mutants deficient in the biosynthesis of coumarin scopoletin exhibited enhanced susceptibility to A. brassicae. The supplementation of scopoletin to medium or exogenous application resulted in a significant reduction in the A. brassicae growth. Our study provides new insights into the transcriptome dynamics in A. brassicae-challenged Arabidopsis and demonstrates the involvement of coumarins in plant immunity against the Brassica pathogen A. brassicae.

Comparative Transcriptome and sRNAome Analysis Suggest Coordinated Citrus Immune Responses against Huanglongbing Disease

Citrus Huanglongbing (HLB), caused by the phloem-inhibiting bacterium Candidatus Liberibacter asiaticus (CLas), is the most devastating citrus disease, intimidating citrus production worldwide. Although commercially cultivated citrus cultivars are vulnerable to CLas infection, HLB-tolerant attributes have, however, been observed in certain citrus varieties, suggesting a possible pathway for identifying innate defense regulators that mitigate HLB. By adopting transcriptome and small RNAome analysis, the current study compares the responses of HLB-tolerant lemon (Citrus limon L.) with HLB-susceptible Shatangju mandarin (Citrus reticulata Blanco cv. Shatangju) against CLas infection. Transcriptome analysis revealed significant differences in gene expression between lemon and Shatangju. A total of 1751 and 3076 significantly differentially expressed genes were identified in Shatangju and lemon, respectively. Specifically, CLas infected lemon tissues demonstrated higher expressions of genes involved in antioxidant enzyme activity, protein phosphorylation, carbohydrate, cell wall, and lipid metabolism than Shatangju. Wet-lab experiments further validated these findings, demonstrating increased antioxidant enzyme activity in lemon: APX (35%), SOD (30%), and CAT (64%) than Shatangju. Conversely, Shatangju plants exhibited higher levels of oxidative stress markers like H2O2 (44.5%) and MDA content (65.2%), alongside pronounced ion leakage (11.85%), than lemon. Moreover, microscopic investigations revealed that CLas infected Shatangju phloem exhibits significantly more starch and callose accumulation than lemon. Furthermore, comparative sRNA profiles revealed the potential defensive regulators for HLB tolerance. In Shatangju, increased expression of csi-miR166 suppresses the expression of disease-resistant proteins, leading to inadequate defense against CLas. Conversely, reduced expression of csi-miR166 in lemon plants enables them to combat HLB by activating disease-resistance proteins. The above findings indicate that when infected with CLas, lemon exhibits stronger antioxidative activity and higher expression of disease-resistant genes, contributing to its enhanced tolerance to HLB. In contrast, Shatangju shows lower antioxidative activity, reduced expression of disease-resistant genes, significant ion leakage, and extensive callose deposition, possibly related to damage to plant cell structure and blockage of phloem sieve tubes, thereby promoting the development of HLB symptoms.

Nitrogen and Silicon Contribute to Wheat Defense's to Pyrenophora tritici-repentis, but in an Independent Manner

Nitrogen (N) and silicon (Si) are mineral elements that have shown a reduction in the damage caused by tan spot (Pyrenophora tritici-repentis (Ptr)) in wheat. However, the effects of these elements were studied separately, and the N and Si interaction effect on wheat resistance to tan spot remains elusive. Histocytological and biochemical defense responses against Ptr in wheat leaves treated with Si (+Si) at low (LN) and high N (HN) inputs were investigated. Soil amendment with Si reduced the tan spot severity in 18% due to the increase in the leaf Si concentration (around 30%), but it was affected by the N level used. The superoxide dismutase (SOD) activity was higher in +Si plants and inoculated with Ptr, leading to early and higher H2O2 and callose accumulation in wheat leaf. Interestedly, phenylalanine ammonia-lyase (PAL) activity was induced by the Si supplying, being negatively affected by the HN rate. Meanwhile, catalase (CAT), and peroxidase (POX) activities showed differential response patterns according to the Si and N rates used. Tan spot severity was reduced by both elements, but their interaction does not evidence synergic effects in this disease's control. Wheat plants from -Si and HN and +Si and LN treatments recorded lower tan spot severity.

Theory to practice: a success in breeding sugarcane variety YZ08-1609 known as the King of Sugar

Sugarcane, a significant cash crop in tropical and subtropical regions, contributes to 80% of sugar production and 40% of bioethanol production in the world. It is a key sugar crop, accounting for 85% of sugar production in China. Developing new varieties with high yield, high sugar, and better stress resistance is crucial for the sustainable growth of sugar industry. Hybrid breeding is the most widely used and effective method, with over 98% of Chinese sugarcane varieties resulting from this approach. Over the past two decades, Chinese breeders have developed the theory of high-heterogeneous composite high-sugar breeding, leading to the successful breeding of the fifth-generation sugarcane varieties. Among them, YZ08-1609, a complex hybrid of Saccharum spp., was developed by Sugarcane Research Institute (YSRI) of Yunnan Academy of Agricultural Sciences. The average cane yield of YZ08-1609 was 14.4% higher than ROC22. It is highly resistant to mosaic disease, and highly tolerant to drought stress, but moderately susceptible to smut disease. Notably, YZ08-1609 stands out with a sucrose content of 20.3%, setting an international record, earning the reputation as "King of Sugar". To summarize experience and inspire breeding, we provided here the detailed insights into the selection of parents, breeding process, and characteristics of YZ08-1609. Besides, the biological mechanisms underlying its high yield and high sugar was excavated at both transcriptional and metabolic levels. The challenges and prospects in breeding sugarcane varieties especially with high sugar were also discussed, offering a foundation for the future development of high-sugar varieties.

Biochemical Responses in Populus tremula: Defending against Sucking and Leaf-Chewing Insect Herbivores

The main biochemical traits were estimated in poplar leaves under biotic attack (aphids and spongy moth infestation). Changes in the abundance of bioactive compounds in genetically uniform individuals of European aspen (Populus tremula), such as proline, polyphenolic compounds, chlorophylls a and b, and volatile compounds, were determined between leaves damaged by sucking insects (aphid-Chaitophorus nassonowi) and chewing insects (spongy moth-Lymantria dispar) compared to uninfected leaves. Among the nine analyzed phenolic compounds, only catechin and procyanidin showed significant differences between the control leaves and leaves affected by spongy moths or aphids. GC-TOF-MS volatile metabolome analysis showed the clear separation of the control versus aphids-infested and moth-infested leaves. In total, the compounds that proved to have the highest explanatory power for aphid-infested leaves were 3-hexenal and 5-methyl-2-furanone, and for moth-infested leaves, trans-α-farnesene and 4-cyanocyclohexane. The aphid-infested leaves contained around half the amount of chlorophylls and twice the amount of proline compared to uninfected leaves, and these results evidenced that aphids influence plant physiology more than chewing insects.

Effect of Elicitor Treatments on Quality Attributes in Blueberry: Implications of Cultivar and Environmental Conditions

Elicitors of plant defence responses can trigger defence mechanisms that are able to protect plant tissues from biotic or abiotic stresses. Since one defence response involves the activation of secondary metabolites' biosynthesis, the purpose of this study was to evaluate the effect of chitosan and melatonin pre-harvest treatments on the quality and the nutritional parameters of the fruits of blueberry (Vaccinium corymbosum L.). Across the two years of experiment, three different cultivars (cv.s. 'Cosmopolitan', 'Hortblue Poppins' and 'Legacy') were treated with 1% chitosan or 100 µM melatonin every two weeks during the ripening season and ripe fruits were progressively harvested and analysed. The treatment with both elicitors had only slight effects on dry matter, soluble solids content, titratable acidity and pH, with a cultivar-dependent response. On the other hand, elicitors significantly affected the levels of phenylpropanoid and antioxidant compounds in all cvs. in both years, with a higher accumulation of total anthocyanins and phenolics and the enhancement of the antioxidant capacity, with positive effects on the nutraceutical quality of fruits. The anthocyanin profile in terms of both absolute concentrations and the relative proportion of single anthocyanins was affected by both harvest year and cv., highlighting the role of the genetic background in the plant response to environmental conditions (with particular reference to summer heat stress) and to elicitor treatments.

Integrating transcriptomics and metabolomics to analyze the defense response of Morus notabilis to mulberry ring rot disease

Introduction

The mulberry industry has thrived in China for millennia, offering significant ecological and economic benefits. However, the prevalence of mulberry ring rot disease poses a serious threat to the quality and yield of mulberry leaves.

Methods

In this study, we employed a combination of transcriptomic and metabolomic analyses to elucidate the changes occurring at the transcriptional and metabolic levels in Morus notabilis in response to this disease infestation. Key metabolites identified were further validated through in vitro inhibition experiments.

Results

The findings revealed significant enrichment in Kyoto Encyclopedia of Genes and Genomes pathways, particularly those related to flavonoid biosynthesis. Notably, naringenin, kaempferol, and quercetin emerged as pivotal players in M. notabilis' defense mechanism against this disease pathogen. The upregulation of synthase genes, including chalcone synthase, flavanone-3-hydroxylase, and flavonol synthase, suggested their crucial roles as structural genes in this process. In vitro inhibition experiments demonstrated that kaempferol and quercetin exhibited broad inhibitory properties, while salicylic acid and methyl jasmonate demonstrated efficient inhibitory effects.

Discussion

This study underscores the significance of the flavonoid biosynthesis pathway in M. notabilis' defense response against mulberry ring rot disease, offering a theoretical foundation for disease control measures.

Transcriptomics combined with physiological analysis provided new insights into the Zn enrichment capacity and tolerance mechanism of Dendrobium denneanum Kerr

In this study, we investigated the tolerance and accumulation capacity of Dendrobium denneanum Kerr (D.denneanum) by analyzing the growth and physiological changes of D.denneanum under different levels of Zn treatments, and further transcriptome sequencing of D.denneanum leaves to screen and analyze the differentially expressed genes. The results showed that Zn400 treatment (400 mg·kg-1) promoted the growth of D.denneanum while both Zn800 (800 mg·kg-1) and Zn1600 treatment (1600 mg·kg-1) caused stress to D.denneanum. Under Zn800 treatment (800 mg·kg-1), the resistance contribution of physiological indexes was the most obvious: antioxidant system, photosynthetic pigment, osmoregulation, phytochelatins, and ASA-GSH cycle (Ascorbic acid-Glutathione cycle). D.denneanum leaves stored the most Zn, followed by stems and roots. The BCF(Bioconcentration Factor) of the D.denneanum for Zn were all more than 1.0 under different Zn treatments, with the largest BCF (1.73) for Zn400. The transcriptome revealed that there were 1500 differentially expressed genes between Zn800 treatment and group CK, of which 842 genes were up-regulated and 658 genes were down-regulated. The genes such as C4H, PAL, JAZ, MYC2, PP2A, GS, and GST were significantly induced under the Zn treatments. The differentially expressed genes were associated with phenylpropane biosynthesis, phytohormone signaling, and glutathione metabolism. There were three main pathways of response to Zn stress in Dendrobium: antioxidant action, compartmentalization, and cellular chelation. This study provides new insights into the response mechanisms of D.denneanum to Zn stress and helps to evaluate the phytoremediation potential of D.denneanum in Zn-contaminated soils.

Comparative analyses reveal a phenylalanine ammonia lyase dependent and salicylic acid mediated host resistance in Zingiber zerumbet against the necrotrophic soft rot pathogen Pythium myriotylum

Little is known about the molecular basis of host defense in resistant wild species Zingiber zerumbet (L.) Smith against the soil-borne, necrotrophic oomycete pathogen Pythium myriotylum Drechsler, which causes the devastating soft rot disease in the spice crop ginger (Zingiber officinale Roscoe). We investigated the pattern of host defense between Z. zerumbet and ginger in response to P. myriotylum inoculation. Analysis of gene expression microarray data revealed enrichment of phenylpropanoid biosynthetic genes, particularly lignin biosynthesis genes, in pathogen-inoculated Z. zerumbet compared to ginger. RT-qPCR analysis showed the robust activation of phenylpropanoid biosynthesis genes in Z. zerumbet, including the core genes PAL, C4H, 4CL, and the monolignol biosynthesis and polymerization genes such as CCR, CAD, C3H, CCoAOMT, F5H, COMT, and LAC. Additionally, Z. zerumbet exhibited the accumulation of the phenolic acids including p-coumaric acid, sinapic acid, and ferulic acid that are characteristic of the cell walls of commelinoid monocots like Zingiberaceae and are involved in cell wall strengthening by cross linking with lignin. Z. zerumbet also had higher total lignin and total phenolics content compared to pathogen-inoculated ginger. Phloroglucinol staining revealed the enhanced fortification of cell walls in Z. zerumbet, specifically in xylem vessels and surrounding cells. The trypan blue staining indicated inhibition of pathogen growth in Z. zerumbet at the first leaf whorl, while ginger showed complete colonization of the pith within 36 h post inoculation (hpi). Accumulation of salicylic acid (SA) and induction of SA regulator NPR1 and the signaling marker PR1 were observed in Z. zerumbet. Silencing of PAL in Z. zerumbet through VIGS suppressed downstream genes, leading to reduced phenylpropanoid accumulation and SA level, resulting in the susceptibility of plants to P. myriotylum. These findings highlight the essential role of PAL-dependent mechanisms in resistance against P. myriotylum in Z. zerumbet. Moreover, our results suggest an unconventional role for SA in mediating host resistance against a necrotroph. Targeting the phenylpropanoid pathway could be a promising strategy for the effective management of P. myriotylum in ginger.

Molecular mechanism of drought resistance in soybean roots revealed using physiological and multi-omics analyses

Soybeans are one of the most cultivated crops worldwide and drought can seriously affect their growth and development. Many studies have elucidated the mechanisms through which soybean leaves respond to drought; however, little is known about these mechanisms in roots. We used two soybean varieties with different drought tolerances to study the morphological, physiological, and molecular response mechanisms of the root system to drought stress in seedlings. We found that drought stress led to a significant decrease in the root traits and an increase in antioxidant enzyme activity in the two varieties. Drought-resistant varieties accumulate large amounts of flavonoids and phenolic acids at the metabolic level, which causes variations in drought resistance. Additionally, differences in gene expression and drought-resistance pathways between the two varieties were clarified using transcriptome analysis. Through a multi-omics joint analysis, phenylpropanoid and isoflavonoid biosynthesis were identified as the core drought resistance pathways in soybean roots. Candidate genes and marker metabolites affecting drought resistance were identified. The phenylpropanoid pathway confers drought tolerance to roots by maintaining a high level of POD activity and mediates the biosynthesis of various secondary drought-resistant metabolites to resist drought stress. This study provides useful data for investigating plant root drought responses and offers theoretical support for plant breeding for drought resistance.

A review on endophytic fungi: a potent reservoir of bioactive metabolites with special emphasis on blight disease management

Phytopathogenic microorganisms have caused blight diseases that present significant challenges to global agriculture. These diseases result in substantial crop losses and have a significant economic impact. Due to the limitations of conventional chemical treatments in effectively and sustainably managing these diseases, there is an increasing interest in exploring alternative and environmentally friendly approaches for disease control. Using endophytic fungi as biocontrol agents has become a promising strategy in recent years. Endophytic fungi live inside plant tissues, forming mutually beneficial relationships, and have been discovered to produce a wide range of bioactive metabolites. These metabolites demonstrate significant potential for fighting blight diseases and provide a plentiful source of new biopesticides. In this review, we delve into the potential of endophytic fungi as a means of biocontrol against blight diseases. We specifically highlight their significance as a source of biologically active compounds. The review explores different mechanisms used by endophytic fungi to suppress phytopathogens. These mechanisms include competing for nutrients, producing antifungal compounds, and triggering plant defense responses. Furthermore, this review discusses the challenges of using endophytic fungi as biocontrol agents in commercial applications. It emphasizes the importance of conducting thorough research to enhance their effectiveness and stability in real-world environments. Therefore, bioactive metabolites from endophytic fungi have considerable potential for sustainable and eco-friendly blight disease control. Additional research on endophytes and their metabolites will promote biotechnology solutions.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9

The plant growth-promoting rhizobacterium Tsukamurella tyrosinosolvens P9 can improve peanut growth. In this study, a co-culture system of strain P9 and peanut was established to analyze the transcriptome of peanut roots interacting with P9 for 24 and 72 h. During the early stage of co-culturing, genes related to mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction, ethylene synthesis, and cell wall pectin degradation were induced, and the up-regulation of phenylpropanoid derivative, flavonoid, and isoflavone synthesis enhanced the defense response of peanut. The enhanced expression of genes associated with photosynthesis and carbon fixation, circadian rhythm regulation, indoleacetic acid (IAA) synthesis, and cytokinin decomposition promoted root growth and development. At the late stage of co-culturing, ethylene synthesis was reduced, whereas Ca2+ signal transduction, isoquinoline alkaloid synthesis, and ascorbate and aldarate metabolism were up-regulated, thereby maintaining root ROS homeostasis. Sugar decomposition and oxidative phosphorylation and nitrogen and fatty acid metabolism were induced, and peanut growth was significantly promoted. Finally, the gene expression of seedlings inoculated with strain P9 exhibited temporal differences. The results of our study, which explored transcriptional alterations of peanut root during interacting with P9, provide a basis for elucidating the growth-promoting mechanism of this bacterial strain in peanut.

Leaf rust (Puccinia recondita f. sp. secalis) triggers substantial changes in rye (Secale cereale L.) at the transcriptome and metabolome levels

BACKGROUND

Rye (Secale cereale L.) is a cereal crop highly tolerant to environmental stresses, including abiotic and biotic stresses (e.g., fungal diseases). Among these fungal diseases, leaf rust (LR) is a major threat to rye production. Despite extensive research, the genetic basis of the rye immune response to LR remains unclear.

RESULTS

An RNA-seq analysis was conducted to examine the immune response of three unrelated rye inbred lines (D33, D39, and L318) infected with compatible and incompatible Puccinia recondita f. sp. secalis (Prs) isolates. In total, 877 unique differentially expressed genes (DEGs) were identified at 20 and 36 h post-treatment (hpt). Most of the DEGs were up-regulated. Two lines (D39 and L318) had more up-regulated genes than down-regulated genes, whereas the opposite trend was observed for line D33. The functional classification of the DEGs helped identify the largest gene groups regulated by LR. Notably, these groups included several DEGs encoding cytochrome P450, receptor-like kinases, methylesterases, pathogenesis-related protein-1, xyloglucan endotransglucosylases/hydrolases, and peroxidases. The metabolomic response was highly conserved among the genotypes, with line D33 displaying the most genotype-specific changes in secondary metabolites. The effect of pathogen compatibility on metabolomic changes was less than the effects of the time-points and genotypes. Accordingly, the secondary metabolome of rye is altered by the recognition of the pathogen rather than by a successful infection. The results of the enrichment analysis of the DEGs and differentially accumulated metabolites (DAMs) reflected the involvement of phenylpropanoid and diterpenoid biosynthesis as well as thiamine metabolism in the rye immune response.

CONCLUSION

Our work provides novel insights into the genetic and metabolic responses of rye to LR. Numerous immune response-related DEGs and DAMs were identified, thereby clarifying the mechanisms underlying the rye response to compatible and incompatible Prs isolates during the early stages of LR development. The integration of transcriptomic and metabolomic analyses elucidated the contributions of phenylpropanoid biosynthesis and flavonoid pathways to the rye immune response to Prs. This combined analysis of omics data provides valuable insights relevant for future research conducted to enhance rye resistance to LR.

Volatile Organic Compounds Emitted by Flowers: Ecological Roles, Production by Plants, Extraction, and Identification

Volatile organic compounds (VOCs) with a large chemical diversity are emitted by plant flowers. These compounds play an important role in the ecology of plants. This review presents the different ecological roles of VOCs present in the odor plumes of plant flowers, such as pollination, defense, adaptation to their environment, and communication with other organisms. The production and accumulation sites of VOCs in plants with their spatial and temporal variations, including environmental issues, are also summarized. To evaluate the qualitative and quantitative chemical composition of VOCs, several methods of extraction and analysis were used. Headspace (HS) sampling coupled with solid phase microextraction (SPME) is now well-developed for the extraction process. Parameters are known, and several fibers are now available to optimize this extraction. Most of the time, SPME is coupled with gas chromatography-mass spectrometry (GC-MS) to determine the structural identification of the VOCs, paying attention to the use of several complementary methods for identification like the use of databases, retention indices, and, when available, comparison with authentic standards analyses. The development of the knowledge on VOCs emitted by flowers is of great importance for plant ecology in the context of environmental and climate changes.

Comparative transcriptome and metabolome analyses revealed quality difference between beauty tea processed through indoor withering and outdoor solar withering

BACKGROUND

Withering is the first processing procedure of beauty tea, and there are few reports on the impact of withering methods on the quality of beauty tea and its regulatory mechanisms.

RESULTS

Through comparison of fresh tea leaves (FT) with the leaves after indoor natural withering for 18 h (IWT-18) and outdoor solar withering for 6 h (OWT-6), which were collected at the end of the two withering processes, 17 282 and 13 984 differentially expressed genes (DEGs) were respectively screened and 267 and 154 differential metabolites (DMs) were respectively identified. The coexpression network revealed that a large number of DEGs and DMs were enriched in phenylpropanoid, flavonoid, and adenosine triphosphate binding cassette (ABC) transporter pathways, and the number of DMs and DEGs in IWT-18 versus FT exceeded that in OWT-6 versus FT. Both withering methods promoted a significant increase in content of phenylalanine and upregulation of β-glucoside expression in the phenylpropanoid metabolism pathway. Five theaflavin-type proanthocyanidins in the flavonoid synthesis pathway were more significantly accumulated in FT versus IWT-18 than in FT versus OWT-6. Meanwhile, both withering methods can affect the ABC transporter pathway to promote the accumulation of amino acids and their derivatives, but different withering methods affect different ABC transporter families. Outdoor withering with more severe abiotic stress has a greater impact on the ABCG family, whereas indoor withering has a more significant effect on the ABCC family. Sensory evaluation results showed that the dry tea of IWT-18 was slightly better than that of OWT-6 because of the longer withering time and more thorough substance transformation.

CONCLUSION

In conclusion, the formation of honey flavor in beauty tea may be closely related to the DEGs and DMs in these three pathways. Our research provides theoretical data support for further revealing the mechanism of quality formation during the withering process of beauty tea. © 2023 Society of Chemical Industry.

Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review

Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.

Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics

KEY MESSAGE

Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.

Biodegradation of sulfadiazine by ryegrass (Lolium perenne L.) in a soil system: Analysis of detoxification mechanisms, transcriptome, and bacterial communities

The indiscriminate use of sulfadiazine has caused severe harm to the environment, and biodegradation is a viable method for the removal of sulfadiazine. However, there are few studies that consider sulfadiazine biodegradation mechanisms. To comprehensively investigate the process of sulfadiazine biodegradation by plants in a soil system, a potted system that included ryegrass and soil was constructed in this study. The removal of sulfadiazine from the system was found to be greater than 95% by determining the sulfadiazine residue. During the sulfadiazine removal process, a significant decrease in ryegrass growth and a significant increase in antioxidant enzyme activity were observed, which indicates the toxic response and detoxification mechanism of sulfadiazine on ryegrass. The ryegrass transcriptome and soil bacterial communities were further investigated. These results revealed that most of the differentially expressed genes (DEGs) were enriched in the CYP450 enzyme family and phenylpropanoid biosynthesis pathway after sulfadiazine exposure. The expression of these genes was significantly upregulated. Sulfadiazine significantly increased the abundance of Vicinamibacteraceae, RB41, Ramlibacter, and Microvirga in the soil. These key genes and bacteria play an important role in sulfadiazine biodegradation. Through network analysis of the relationship between the DEGs and soil bacteria, it was found that many soil bacteria promote the expression of plant metabolic genes. This mutual promotion enhanced the sulfadiazine biodegradation in the soil system. This study demonstrated that this pot system could substantially remove sulfadiazine and elucidated the biodegradation mechanism through changes in plants and soil bacteria.

Internalization, physiological responses and molecular mechanisms of lettuce to polystyrene microplastics of different sizes: Validation of simulated soilless culture

Microplastics (MPs) exists widely in the environment, and the resulting pollution of MPs has become a global environmental problem. Plants can absorb MPs through their roots. However, studies on the mechanism of the effect of root exposure to different size MPs on vegetables are limited. Here, we use Polystyrene (PS) MPs with different particle sizes to investigate the internalization, physiological response and molecular mechanism of lettuce to MPs. MPs may accumulate in large amounts in lettuce roots and migrate to the aboveground part through the vascular bundle, while small particle size MPs (SMPs, 100 nm) have stronger translocation ability than large particle size MPs (LMPs, 500 nm). MPs can cause physiological and biochemical responses and transcriptome changes in lettuce. SMPs and LMPs resulted in reduced biomass (38.27 % and 48.22 % reduction in fresh weight); caused oxidative stress (59.33 % and 47.74 % upregulation of SOD activity in roots) and differential gene expression (605 and 907 DEGs). Signal transduction, membrane transport and alteration of synthetic and metabolic pathways may be the main causes of physiological toxicity of lettuce. Our study provides important information for understanding the behavior and fate of MPs in edible vegetables, especially the physiological toxicity of MPs to edible vegetables, in order to assess the potential threat of MPs to food safety and agricultural sustainable development.

Transcriptomic-Proteomic Analysis Revealed the Regulatory Mechanism of Peanut in Response to Fusarium oxysporum

Peanut Fusarium rot, which is widely observed in the main peanut-producing areas in China, has become a significant factor that has limited the yield and quality in recent years. It is highly urgent and significant to clarify the regulatory mechanism of peanuts in response to Fusarium oxysporum. In this study, transcriptome and proteome profiling were combined to provide new insights into the molecular mechanisms of peanut stems after F. oxysporums infection. A total of 3746 differentially expressed genes (DEGs) and 305 differentially expressed proteins (DEPs) were screened. The upregulated DEGs and DEPs were primarily enriched in flavonoid biosynthesis, circadian rhythm-plant, and plant-pathogen interaction pathways. Then, qRT-PCR analysis revealed that the expression levels of phenylalanine ammonia-lyase (PAL), chalcone isomerase (CHI), and cinnamic acid-4-hydroxylase (C4H) genes increased after F. oxysporums infection. Moreover, the expressions of these genes varied in different peanut tissues. All the results revealed that many metabolic pathways in peanut were activated by improving key gene expressions and the contents of key enzymes, which play critical roles in preventing fungi infection. Importantly, this research provides the foundation of biological and chemical analysis for peanut disease resistance mechanisms.

The phenylalanine ammonia-lyase inhibitor AIP induces rice defence against the root-knot nematode Meloidogyne graminicola

The phenylalanine ammonia-lyase (PAL) enzyme catalyses the conversion of l-phenylalanine to trans-cinnamic acid. This conversion is the first step in phenylpropanoid biosynthesis in plants. The phenylpropanoid pathway produces diverse plant metabolites that play essential roles in various processes, including structural support and defence. Previous studies have shown that mutation of the PAL genes enhances disease susceptibility. Here, we investigated the functions of the rice PAL genes using 2-aminoindan-2-phosphonic acid (AIP), a strong competitive inhibitor of PAL enzymes. We show that the application of AIP can significantly reduce the PAL activity of rice crude protein extracts in vitro. However, when AIP was applied to intact rice plants, it reduced infection of the root-knot nematode Meloidogyne graminicola. RNA-seq showed that AIP treatment resulted in a rapid but transient upregulation of defence-related genes in roots. Moreover, targeted metabolomics demonstrated higher levels of jasmonates and antimicrobial flavonoids and diterpenoids accumulating after AIP treatment. Furthermore, chemical inhibition of the jasmonate pathway abolished the effect of AIP on nematode infection. Our results show that disturbance of the phenylpropanoid pathway by the PAL inhibitor AIP induces defence in rice against M. graminicola by activating jasmonate-mediated defence.

The Changes in Metabolites, Quality Components, and Antioxidant Activity of Tea (Camellia sinensis) Infected with Exobasidium vexans by Applying UPLC-MS/MS-Based Widely Targeted Metabolome and Biochemical Analysis

Blister blight infection with Exobasidium vexans is one of the most destructive foliar diseases that seriously affect the quality and yield of tea. This research investigated the metabolite changes of healthy and infected leaves on tea cultivar 'Fuding Dabaicha' and further explored the potential antimicrobial substances against E. vexans infection. In total, 1,166 compounds were identified during the entire course of an infection, among which 73 different common compounds were significantly accumulated involved in the important antimicrobial substances of flavonoids and phenolic acids, including kaempferol (3,5,7,4'-tetrahydroxyflavone), kaempferol-3-O-sophoroside-7-O-glucoside, phloretin, 2,4,6-trihydroxybenzoic acid, galloylprocyanidin B4, and procyanidin C1 3'-O-gallate, which indicated that these metabolites might positively dominate resistance to E. vexans. Furthermore, relevant biological pathways, such as the flavone and flavonol biosynthesis, flavonoid biosynthesis, and phenylpropane pathways, were more closely related to resistance to E. vexans. Additionally, total flavonoids, phenolics, alkaloids, and terpenoids contributing to antimicrobial and antioxidant capacity were significantly altered during four different infection periods, especially the Leaf_S2 stage (the second stage of infection), in which the most concentration accumulated. The leaves affected by E. vexans infection at the second stage had the relatively highest antioxidant activity. Accordingly, this study provides a theoretical support for and comprehensive insights into the effects on the metabolite changes, tea quality components, and antioxidant activity of blister blight caused by E. vexans.

Integrative analysis of transcriptome and metabolome reveals the sesquiterpenoids and polyacetylenes biosynthesis regulation in Atractylodes lancea (Thunb.) DC

Atractylodes lancea (Thunb.) is a perennial medicinal herb, with its dry rhizomes are rich in various sesquiterpenoids and polyacetylenes components (including atractylodin, atractylon and β-eudesmol). However, the contents of these compounds are various and germplasms specific, and the mechanisms of biosynthesis in A. lancea are still unknown. In this study, we identified the differentially expressed candidate genes and metabolites involved in the biosynthesis of sesquiterpenoids and polyacetylenes, and speculated the anabolic pathways of these pharmaceutical components by transcriptome and metabolomic analysis. In the sesquiterpenoids biosynthesis, a total of 28 differentially expressed genes (DEGs) and 6 differentially expressed metabolites (DEMs) were identified. The beta-Selinene is likely to play a role in the synthesis of atractylon and β-eudesmol. Additionally, the polyacetylenes biosynthesis showed the presence of 3 DEGs and 4 DEMs. Notably, some fatty acid desaturase (FAB2 and FAD2) significantly down-regulated in polyacetylenes biosynthesis. The gamma-Linolenic acid is likely involved in the biosynthesis of polyacetylenes and thus further synthesis of atractylodin. Overall, these studies have investigated the biosynthetic pathways of atractylodin, atractylon and β-eudesmol in A. lancea for the first time, and present potential new anchor points for further exploration of sesquiterpenoids and polyacetylenes compound biosynthesis pathways in A. lancea.

Multiomics Reveals the Key Microorganisms and Metabolites in the Resistance to Root Rot Disease of Paris polyphylla

Root rot of Paris polyphylla has received widespread attention due to its threat to yield and leads to serious economic losses. However, the relationship among the rhizosphere microbial community, metabolites and root rot disease remained largely unexplored. Herein, we used integrated 16S rRNA, ITS, RNA sequencing and UPLC-MS/MS to systematically investigate the differences between healthy and diseased P. polyphylla. We found that root rot reduced the microbial diversity in the diseased P. polyphylla compared with the healthy control. The relative abundance of the bacterial phylum Actinobacteria increased in the diseased rhizome of P. polyphylla. For the fungal community, root rot disease contributed to an increased relative abundance of Ascomycota and decreased Glomeromycota at the phylum level. The transcriptomic results showed that the differently expressed genes were significantly enriched in the "Biosynthesis of various alkaloids", "flavonoid biosynthesis" and "isoflavonoid biosynthesis" and "Phenylpropanoid biosynthesis" was dramatically enriched in healthy P. polyphylla compared with that in diseased P. polyphylla. Likewise, the metabolomic results showed that the biosynthesis of secondary metabolites and metabolic pathways was found to be significantly enriched by differential metabolites. Taken together, the study of combining metabolomics with microbiomes can help us enhance our understanding of the mechanisms of plant resistance to root rot disease, thereby discovering specific metabolites and microorganisms that can resist pathogen infection in P. polyphylla.

An expeditive and green chemo-enzymatic route to diester sinapoyl-l-malate analogues: sustainable bioinspired and biosourced UV filters and molecular heaters

Sinapoyl malate, naturally present in plants, has proved to be an exceptional UV filter and molecular heater for plants. Although there are nowadays industrially relevant sustainable synthetic routes to sinapoyl malate, its incorporation into certain cosmetic formulations, as well as its adsorption on plant leaves, is limited by its hydrophilicity. To overcome these obstacles, it is important to find a way to effectively control the hydrophilic-lipophilic balance of sinapoyl malate to make it readily compatible with the cosmetic formulations and stick on the waxy cuticle of leaves. To this end, herein, we describe a highly regioselective chemo-enzymatic synthesis of sinapoyl malate analogues possessing fatty aliphatic chains of variable length, enabling the lipophilicity of the compounds to be modulated. The potential toxicity (i.e., mutagenicity, carcinogenicity, endocrine disruption, acute and repeated-dose toxicity), bioaccumulation, persistence and biodegradability potential of these new analogues were evaluated in silico, along with the study of their transient absorption spectroscopy, their photostability as well as their photodegradation products.

Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties

Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome for the first time from the world's largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. We also sequenced and assembled the transcriptome of S. cumini in this study. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families resulting from gene duplication events compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.

Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources

Cassava (Manihot esculenta Crantz) is a food and industrial storage root crop with substantial potential to contribute to managing risk associated with climate change due to its inherent resilience and in providing a biodegradable option in manufacturing. In Africa, cassava production is challenged by two viral diseases, cassava brown streak disease (CBSD) and cassava mosaic disease. Here we detect quantitative trait loci (QTL) associated with CBSD in a biparental mapping population of a Tanzanian landrace, Nachinyaya and AR37-80, phenotyped in two locations over three years. The purpose was to use the information to ultimately facilitate either marker-assisted selection or adjust weightings in genomic selection to increase the efficiency of breeding. Results from this study were considered in relation to those from four other biparental populations, of similar genetic backgrounds, that were phenotyped and genotyped simultaneously. Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. Of significance within the candidate genes underlying the QTL on chromosome 4 are Phenylalanine ammonia-lyase (PAL) and Cinnamoyl-CoA reductase (CCR) genes and three PEPR1-related kinases associated with the lignin pathway. In addition, a CCR gene was also underlying the root necrosis-resistant QTL on chromosome 11. Upregulation of key genes in the cassava lignification pathway from an earlier transcriptome study, including PAL and CCR, in a CBSD-resistant landrace compared to a susceptible landrace suggests a higher level of basal lignin deposition in the CBSD-resistant landrace. Earlier RNAscope® in situ hybridisation imaging experiments demonstrate that cassava brown streak virus (CBSV) is restricted to phloem vessels in CBSV-resistant varieties, and phloem unloading for replication in mesophyll cells is prevented. The results provide evidence for the involvement of the lignin pathway. In addition, five eukaryotic initiation factor (eIF) genes associated with plant virus resistance were found within the priority QTL regions.

Microbial consortium mediated acceleration of the defense response in potato against Alternaria solani through prodigious inflation in phenylpropanoid derivatives and redox homeostasis

The present study was carried out in a pot experiment to examine the bioefficacy of three biocontrol agents, viz., Trichoderma viride, Bacillus subtilis, and Pseudomonas fluorescens, either alone or in consortium, on plant growth promotion and activation of defense responses in potato against the early blight pathogen Alternaria solani. The results demonstrate significant enhancement in growth parameters in plants bioprimed with the triple-microbe consortium compared to other treatments. In potato, the disease incidence percentage was significantly reduced in plants treated with the triple-microbe consortium compared to untreated control plants challenged with A. solani. Potato tubers treated with the consortium and challenged with pathogen showed significant activation of defense-related enzymes such as peroxidase (PO) at 96 h after pathogen inoculation (hapi) while, both polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) at 72 hapi, compared to the individual and dual microbial consortia-treated plants. The expression of antioxidant enzymes like superoxide dismutase (SOD) and catalase (CAT) and the accumulation of pathogenesis-related proteins such as chitinase and β-1,3-glucanase were observed to be highest at 72 hapi in the triple microbe consortium as compared to other treatments. HPLC analysis revealed significant induction in polyphenolic compounds in triple-consortium bioprimed plants compared to the control at 72 hapi. Histochemical analysis of hydrogen peroxide (H2O2) clearly showed maximum accumulation of H2O2 in pathogen-inoculated control plants, while the lowest was observed in triple-microbe consortium at 72 hapi. The findings of this study suggest that biopriming with a microbial consortium improved plant growth and triggered defense responses against A. solani through the induction of systemic resistance via modulation of the phenylpropanoid pathway and antioxidative network.

Comparative Transcriptomic Analysis of Wheat Cultivars in Response to Xanthomonas translucens pv. cerealis and Its T2SS, T3SS, and TALEs Deficient Strains

Xanthomonas translucens pv. cerealis causes bacterial leaf streak disease on small grain cereals. Type II and III secretion systems (T2SS and T3SS) play a pivotal role in the pathogenicity of the bacterium, while no data are available on the transcriptomic profile of wheat cultivars infected with either wild type (WT) or mutants of the pathogen. In this study, WT, TAL-effector mutants, and T2SS/T3SS mutants of X. translucens pv. cerealis strain NXtc01 were evaluated for their effect on the transcriptomic profile of two wheat cultivars, 'Chinese Spring' and 'Yangmai-158', using Illumina RNA-sequencing technology. RNA-Seq data showed that the number of differentially expressed genes (DEGs) was higher in Yangmai-158 than in Chinese Spring, suggesting higher susceptibility of Yangmai-158 to the pathogen. In T2SS, most suppressed DEGs were related to transferase, synthase, oxidase, WRKY, and bHLH transcription factors. The gspD mutants showed significantly decreased disease development in wheat, suggesting an active contribution of T2SS in virulence. Moreover, the gspD mutant restored full virulence and its multiplication in planta by addition of gspD in trans. In the T3SS-deficient strain, downregulated DEGs were associated with cytochrome, peroxidases, kinases, phosphatases, WRKY, and ethylene-responsive transcription factors. In contrast, upregulated DEGs were trypsin inhibitors, cell number regulators, and calcium transporter. Transcriptomic analyses coupled with quantitative real-time-PCR indicated that some genes are upregulated in Δtal1/Δtal2 compared with the tal-free strain, but no direct interaction was observed. These results provide novel insight into wheat transcriptomes in response to X. translucens infection and pave the way for understanding host-pathogen interactions.

Phenylpropanoid Derivatives and Their Role in Plants' Health and as antimicrobials

Phenylpropanoids belong to a wide group of compounds commonly secreted by plants and involved in different roles related with plant growth and development and the defense against plant pathogens. Some key intermediates from shikimate pathway are used to synthesize these compounds. In this way, by the phenylpropanoid pathway several building blocks are achieved to obtain flavonoids, isoflavonoids, coumarins, monolignols, phenylpropenes, phenolic acids, stilbenes and stilbenoids, and lignin, suberin and sporopollenin for plant-microbe interactions, structural support and mechanical strength, organ pigmentation, UV protection and acting against pathogens. Some reviews have revised phenylpropanoid biosynthesis and regulation of the biosynthetic pathways. In this review, the most important chemical structures about phenylpropanoid derivatives are summarized grouping them in different sections according to their structure. We have put special attention on their different roles in plants especially in plant health, growth and development and plant-environment interactions. Their interaction with microorganisms is discussed including their role as antimicrobials. We summarize all new findings about new developed structures and their involvement in plants health.

Response of salt stress resistance in highland barley (Hordeum vulgare L. var. nudum) through phenylpropane metabolic pathway

Highland barley (Hordeum vulgare L. var. nudum) is a grain crop that grows on the plateau under poor and high salt conditions. Therefore, to cultivate high-quality highland barley varieties, it is necessary to study the molecular mechanism of strong resistance in highland barley, which has not been clearly explained. In this study, a high concentration of NaCl (240 mmol/L), simulating the unfavorable environment, was used to spray the treated highland barley seeds. Transcriptomic analysis revealed that the expression of more than 8,000 genes in highland barley seed cells was significantly altered, suggesting that the metabolic landscape of the cells was deeply changed under salt stress. Through the KEGG analysis, the phenylpropane metabolic pathway was significantly up-regulated under salt stress, resulting in the accumulation of polyphenols, flavonoids, and lignin, the metabolites for improving the stress resistance of highland barley seed cells, being increased 2.71, 1.22, and 1.17 times, respectively. This study discovered that the phenylpropane metabolic pathway was a significant step forward in understanding the stress resistance of highland barley, and provided new insights into the roles of molecular mechanisms in plant defense.

Responses of salicylic acid encapsulation on growth, photosynthetic attributes and ROS scavenging system in Lactuca sativa exposed to polycyclic aromatic hydrocarbon pollution

Salicylic acid (SA) is a phytohormone that plays a key role in the regulation of the defense response against environmental variables in plants, and it provides increased yield and stress tolerance when exogenously applied to plants as a growth regulator. The role of SA-mediated signals in abiotic stress tolerance varies according to the species, stressor, application method, and dose. This study investigated the effects of salicylic acid (SA, 0.1 mg ml-1) or β-cyclodextrin encapsulated salicylic acid (e-SA, 0.1 mg ml-1) treatments on growth parameters, gas exchange, photosynthesis efficiency, and antioxidant capacity in lettuce seedlings exposed to polycyclic aromatic hydrocarbon pollution. Fluorene (FLN, 100 mg L-1) contamination resulted in a 27% growth rate and a 14% water content reduction in lettuce leaves. Significant suppressions of stomatal conductance, carbon assimilation, and PSII photochemistry were detected in plants under stress. FLN + SA and FLN + e-SA treatments regulated plant-water relations by stimulating proline accumulation and relieving stomatal limitations. As indicated by the high Fv/Fm ratio, photosynthesis efficiency was recovered in FLN + SA and FLN + e-SA group plants. FLN stress caused high oxidative stress in lettuce leaves and increased lipid peroxidation level by 40%. However, especially e-SA application to plants under stress, increased SOD activity by 3-fold and CAT activity by 80% and was successful in preventing H2O2 accumulation and lipid peroxidation. Both SA and e-SA treatments partially activated the AsA-GSH cycle. As a result, direct SA application was effective in mitigating stress-induced physiological limitations with high SA accumulation in the tissues, while encapsulated SA treatment was more effective in regulating photosynthetic and biochemical reactions, alleviating oxidative damage by activating the antioxidant defense, and promoting growth under stress with moderate SA accumulation.

Molecular, biochemical and metabolomics analyses reveal constitutive and pathogen-induced defense responses of two sugarcane contrasting genotypes against leaf scald disease

Leaf scald caused by the bacteria Xanthomonas albilineans is one of the major concerns to sugarcane production. To breed for resistance, mechanisms underlying plant-pathogen interaction need deeper investigations. Herein, we evaluated sugarcane defense responses against X. albilineans using molecular and biochemical approaches to assess pathogen-triggered ROS, phytohormones and metabolomics in two contrasting sugarcane genotypes from 0.5 to 144 h post-inoculation (hpi). In addition, the infection process was monitored using TaqMan-based quantification of X. albilineans and the disease symptoms were evaluated in both genotypes after 15 d post-inoculation (dpi). The susceptible genotype presented a response to the infection at 0.5 hpi, accumulating defense-related metabolites such as phenolics and flavonoids with no significant defense responses thereafter, resulting in typical symptoms of leaf scald at 15 dpi. The resistant genotype did not respond to the infection at 0.5 hpi but constitutively presented higher levels of salicylic acid and of the same metabolites induced by the infection in the susceptible genotype. Moreover, two subsequent pathogen-induced metabolic responses at 12 and 144 hpi were observed only in the resistant genotype in terms of amino acids, quinic acids, coumarins, polyamines, flavonoids, phenolics and phenylpropanoids together with an increase of hydrogen peroxide, ROS-related genes expression, indole-3-acetic-acid and salicylic acid. Multilevel approaches revealed that constitutive chemical composition and metabolic reprogramming hampers the development of leaf scald at 48 and 72 hpi, reducing the disease symptoms in the resistant genotype at 15 dpi. Phenylpropanoid pathway is suggested as a strong candidate marker for breeding sugarcane resistant to leaf scald.

Senolytic and senomorphic secondary metabolites as therapeutic agents in Drosophila melanogaster models of Parkinson's disease

Drosophila melanogaster is a valuable model organism for a wide range of biological exploration. The well-known advantages of D. melanogaster include its relatively simple biology, the ease with which it is genetically modified, the relatively low financial and time costs associated with their short gestation and life cycles, and the large number of offspring they produce per generation. D. melanogaster has facilitated the discovery of many significant insights into the pathology of Parkinson's disease (PD) and has served as an excellent preclinical model of PD-related therapeutic discovery. In this review, we provide an overview of the major D. melanogaster models of PD, each of which provide unique insights into PD-relevant pathology and therapeutic targets. These models are discussed in the context of their past, current, and future potential use for studying the utility of secondary metabolites as therapeutic agents in PD. Over the last decade, senolytics have garnered an exponential interest in their ability to mitigate a broad spectrum of diseases, including PD. Therefore, an emphasis is placed on the senolytic and senomorphic properties of secondary metabolites. It is expected that D. melanogaster will continue to be critical in the effort to understand and improve treatment of PD, including their involvement in translational studies focused on secondary metabolites.