Integrated Transcriptome and Metabolome Analysis Revealed That Flavonoid Biosynthesis May Dominate the Resistance of Zanthoxylum bungeanum against Stem Canker

Multi-omics analyses reveal mechanism for high resistant starch formation in an indica rice SSIIIa mutant

Soluble starch synthase IIIa (SSIIIa) is a key enzyme involved in amylopectin biosynthesis in rice, and deficiency of SSIIIa results in high content of resistant starch, which is benefit to human health. However, little is known about metabolic differences and carbon re-allocation in the seeds of the indica rice ss3a mutant. We found that SSIIIa deficiency impaired the storage of starch, but increased the soluble sugars, free amino acids and lipids. By multi-omic analyses, we found inactivation of SSIIIa triggered carbon repartitioning by downregulating sucrose synthase, grain incomplete filling 1, fructokinase and hexokinase (HK), and promoted the accumulation of soluble sugars. Meanwhile, the downregulation of HK and upregulation of plastidic phosphoglucomutase reduced the carbon flow through glycolysis and promoted glycogenesis. The downregulation of OsbZIP58 and the deleterious effect on ribosome formation might result in the reduction of storage protein synthesis and increased free amino acids content in ss3a. The higher levels of amylose and lipids could form more amylose-lipid complexes (starch phospholipids), resulting in a higher resistant starch content. Taken together, our study unraveled a functional cross talk between starch, protein and lipids in rice endosperm during seed development of ss3a, providing new insights for formation of high resistant starch in rice.

The Critical Role of Phenylpropanoid Biosynthesis Pathway in Lily Resistance Against Gray Mold

Gray mold caused by Botrytis elliptica is one of the most determinative factors of lily growth and has become a major threat to lily productivity. However, the nature of the lily B. elliptica interaction remains largely unknown. Here, comparative transcriptomic and metabolomic were used to investigate the defense responses of resistant ('Sorbonne') and susceptible ('Tresor') lily cultivars to B. elliptica infection at 24 hpi. In total, 1326 metabolites were identified in 'Sorbonne' and 'Tresor' after infection, including a large number of phenylpropanoids. Specifically, the accumulation of four phenylpropanes, including eriodictyol, hesperetin, ferulic acid, and sinapyl alcohol, was significantly upregulated in the B. elliptica-infected 'Sorbonne' compared with the infected 'Tresor', and these phenylpropanes could significantly inhibit B. elliptica growth. At the transcript level, higher expression levels of F3'M, COMT, and CAD led to a higher content of resistance-related phenylpropanes (eriodictyol, ferulic acid, and sinapyl alcohol) in 'Sorbonne' following B. elliptica infection. It can be assumed that these phenylpropanes cause the resistance difference between 'Sorbonne' and 'Tresor', and could be the potential marker metabolites for gray mold resistance in the lily. Further transcriptional regulatory network analysis suggested that members of the AP2/ERF, WRKY, Trihelix, and MADS-M-type families positively regulated the biosynthesis of resistance-related phenylpropanes. Additionally, the expression patterns of genes involved in phenylpropanoid biosynthesis were confirmed using qRT-PCR. Therefore, we speculate that the degree of gray mold resistance in the lily is closely related to the contents of phenylpropanes and the transcript levels of the genes in the phenylpropanoid biosynthesis pathway. Our results not only improve our understanding of the lily's resistance mechanisms against B. elliptica, but also facilitate the genetic improvement of lily cultivars with gray mold resistance.

Infection mechanism of Botryosphaeria dothidea and the disease resistance strategies of Chinese hickory (Carya cathayensis)

Botryosphaeria dothidea is the main fungal pathogen responsible for causing Chinese hickory (Carya cathayensis) dry rot disease, posing a serious threat to the Chinese hickory industry. Understanding the molecular basis of B. dothidea infection and the host's resistance mechanisms is crucial for controlling and managing the ecological impact of Chinese hickory dry rot disease. This study utilized ultrastructural observations to reveal the process of B. dothidea infection and colonization in Chinese hickory, and investigated the impact of B. dothidea infection on Chinese hickory biochemical indicators and plant hormone levels. Through high-throughput transcriptome sequencing, the gene expression profiles associated with different stages of B. dothidea infection in Chinese hickory and their corresponding defense responses were described. Additionally, a series of key genes closely related to non-structural carbohydrate metabolism, hormone metabolism, and plant-pathogen interactions during B. dothidea infection in Chinese hickory were identified, including genes encoding DUF, Myb_DNA-binding, and ABC transporter proteins. These findings provide important insights into elucidating the pathogenic mechanisms of B. dothidea and the resistance genes in Chinese hickory.

Combined transcriptomic and metabolomic analysis of the mechanism by which Bacillus velezensis induces resistance to anthracnose in walnut

Walnut (Juglans spp.), a significant deciduous tree of economic and ecological importance, faces substantial threats from walnut anthracnose, primarily caused by Colletotrichum gloeosporioides. Bacillus velezensis has shown promise in mitigating this fungal pathogen. To delve deeper into the induction mechanism of B. velezensis on walnut plant resistance, we conducted a metabolomic analysis on walnut leaves from six different treatment groups. Specifically, the groups were defined as follows: Group B.v. was inoculated with B. velezensis alone, Group CK served as the blank control, and Group C.g. was inoculated solely with C. gloeosporioides. Group B.v.-C.g. received B. velezensis followed by C. gloeosporioides inoculation. Group B.v.+C.g. underwent simultaneous inoculation with both B. velezensis and C. gloeosporioides, while Group C.g.-B.v. was treated first with C. gloeosporioides then B. velezensis. A total of 1,503 metabolites were detected, mainly including flavonoids, terpenoids, and steroids. The results revealed that B. velezensis spraying not only enhanced the inherent resistance of walnut plants but also significantly regulated walnut plants already infected with C. gloeosporioides. This was mainly achieved by inducing walnut plants to adjust their metabolic pathways such as salicylic acid, jasmonic acid, and abscisic acid, thereby strengthening their stress response. Transcriptomic and metabolomic correlation analyses showed that in the comparisons of B.v. vs. CK, C.g. vs. CK, and C.g.-B.v. vs. C.g., 59, 244, and 122 differential abundance metabolites were detected, along with 7860, 3677, and 5587 differential genes, respectively. Amino acid synthesis, starch and sucrose metabolism, photosynthesis, phenylpropane metabolism, purine metabolism, and glutathione metabolism played crucial roles in walnut's disease resistance mechanism. Further analysis revealed that B. velezensis induced walnut plants to regulate multiple genes, such as LOC109005403, LOC108985444 and LOC118344177, resulting in the production of defensive metabolites such as palmitic acid, coumarin and ferulic acid, thereby enhancing their resistance to C. gloeosporioides. In summary, B. velezensis induces systemic resistance in walnut plants by modulating the metabolic pathways of salicylic acid, jasmonic acid, and abscisic acid. It enhances this resistance by strengthening cell walls, synthesizing defensive secondary metabolites, and regulating energy metabolism and stress responses. These findings provide a solid theoretical foundation for the future field application of B. velezensis in controlling walnut anthracnose.

Integrated Transcriptome and Metabolome Analysis Revealed the Key Role of the Flavonoid Biosynthesis in Olive Defense Against Alternaria alternata

The olive tree is an important oil woody plant with high economic value, yet it is vulnerable to the attack of numerous fungi. The successful control of olive fungal diseases requires a comprehensive understanding of the disease resistance mechanisms in plants. Here, we isolated Alternaria alternata from the diseased leaves of olive plants, and screened a resistant ("Leccino") and susceptible ("Manzanilla de Sevilla") cultivar from eight olive cultivars to explore their resistance mechanisms. Transcriptomic and metabolomic analyses identified the flavonoid biosynthesis as a key defense pathway against A. alternata. Five important transcription factors associated with flavonoid biosynthesis were also determined. The overexpression of OeWRKY40 significantly enhanced the disease resistance of the susceptible cultivar and upregulated the expression of genes involved in flavonoid biosynthesis and the accumulation of related metabolites. LUC assays further proved that OeWRKY40 can activate the expression of OeC4H. These results help to better clarify the molecular mechanisms of flavonoid biosynthesis against A. alternata. Our study provides key information for further exploration of the molecular pathways of olive plants and their resistance to fungi, an important factor for molecular breeding and utilization of resistant cultivars.

Integrated transcriptomic and metabolomic analysis reveals the molecular profiles of dynamic variation in Lilium brownii var. viridulum suffering from bulb rot

Lilium brownii var. viridulum, known as Longya lily, is a well-known medicinal and edible plant in China. Bulb rot is a common disease in Longya lily cultivation that severely affects the yield and quality of lilies. According field investigations, we found that different Longya lily plants in the same field had different degrees of resistance to root rot. To find the reasons leading to the difference, we performed metabolomic and transcriptomic analyses of Longya lily with different degrees of disease. The transcriptomic analyses showed that the number of differentially expressed genes increased in early and mid-stage infections (LYBH2 and LYBH3), while decreased in late-stage infection (LYBH4). A total of 2309 DEGs showed the same expression trend in diseased bulb compared healthy bulb (LYBH1). The transcription factors (TFs) analysis of DEGs showed that several common TFs, like WRKY, bHLH, AP2/ERF-ERF and MYB, were significantly activated in bulbs after decay. The metabolomic analyses showed that there were 794 differentially accumulated metabolites, and metabolites with significant changes in relative content largely were phenolic acids, followed by flavonoids and amino acids and derivatives. The combined analysis of transcriptome and metabolome indicated that phenylpropanoid biosynthesis pathway was crucial in Longya lily resistance to bulb rot. Therefore, we speculated that the different degree of resistance to bulb rot in Longya lily may be related to the transcript levels of gene and contents of metabolites in the phenylpropanoid biosynthesis pathway. Overall, these results elucidate the molecular responses of Longya lily to bulb rot and lay a theoretical foundation for breeding resistant varieties.

Joint metabolomic and transcriptomic analysis identify unique phenolic acid and flavonoid compounds associated with resistance to fusarium wilt in cucumber (Cucumis sativus L.)

Introduction

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease in cucumber (Cucumis sativus. L). However, there remains limited knowledge on the molecular mechanisms underlying FW resistance-mediated defense responses in cucumber.

Methods

In this study, metabolome and transcriptome profiling were carried out for two FW resistant (NR) and susceptible (NS), near isogenic lines (NILs) before and after Foc inoculation. NILs have shown consistent and stable resistance in multiple resistance tests conducted in the greenhouse and in the laboratory. A widely targeted metabolomic analysis identified differentially accumulated metabolites (DAMs) with significantly greater NR accumulation in response to Foc infection, including many phenolic acid and flavonoid compounds from the flavonoid biosynthesis pathway.

Results

Transcriptome analysis identified differentially expressed genes (DEGs) between the NILs upon Foc inoculation including genes for secondary metabolite biosynthesis and transcription factor genes regulating the flavonoid biosynthesis pathway. Joint analysis of the metabolomic and transcriptomic data identified DAMs and DEGs closely associated with the biosynthesis of phenolic acid and flavonoid DAMs. The association of these compounds with NR-conferred FW resistance was exemplified by in vivo assays. These assays found two phenolic acid compounds, bis (2-ethylhexyl) phthalate and diisooctyl phthalate, as well as the flavonoid compound gallocatechin 3-O-gallate to have significant inhibitory effects on Foc growth. The antifungal effects of these three compounds represent a novel finding.

Discussion

Therefore, phenolic acids and flavonoids play important roles in NR mediated FW resistance breeding in cucumber.

Identification and Characterization of Hibiscus mutabilis Varieties Resistant to Bemisia tabaci and Their Resistance Mechanisms

Hibiscus mutabilis, the city flower of Chengdu, is culturally significant and has nutritional and medicinal benefits. However, frequent infestations of Bemisia tabaci have caused economic losses. This study aimed to identify insect-resistant H. mutabilis varieties. Over two years, varieties like Jinqiusong, Zuiyun, and Zuifurong showed moderate to high resistance based on reproductive indices. Assessments of antixenosis and developmental impacts revealed that adult B. tabaci exhibited low selectivity toward these resistant varieties, indicating a strong repellent effect. Gas chromatography-mass spectrometry analysis identified volatile organic compounds, such as alcohols, alkanes, and terpenes. Notably, 2-ethylhexanol and 6-methylheptanol exhibited repellent properties. Using nontargeted metabolomics, this study compared the metabolite profiles of the insect-resistant variety Jinqiusong (JQS), moderately resistant Bairihuacai (BRHC), and highly susceptible Chongbanbai (CBB) post B. tabaci infestation. Fifteen key metabolites were linked to resistance, emphasizing the phenylpropanoid biosynthesis pathway as crucial in defense. These findings offer a theoretical foundation for breeding insect-resistant H. mutabilis varieties and developing eco-friendly strategies against B. tabaci infestations.

Melatonin enhances resistance to Botryosphaeria dothidea in pear by promoting jasmonic acid and phlorizin biosynthesis

Ring rot, caused by Botryosphaeria dothidea, is an important fungal disease of pear fruit during postharvest storage. Melatonin, as a plant growth regulator, plays an important role in enhancing the stress resistance of pear fruits. It enhances the resistance of pear fruits to ring rot by enhancing their antioxidant capacity. However, the underlying mechanism remains unclear. In this study, we examined the effect of melatonin on the growth of B. dothidea. Results showed that melatonin did not limit the growth of B. dothidea during in vitro culture. However, metabolomics and transcriptomics analyses of 'Whangkeumbae' pear (Pyrus pyrifolia) revealed that melatonin increased the activity of antioxidant enzymes, including peroxidase (POD), superoxide dismutase (SOD), and polyphenol oxidase (PPO), in the fruit and activated the phenylpropanoid metabolic pathway to improve fruit resistance. Furthermore, melatonin treatment significantly increased the contents of jasmonic acid and phlorizin in pear fruit, both of which could improve disease resistance. Jasmonic acid regulates melatonin synthesis and can also promote phlorizin synthesis, ultimately improving the resistance of pear fruit to ring rot. In summary, the interaction between melatonin and jasmonic acid and phlorizin enhances the antioxidant defense response and phenylpropanoid metabolism pathway of pear fruit, thereby enhancing the resistance of pear fruit to ring rot disease. Our results provide new insights into the application of melatonin in the resistance to pear fruit ring rot.

Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash

BACKGROUND

Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker.

RESULTS

In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family.

CONCLUSION

This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.

Integrative metabolomic and transcriptomic analyses reveals the accumulation patterns of key metabolites associated with flavonoids and terpenoids of Gynostemma pentaphyllum (Thunb.) Makino

Gynostemma pentaphyllum (Thunb.) Makino (G. pentaphyllum) is a medicinal and edible plant with multiple functions of liver protection, anti-tumor, anti-inflammation, balancing blood sugar and blood lipids. The nutritional value of the G. pentaphyllum plant is mainly due to its rich variety of biologically active substances, such as flavonoids, terpenes and polysaccharides. In this study, we performed a comprehensive analysis combining metabolomics and root, stem and leaf transcriptomic data of G. pentaphyllum. We used transcriptomics and metabolomics data to construct a dynamic regulatory network diagram of G. pentaphyllum flavonoids and terpenoids, and screened the transcription factors involved in flavonoids and terpenoids, including basic helix-loop-helix (bHLH), myb-related, WRKY, AP2/ERF. Transcriptome analysis results showed that among the DEGs related to the synthesis of flavonoids and terpenoids, dihydroflavonol 4-reductase (DFR) and geranylgeranyl diphosphate synthases (GGPPS) were core genes. This study presents a dynamic image of gene expression in different tissues of G. pentaphyllum, elucidating the key genes and metabolites of flavonoids and terpenoids. This study is beneficial to a deeper understanding of the medicinal plants of G. pentaphyllum, and also provides a scientific basis for further regulatory mechanisms of plant natural product synthesis pathways and drug development.

Comparative transcriptomics and proteomics analysis of the symbiotic germination of Paphiopedilum barbigerum with Epulorhiza sp. FQXY019

Introduction

Paphiopedilum barbigerum is currently the rarest and most endangered species of orchids in China and has significant ornamental value. The mature seeds of P. barbigerum are difficult to germinate owing to the absence of an endosperm and are highly dependent on mycorrhizal fungi for germination and subsequent development. However, little is known about the regulation mechanisms of symbiosis and symbiotic germination of P. barbigerum seeds.

Methods

Herein, transcriptomics and proteomics were used to explore the changes in the P. barbigerum seeds after inoculation with (FQXY019 treatment group) or without (control group) Epulorhiza sp. FQXY019 at 90 days after germination.

Results

Transcriptome sequencing revealed that a total of 10,961 differentially expressed genes (DEGs; 2,599 upregulated and 8,402 downregulated) were identified in the control and FQXY019 treatment groups. These DEGs were mainly involved in carbohydrate, fatty acid, and amino acid metabolism. Furthermore, the expression levels of candidate DEGs related to nodulin, Ca2+ signaling, and plant lectins were significantly affected in P. barbigerum in the FQXY019 treatment groups. Subsequently, tandem mass tag-based quantitative proteomics was performed to recognize the differentially expressed proteins (DEPs), and a total of 537 DEPs (220 upregulated and 317 downregulated) were identified that were enriched in processes including photosynthesis, photosynthesis-antenna proteins, and fatty acid biosynthesis and metabolism.

Discussion

This study provides novel insight on the mechanisms underlying the in vitro seed germination and protocorm development of P. barbigerum by using a compatible fungal symbiont and will benefit the reintroduction and mycorrhizal symbiotic germination of endangered orchids.

The endophytic fungal community plays a crucial role in the resistance of host plants to necrotic bacterial pathogens

Konjac species (Amorphophallus spp.) are the only plant species in the world that are rich in a large amount of konjac glucomannan (KGM). These plants are widely cultivated as cash crops in tropical and subtropical countries in Asia, including China. Pectobacterium carotovorum subsp. carotovorum (Pcc) is one of the most destructive bacterial pathogens of konjac. Here, we analyzed the interactions between Pcc and susceptible and resistant konjac species from multiple perspectives. At the transcriptional and metabolic levels, the susceptible species A. konjac and resistant species A. muelleri exhibit similar molecular responses, activating plant hormone signaling pathways and metabolizing defense compounds such as phenylpropanoids and flavonoids to resist infection. Interestingly, we found that Pcc stress can lead to rapid recombination of endophytic microbial communities within a very short period (96 h). Under conditions of bacterial pathogen infection, the relative abundance of most bacterial communities in konjac tissue decreased sharply compared with that in healthy plants, while the relative abundance of some beneficial fungal communities increased significantly. The relative abundance of Cladosporium increased significantly in both kinds of infected konjac compared to that in healthy plants, and the relative abundance in resistant A. muelleri plants was greater than that in susceptible A. konjac plants. Among the isolated cultivable microorganisms, all three strains of Cladosporium strongly inhibited Pcc growth. Our results further elucidate the potential mechanism underlying konjac resistance to Pcc infection, highlighting the important role of endophytic microbial communities in resisting bacterial pathogen infections, especially the more direct role of fungal communities in inhibiting pathogen growth.

Microbial exopolysaccharide EPS66A inducing walnut (Juglans regia) resistance to bacterial blight

Bacterial blight caused by Xanthomonas arboricola pv. juglandis is a major obstacle to walnut production. EPS66A, derived from Streptomyces sp. strain HL-66, has various beneficial properties, including broad-spectrum microbe inhibition and plant disease resistance induction. To understand the effects of Xaj and EPS66A on walnut, a comprehensive analysis of the metabolome and transcriptome was conducted. While EPS66A did not directly inhibit Xaj on agar media, applying it at 200 μg/mL, 24 h after Xaj inoculation on walnut leaves, significantly reduced bacterial blight in a greenhouse. Additionally, EPS66A increased phenolic and flavonoid concentrations and enhanced enzymatic activities associated with resistance, such as catalase, superoxide dismutase, peroxidase, and phenylalanine ammonia lyase. Differential expression of eleven metabolites and fourteen genes related to flavonoid biosynthesis pathway was observed. Consequently, EPS66A application induced systemic resistance in walnuts, effectively preventing Xaj infection. This study provides insights into the flavonoid biosynthesis mechanism underlying EPS66A-induced resistance in walnuts.

Comparative transcriptome and metabolome analysis revealed diversity in the response of resistant and susceptible rose (Rosa hybrida) varieties to Marssonina rosae

Rose black spot disease caused by Marssonina rosae is among the most destructive diseases that affects the outdoor cultivation and production of roses; however, the molecular mechanisms underlying the defensive response of roses to M. rosae have not been clarified. To investigate the diversity of response to M. rosae in resistant and susceptible rose varieties, we performed transcriptome and metabolome analyses of resistant (KT) and susceptible (FG) rose varieties and identified differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in response to M. rosae at different time points. In response to M. rosae, DEGs and DAMs were mainly upregulated compared to the control and transcription factors were concentrated in the WRKY and AP2/ERF families. Gene Ontology analysis showed that the DEGs of FG were mainly enriched in biological processes, such as the abscisic acid-activated signaling pathway, cell wall, and defense response, whereas the DEGs of KT were mainly enriched in Golgi-mediated vesicle transport processes. Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs of both varieties were concentrated in plant-pathogen interactions, plant hormone signal transduction, and mitogen-activated protein kinase signaling pathways, with the greatest number of DEGs associated with brassinosteroid (BR) in the plant hormone signal transduction pathway. The reliability of the transcriptome results was verified by qRT-PCR. DAMs of KT were significantly enriched in the butanoate metabolism pathway, whereas DAMs of FG were significantly enriched in BR biosynthesis, glucosinolate biosynthesis, and tryptophan metabolism. Moreover, the DAMs in these pathways were significantly positively correlated with the DEGs. Disease symptoms were aggravated when FG leaves were inoculated with M. rosae after 24-epibrassinolide treatment, indicating that the response of FG to M. rosae involves the BR signaling pathway. Our results provide new insights into the molecular mechanisms underlying rose response to M. rosae and lay a theoretical foundation for formulating rose black spot prevention and control strategies and cultivating resistant varieties.

Identification of adult resistant genes to stripe rust in wheat from southwestern China based on GWAS and WGCNA analysis

KEY MESSAGE

In this study, genome-wide association studies combined with transcriptome data analysis were utilized to reveal potential candidate genes for stripe rust resistance in wheat, providing a basis for screening wheat varieties for stripe rust resistance. Wheat stripe rust, which is caused by the wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) is one of the world's most devastating diseases of wheat. Genetic resistance is the most effective strategy for controlling diseases. Although wheat stripe rust resistance genes have been identified to date, only a few of them confer strong and broad-spectrum resistance. Here, the resistance of 335 wheat germplasm resources (mainly wheat landraces) from southwestern China to wheat stripe rust was evaluated at the adult stage. Combined genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) based on RNA sequencing from stripe rust resistant accession Y0337 and susceptible accession Y0402, five candidate resistance genes to wheat stripe rust (TraesCS1B02G170200, TraesCS2D02G181000, TraesCS4B02G117200, TraesCS6A02G189300, and TraesCS3A02G122300) were identified. The transcription level analyses showed that these five genes were significantly differentially expressed between resistant and susceptible accessions post inoculation with Pst at different times. These candidate genes could be experimentally transformed to validate and manipulate fungal resistance, which is beneficial for the development of the wheat cultivars resistant to stripe rust.

Exogenous priming of chitosan induces resistance in Chinese prickly ash against stem canker caused by Fusarium zanthoxyli

Stem canker is a highly destructive disease that threatens prickly ash plantations in China. This study demonstrated the effective control of stem canker in prickly ash using chitosan priming, reducing lesion areas by 46.77 % to 75.13 % across all chitosan treatments. The mechanisms underlying chitosan-induced systemic acquired resistance (SAR) in prickly ash were further investigated. Chitosan increased H2O2 levels and enhanced peroxidase and catalase enzyme activities. A well-constructed regulatory network depicting the genes involved in the SAR and their corresponding expression levels in prickly ash plants primed with chitosan was established based on transcriptomic analysis. Additionally, 224 ZbWRKYs were identified based on the whole genome of prickly ash, and their phylogenetic evolution, conserved motifs, domains and expression patterns of ZbWRKYs were comprehensively illustrated. The expression of 12 key genes related to the SAR was significantly increased by chitosan, as determined using reverse transcription-quantitative polymerase chain reaction. Furthermore, the activities of defensive enzymes and the accumulation of lignin and flavonoids in prickly ash were significantly enhanced by chitosan treatment. Taken together, this study provides valuable insights into the chitosan-mediated activation of the immune system in prickly ash, offering a promising eco-friendly approach for forest stem canker control.

Changes in root metabolites and soil microbial community structures in rhizospheres of sugarcanes under different propagation methods

Root metabolites and soil microbial community structure in the rhizosphere play critical roles in crop growth. Here, we assessed the efficiency of conventional and tissue culture propagation methods in modulating the soil health and microbiota in the rhizosphere of sugarcane (Saccharum officinarum L.) plants. The seeding canes were obtained using newly planted and two-year ratooned canes propagated by conventional (CSN and CSR) or tissue culture (TCN and TCR) methods. Changes in soil fertility, root metabolites and soil microbial community structure in the rhizosphere of sugarcane plants obtained using these canes were assessed. The activities of soil β-glucosidase and aminopeptidase, soil microbial biomass nitrogen, and abundances of soil beneficial microbes, both at phyla and genera levels, were significantly higher in the rhizosphere of sugarcane plants in TCN and TCR treatments than those in that of plants in CSN and CSR treatments. Furthermore, flavonoid and flavonol biosynthesis and alanine, aspartate and glutamate metabolism were significantly upregulated in the roots of TCR and TCN plants compared with those in the roots of CSN and CSR plants. These results suggest that the tissue culture propagation method is a sustainable method for sugarcane cultivation to improve soil fertility and health in sugarcane rhizosphere.

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.

Comparative Analysis of Transcriptomics and Metabolomics Reveals Defense Mechanisms in Melon Cultivars against Pseudoperonospora cubensis Infection

Melon (Cucumis melo L.) represents an agriculturally significant horticultural crop that is widely grown for its flavorful fruits. Downy mildew (DM), a pervasive foliar disease, poses a significant threat to global melon production. Although several quantitative trait loci related to DM resistance have been identified, the comprehensive genetic underpinnings of this resistance remain largely uncharted. In this study, we utilized integrative transcriptomics and metabolomics approaches to identify potential resistance-associated genes and delineate the strategies involved in the defense against DM in two melon cultivars: the resistant 'PI442177' ('K10-1') and the susceptible 'Huangdanzi' ('K10-9'), post-P. cubensis infection. Even in the absence of the pathogen, there were distinctive differentially expressed genes (DEGs) between 'K10-1' and 'K10-9'. When P. cubensis was infected, certain genes, including flavin-containing monooxygenase (FMO), receptor-like protein kinase FERONIA (FER), and the HD-ZIP transcription factor member, AtHB7, displayed pronounced expression differences between the cultivars. Notably, our data suggest that following P. cubensis infection, both cultivars suppressed flavonoid biosynthesis via the down-regulation of associated genes whilst concurrently promoting lignin production. The complex interplay of transcriptomic and metabolic responses elucidated by this study provides foundational insights into melon's defense mechanisms against DM. The robust resilience of 'K10-1' to DM is attributed to the synergistic interaction of its inherent transcriptomic and metabolic reactions.

Transcriptome and metabolome analyses revealed the response mechanism of pepper roots to Phytophthora capsici infection

BACKGROUND

Phytophthora root rot caused by the oomycete Phytophthora capsici is the most devastating disease in pepper production worldwide, and current management strategies have not been effective in preventing this disease. Therefore, the use of resistant varieties was regarded as an important part of disease management of P. capsici. However, our knowledge of the molecular mechanisms underlying the defense response of pepper roots to P. capsici infection is limited.

METHODS

A comprehensive transcriptome and metabolome approaches were used to dissect the molecular response of pepper to P. capsici infection in the resistant genotype A204 and the susceptible genotype A198 at 0, 24 and 48 hours post-inoculation (hpi).

RESULTS

More genes and metabolites were induced at 24 hpi in A204 than A198, suggesting the prompt activation of defense responses in the resistant genotype, which can attribute two proteases, subtilisin-like protease and xylem cysteine proteinase 1, involved in pathogen recognition and signal transduction in A204. Further analysis indicated that the resistant genotype responded to P. capsici with fine regulation by the Ca2+- and salicylic acid-mediated signaling pathways, and then activation of downstream defense responses, including cell wall reinforcement and defense-related genes expression and metabolites accumulation. Among them, differentially expressed genes and differentially accumulated metabolites involved in the flavonoid biosynthesis pathways were uniquely activated in the resistant genotype A204 at 24 hpi, indicating a significant role of the flavonoid biosynthesis pathways in pepper resistance to P. capsici.

CONCLUSION

The candidate transcripts may provide genetic resources that may be useful in the improvement of Phytophthora root rot-resistant characters of pepper. In addition, the model proposed in this study provides new insight into the defense response against P. capsici in pepper, and enhance our current understanding of the interaction of pepper-P. capsici.

Integrated Transcriptome and Metabolome Analysis Reveals the Molecular Mechanism of Rust Resistance in Resistant (Youkang) and Susceptive (Tengjiao) Zanthoxylum armatum Cultivars

Chinese pepper rust is a live parasitic fungal disease caused by Coleosporium zanthoxyli, which seriously affects the cultivation and industrial development of Z. armatum. Cultivating and planting resistant cultivars is considered the most economical and environmentally friendly strategy to control this disease. Therefore, the mining of excellent genes for rust resistance and the analysis of the mechanism of rust resistance are the key strategies to achieve the targeted breeding of rust resistance. However, there is no relevant report on pepper rust resistance at present. The aim of the present study was to further explore the resistance mechanism of pepper by screening the rust-resistant germplasm resources in the early stage. Combined with the analysis of plant pathology, transcriptomics, and metabolomics, we found that compared with susceptible cultivar TJ, resistant cultivar YK had 2752 differentially expressed genes (DEGs, 1253 up-, and 1499 downregulated) and 321 differentially accumulated metabolites (DAMs, 133 up- and 188 down-accumulated) after pathogen infection. And the genes and metabolites related to phenylpropanoid metabolism were highly enriched in resistant varieties, which indicated that phenylpropanoid metabolism might mediate the resistance of Z. armatum. This finding was further confirmed by a real-time quantitative polymerase chain reaction analysis, which revealed that the expression levels of core genes involved in phenylpropane metabolism in disease-resistant varieties were high. In addition, the difference in flavonoid and MeJA contents in the leaves between resistant and susceptible varieties further supported the conclusion that the flavonoid pathway and methyl jasmonate may be involved in the formation of Chinese pepper resistance. Our research results not only help to better understand the resistance mechanism of Z. armatum rust but also contribute to the breeding and utilization of resistant varieties.

Transcriptomic and metabolic profiling of watermelon uncovers the role of salicylic acid and flavonoids in the resistance to cucumber green mottle mosaic virus

Understanding the mechanisms underlying plant resistance to virus infections is crucial for viral disease management in agriculture. However, the defense mechanism of watermelon (Citrullus lanatus) against cucumber green mottle mosaic virus (CGMMV) infection remains largely unknown. In this study, we performed transcriptomic, metabolomic, and phytohormone analyses of a CGMMV susceptible watermelon cultivar 'Zhengkang No.2' ('ZK') and a CGMMV resistant wild watermelon accession PI 220778 (PI) to identify the key regulatory genes, metabolites, and phytohormones responsible for CGMMV resistance. We then tested several phytohormones and metabolites for their roles in watermelon CGMMV resistance via foliar application, followed by CGMMV inoculation. Several phenylpropanoid metabolism-associated genes and metabolites, especially those involved in the flavonoid biosynthesis pathway, were found to be significantly enriched in the CGMMV-infected PI plants compared with the CGMMV-infected 'ZK' plants. We also identified a gene encoding UDP-glycosyltransferase (UGT) that is involved in kaempferol-3-O-sophoroside biosynthesis and controls disease resistance, as well as plant height. Additionally, salicylic acid (SA) biogenesis increased in the CGMMV-infected 'ZK' plants, resulting in the activation of a downstream signaling cascade. SA levels in the tested watermelon plants correlated with that of total flavonoids, and SA pre-treatment up-regulated the expression of flavonoid biosynthesis genes, thus increasing the total flavonoid content. Furthermore, application of exogenous SA or flavonoids extracted from watermelon leaves suppressed CGMMV infection. In summary, our study demonstrates the role of SA-induced flavonoid biosynthesis in plant development and CGMMV resistance, which could be used to breed for CGMMV resistance in watermelon.

Metabolomics provide a novel interpretation of the changes in flavonoids during sea buckthorn (Hippophae rhamnoides L.) drying

Flavonoids are major nutrients in sea buckthorn berries. However, the effects of drying methods on flavonoids in sea buckthorn berries are unclear. In this study, ultra-performance liquid chromatography and metabolomics were adopted to analyse the effects of hot air drying (HAD) and infrared drying (IRD) on flavonoid compounds and antioxidant capacity in sea buckthorn berries. In total, 97 metabolites belonging to 12 classes were identified, including 26 flavones, 23 flavonols, and 11 flavanones. Additionally, 32 differential metabolites were identified among groups. Isorhamnetin and quercetin contents increased in response to HAD and IRD, while (-)-epigallocatechin and (-)-gallocatechin contents decreased. Differential metabolism of flavonoid compounds occurred mainly via the flavonoid biosynthesis and secondary metabolite biosynthesis pathways. Flavonoid compound degradation might be associated with antioxidant activity during drying. This study elucidated the effect of drying on nutritional components of sea buckthorn berries and may guide the improvement of quality during food processing.

A Review of Classification, Biosynthesis, Biological Activities and Potential Applications of Flavonoids

Flavonoids represent the main class of plant secondary metabolites and occur in the tissues and organs of various plant species. In plants, flavonoids are involved in many biological processes and in response to various environmental stresses. The consumption of flavonoids has been known to reduce the risk of many chronic diseases due to their antioxidant and free radical scavenging properties. In the present review, we summarize the classification, distribution, biosynthesis pathways, and regulatory mechanisms of flavonoids. Moreover, we investigated their biological activities and discuss their applications in food processing and cosmetics, as well as their pharmaceutical and medical uses. Current trends in flavonoid research are also briefly described, including the mining of new functional genes and metabolites through omics research and the engineering of flavonoids using nanotechnology. This review provides a reference for basic and applied research on flavonoid compounds.

Integrated Transcriptome and Metabolome Analysis Revealed the Causal Agent of Primary Bud Necrosis in 'Summer Black' Grape

Primary bud necrosis of grape buds is a physiological disorder that leads to decreased berry yield and has a catastrophic impact on the double cropping system in sub-tropical areas. The pathogenic mechanisms and potential solutions remain unknown. In this study, the progression and irreversibility patterns of primary bud necrosis in 'Summer Black' were examined via staining and transmission electron microscopy observation. Primary bud necrosis was initiated at 60 days after bud break and was characterized by plasmolysis, mitochondrial swelling, and severe damage to other organelles. To reveal the underlying regulatory networks, winter buds were collected during primary bud necrosis progression for integrated transcriptome and metabolome analysis. The accumulation of reactive oxygen species and subsequent signaling cascades disrupted the regulation systems for cellular protein quality. ROS cascade reactions were related to mitochondrial stress that can lead to mitochondrial dysfunction, lipid peroxidation causing damage to membrane structure, and endoplasmic reticulum stress leading to misfolded protein aggregates. All these factors ultimately resulted in primary bud necrosis. Visible tissue browning was associated with the oxidation and decreased levels of flavonoids during primary bud necrosis, while the products of polyunsaturated fatty acids and stilbenes exhibited an increasing trend, leading to a shift in carbon flow from flavonoids to stilbene. Increased ethylene may be closely related to primary bud necrosis, while auxin accelerated cell growth and alleviated necrosis by co-chaperone VvP23-regulated redistribution of auxin in meristem cells. Altogether, this study provides important clues for further study on primary bud necrosis.

Combined analysis of metabolome and transcriptome of wheat kernels reveals constitutive defense mechanism against maize weevils

Sitophilus zeamais (maize weevil) is one of the most destructive pests that seriously affects the quantity and quality of wheat (Triticum aestivum L.). However, little is known about the constitutive defense mechanism of wheat kernels against maize weevils. In this study, we obtained a highly resistant variety RIL-116 and a highly susceptible variety after two years of screening. The morphological observations and germination rates of wheat kernels after feeding ad libitum showed that the degree of infection in RIL-116 was far less than that in RIL-72. The combined analysis of metabolome and transcriptome of RIL-116 and RIL-72 wheat kernels revealed differentially accumulated metabolites were mainly enriched in flavonoids biosynthesis-related pathway, followed by glyoxylate and dicarboxylate metabolism, and benzoxazinoid biosynthesis. Several flavonoids metabolites were significantly up-accumulated in resistant variety RIL-116. In addition, the expression of structural genes and transcription factors (TFs) related to flavonoids biosynthesis were up-regulated to varying degrees in RIL-116 than RIL-72. Taken together, these results indicated that the biosynthesis and accumulation of flavonoids contributes the most to wheat kernels defense against maize weevils. This study not only provides insights into the constitutive defense mechanism of wheat kernels against maize weevils, but may also play an important role in the breeding of resistant varieties.

Comparative Transcriptome and Widely Targeted Metabolome Analysis Reveals the Molecular Mechanism of Powdery Mildew Resistance in Tomato

Powdery mildew is a serious problem in tomato production; therefore, the PM-resistant tomato inbred line, '63187', and the susceptible tomato variety, 'Moneymaker (MM)', were used as experimental materials for the combined analysis of transcriptome and widely targeted metabolome on tomato leaves at 0 h post inoculation (hpi), 12 hpi, and 48 hpi. The results indicated that 276 genes were expressed in all treatments, and the K-means cluster analysis showed that these genes were divided into eight classes in '63187' and ten classes in 'MM'. KEGG enrichment showed that amino acid metabolism, signal transduction, energy metabolism, and other secondary metabolites biosynthesis pathways were significantly enriched. Interestingly, the analysis of WRKY family transcription factors (TFs) showed that the expression of four TFs in '63187' increased with no obvious change in 'MM'; and the expression of one TF in 'MM' increased with no obvious change in '63187'. The combined analysis revealed that both phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were enriched in '63187' and 'MM'. In '63187', six metabolites involved in this pathway were downregulated, and four genes were highly expressed, while in 'MM', three metabolites were upregulated, four metabolites were downregulated, and ten genes were highly expressed. These metabolites and genes might be candidates for PM resistance or susceptibility in subsequent studies. These results provide favorable molecular information for the study of the different resistances of tomatoes to PM, and they provide a basis for the breeding of tomato varieties resistant to PM.

Integrative transcriptome and metabolome analysis reveals the mechanism of exogenous melatonin alleviating drought stress in maize roots

Melatonin (MT) is essential for plant development and drought adaptation. However, the molecular and metabolic mechanisms underlying MT-induced drought tolerance in maize roots remain largely unclear. Herein, we investigated the effects of MT on drought tolerance in maize roots using integrated transcriptomic and metabolomic analyses, and identified MT-induced genes and metabolites associated with drought resistance. Compared with the untreated control plants, MT application alleviated the deleterious effects of drought on roots, by decreasing the malondialdehyde level and increasing the solute potential, eventually promoting root growth. Transcriptome and metabolome analysis demonstrated that MT significantly upregulates the expression of genes related to flavonoid biosynthesis (PAL, C4H, 4CL, HCT, CHS, CHI, F3'5'H, and DFR), activates drought-responsive transcription factors (ERFs, NACs, MYBs, and bHLHs), and regulates hormone signaling-related genes, especially ethylene response factors (ERF4, ERF81, and ERF110). Moreover, MT increased the accumulation of flavonoid metabolites, particularly apigenin, luteolin, and quercetin, under drought-stress conditions. These findings were further supported by quantitative real-time polymerase chain reaction analysis and total flavonoid measurements. Altogether, our findings suggest that MT promotes maize root growth during drought by regulating flavonoid synthesis pathways, transcription factors, and plant hormone signals. This study provides new insights into the complex mechanisms by which MT enhances crop resistance to drought damage.

Combined Transcriptome and Metabolome Analysis Reveals Adaptive Defense Responses to DON Induction in Potato

Phytophthora infestans poses a serious threat to potato production, storage, and processing. Understanding plant immunity triggered by fungal elicitors is important for the effective control of plant diseases. However, the role of the potato stress response to Fusarium toxin deoxynivalenol (DON)-induced stress is still not fully understood. In this study, the metabolites of DON-treated potato tubers were studied for four time intervals using UPLC-MS/MS. We identified 676 metabolites, and differential accumulation metabolite analysis showed that alkaloids, phenolic acids, and flavonoids were the major differential metabolites that directly determined defense response. Transcriptome data showed that differentially expressed genes (DEGs) were significantly enriched in phenylpropane and flavonoid metabolic pathways. Weighted gene co-expression network analysis (WGCNA) identified many hub genes, some of which modulate plant immune responses. This study is important for understanding the metabolic changes, transcriptional regulation, and physiological responses of active and signaling substances during DON induction, and it will help to design defense strategies against Phytophthora infestans in potato.

The Classification, Molecular Structure and Biological Biosynthesis of Flavonoids, and Their Roles in Biotic and Abiotic Stresses

With the climate constantly changing, plants suffer more frequently from various abiotic and biotic stresses. However, they have evolved biosynthetic machinery to survive in stressful environmental conditions. Flavonoids are involved in a variety of biological activities in plants, which can protect plants from different biotic (plant-parasitic nematodes, fungi and bacteria) and abiotic stresses (salt stress, drought stress, UV, higher and lower temperatures). Flavonoids contain several subgroups, including anthocyanidins, flavonols, flavones, flavanols, flavanones, chalcones, dihydrochalcones and dihydroflavonols, which are widely distributed in various plants. As the pathway of flavonoid biosynthesis has been well studied, many researchers have applied transgenic technologies in order to explore the molecular mechanism of genes associated with flavonoid biosynthesis; as such, many transgenic plants have shown a higher stress tolerance through the regulation of flavonoid content. In the present review, the classification, molecular structure and biological biosynthesis of flavonoids were summarized, and the roles of flavonoids under various forms of biotic and abiotic stress in plants were also included. In addition, the effect of applying genes associated with flavonoid biosynthesis on the enhancement of plant tolerance under various biotic and abiotic stresses was also discussed.

Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure

BACKGROUND

Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C.

RESULTS

The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication.

CONCLUSION

Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.

Integrated transcriptome and metabolome analysis revealed that flavonoids enhanced the resistance of Oryza sativa against Meloidogyne graminicola

Rice is a crucial food crop worldwide, but its yield and quality are significantly affected by Meloidogyne graminicola is a root knot nematode. No rice variety is entirely immune to this nematode disease in agricultural production. Thus, the fundamental strategy to combat this disease is to utilize rice resistance genes. In this study, we conducted transcriptome and metabolome analyses on two rice varieties, ZH11 and IR64. The results indicated that ZH11 showed stronger resistance than IR64. Transcriptome analysis revealed that the change in gene expression in ZH11 was more substantial than that in IR64 after M. graminicola infection. Moreover, GO and KEGG enrichment analysis of the upregulated genes in ZH11 showed that they were primarily associated with rice cell wall construction, carbohydrate metabolism, and secondary metabolism relating to disease resistance, which effectively enhanced the resistance of ZH11. However, in rice IR64, the number of genes enriched in disease resistance pathways was significantly lower than that in ZH11, which further explained susceptibility to IR64. Metabolome analysis revealed that the metabolites detected in ZH11 were enriched in flavonoid metabolism and the pentose phosphate pathway, compared to IR64, after M. graminicola infection. The comprehensive analysis of transcriptome and metabolome data indicated that flavonoid metabolism plays a crucial role in rice resistance to M. graminicola infection. The content of kaempferin, apigenin, and quercetin in ZH11 significantly increased after M. graminicola infection, and the expression of genes involved in the synthetic pathway of flavonoids also significantly increased in ZH11. Our study provides theoretical guidance for the precise analysis of rice resistance and disease resistance breeding in further research.

Autotoxic Ginsenoside Stress Induces Changes in Root Exudates to Recruit the Beneficial Burkholderia Strain B36 as Revealed by Transcriptomic and Metabolomic Approaches

Plants can recruit beneficial microbes to help improve their fitness under abiotic or biotic stress. Our previous studies found that Panax notoginseng could enrich beneficial Burkholderia sp. B36 in the rhizosphere soil under autotoxic ginsenoside stress. Here, we clarified that ginsenoside stress activated the phenylpropanoid biosynthesis and α-linolenic acid metabolism pathways of roots to increase the secretion of cinnamic acid, 2-dodecenoic acid, and 12-oxo-phytodienoic acid. These metabolites could promote the growth of B36. Importantly, cinnamic acid could simultaneously promote the chemotaxis and growth of B36, enhance the colonization of B36 in the rhizosphere, and eventually increase the survival rate of P. notoginseng. Overall, the plants could promote the growth and colonization of beneficial bacteria through key metabolites in root exudates under autotoxin stress. This finding will facilitate the practical application of beneficial bacteria in agricultural production and lead to successful and reproducible biocontrol efficacy by the exogenous addition of key metabolites.

Metabolomics Analysis of Different Tissues of Lonicera japonica Thunb. Based on Liquid Chromatography with Mass Spectrometry

Lonicera japonica Thunb. (LJT) has been widely used as medicines or food additives in Asian countries for thousands of years. The flower buds are often medicinally used, and the other tissues are ignored. However, flowers, leaves and stems have also been reported to have antimicrobial, anti-inflammatory and antioxidant effects. In the current study, un-targeted metabolomics analysis was performed to investigate the metabolic difference among different tissues (flowers, flower buds, stems and leaves) of LJT based on liquid chromatography with mass spectrometry. A total of 171 metabolites were identified, including 28 flavonoids, 35 phenolic acids, 43 iridoids, 9 amino acids, 6 nucleotides, 16 fatty acids, 22 lipids and 12 others. Four new secondary metabolites were discovered. Some flavonoids and iridoids were not detected in leaves and stems. Principal component analysis showed significant differences among four different tissues. Some 27, 81, 113 differential metabolites were found between flowers/flower buds, leaves/flower buds, stems/flower buds, respectively. Primary metabolites showed a higher content in the flowers and flower buds. For the flavonoids, flavones were mainly accumulated in the leaves, flavonols were mainly accumulated in the flower buds, and acylated flavonol glucosides were mainly accumulated in the flowers. Most phenolic acids showed a higher content in the flowers or flower buds, while phenolic acid-glucosides showed significantly higher content in the flower buds. The most abundant iridoids in the LJT also showed a higher content in the flowers and flower buds. These results can provide new insights into the understanding of the metabolites changes in different tissues, and lay a theoretical foundation for the comprehensive utilization of LJT.

Metabolomics analysis unveils important changes involved in the salt tolerance of Salicornia europaea

Salicornia europaea is one of the world's salt-tolerant plant species and is recognized as a model plant for studying the metabolism and molecular mechanisms of halophytes under salinity. To investigate the metabolic responses to salinity stress in S. europaea, this study performed a widely targeted metabolomic analysis after analyzing the physiological characteristics of plants exposed to various NaCl treatments. S. europaea exhibited excellent salt tolerance and could withstand extremely high NaCl concentrations, while lower NaCl conditions (50 and 100 mM) significantly promoted growth by increasing tissue succulence and maintaining a relatively stable K⁺ concentration. A total of 552 metabolites were detected, 500 of which were differently accumulated, mainly consisting of lipids, organic acids, saccharides, alcohols, amino acids, flavonoids, phenolic acids, and alkaloids. Sucrose, glucose, p-proline, quercetin and its derivatives, and kaempferol derivatives represented core metabolites that are responsive to salinity stress. Glycolysis, flavone and flavonol biosynthesis, and phenylpropanoid biosynthesis were considered as the most important pathways responsible for salt stress response by increasing the osmotic tolerance and antioxidant activities. The high accumulation of some saccharides, flavonoids, and phenolic acids under 50 mM NaCl compared with 300 mM NaCl might contribute to the improved salt tolerance under the 50 mM NaCl treatment. Furthermore, quercetin, quercetin derivatives, and kaempferol derivatives showed varied change patterns in the roots and shoots, while coumaric, caffeic, and ferulic acids increased significantly in the roots, implying that the coping strategies in the shoots and roots varied under salinity stress. These findings lay the foundation for further analysis of the mechanism underlying the response of S. europaea to salinity.

Transcriptome and metabolome response of eggplant against Ralstonia solanacearum infection

Bacterial wilt is a soil-borne disease that represents ubiquitous threat to Solanaceae crops. The whole-root transcriptomes and metabolomes of bacterial wilt-resistant eggplant were studied to understand the response of eggplant to bacterial wilt. A total of 2,896 differentially expressed genes and 63 differences in metabolites were identified after inoculation with Ralstonia solanacearum. Further analysis showed that the biosynthesis pathways for phytohormones, phenylpropanoids, and flavonoids were altered in eggplant after inoculation with R. solanacearum. The results of metabolomes also showed that phytohormones played a key role in eggplant response to bacterial wilt. Integrated analyses of the transcriptomic and metabolic datasets indicated that jasmonic acid (JA) content and gene involved in the JA signaling pathway increased in response to bacterial wilt. These findings remarkably improve our understanding of the mechanisms of induced defense response in eggplant and will provide insights intothe development of disease-resistant varieties of eggplant.

Biocontrol endophytes Bacillus subtilis R31 influence the quality, transcriptome and metabolome of sweet corn

During colonization of soil and plants, biocontrol bacteria can effectively regulate the physiological metabolism of plants and induce disease resistance. To illustrate the influence of Bacillus subtilis R31 on the quality, transcriptome and metabolome of sweet corn, field studies were conducted at a corn experimental base in Zhuhai City. The results show that, after application of B. subtilis R31, sweet corn was more fruitful, with a 18.3 cm ear length, 5.0 cm ear diameter, 0.4 bald head, 403.9 g fresh weight of single bud, 272.0 g net weight of single ear, and 16.5 kernels sweetness. Combined transcriptomic and metabolomic analyses indicate that differentially expressed genes related to plant-pathogen interactions, MAPK signaling pathway-plant, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched. Moreover, the 110 upregulated DAMs were mainly involved in the flavonoid biosynthesis and flavone and flavonol biosynthesis pathways. Our study provides a foundation for investigating the molecular mechanisms by which biocontrol bacteria enhance crop nutrition and taste through biological means or genetic engineering at the molecular level.

Early-stage responses to Plasmodiophora brassicae at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed Brassica napus

Clubroot, a devastating soil-borne root disease, in Brassicaceae is caused by Plasmodiophora brassicae Woronin (P. brassicae W.), an obligate biotrophic protist. Plant growth and development, as well as seed yield of Brassica crops, are severely affected due to this disease. Several reports described the molecular responses of B. napus to P. brassicae; however, information on the early stages of pathogenesis is limited. In this study, we have used transcriptomics and metabolomics to characterize P. brassicae pathogenesis at 1-, 4-, and 7-days post-inoculation (DPI) in clubroot resistant (CR) and susceptible (CS) doubled-haploid (DH) canola lines. When we compared between inoculated and uninoculated groups, a total of 214 and 324 putative genes exhibited differential expression (q-value < 0.05) at one or more time-points in the CR and CS genotypes, respectively. When the inoculated CR and inoculated CS genotypes were compared, 4765 DEGs were differentially expressed (q-value < 0.05) at one or more time-points. Several metabolites related to organic acids (e.g., citrate, pyruvate), amino acids (e.g., proline, aspartate), sugars, and mannitol, were differentially accumulated in roots in response to pathogen infection when the CR and CS genotypes were compared. Several DEGs also corresponded to differentially accumulated metabolites, including pyrroline-5-carboxylate reductase (BnaC04g11450D), citrate synthase (BnaC02g39080D), and pyruvate kinase (BnaC04g23180D) as detected by transcriptome analysis. Our results suggest important roles for these genes in mediating resistance to clubroot disease. To our knowledge, this is the first report of an integrated transcriptome and metabolome analysis aimed at characterizing the molecular basis of resistance to clubroot in canola.

Overexpression of dihydroflavonol 4-reductase (CoDFR) boosts flavonoid production involved in the anthracnose resistance

The outbreak of anthracnose caused by Colletotrichum spp. represents a devastating epidemic that severely affects oil tea (Camellia oleifera) production in China. However, the unknown resistance mechanism to anthracnose in C. oleifera has impeded the progress of breeding disease-resistant varieties. In this study, we investigated the physiological responses of resistant and susceptible lines during C. gloeosporioides infection. Our results showed that the accumulation of malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) in both disease-resistant and susceptible lines increased by C. gloeosporioides infection. Also, disease-resistant lines exhibited lower MDA, but higher POD, SOD, and CAT activities compared to susceptible lines. The accumulation of flavonoids in both resistant and susceptible C. oleifera leaves increased following C. gloeosporioides infection, and the increase was greater in resistant lines. Further, we identified and functionally characterized the dihydroflavonol 4-reductase (CoDFR) from the resistant C. oleifera line. We showed that the full-length coding sequence (CDS) of CoDFR is 1044 bp encoding 347 amino acids. The overexpression of CoDFR in tobacco altered the expression of flavonoid biosynthetic genes, resulting in an increased flavonoid content in leaves. CoDFR transgenic tobacco plants exhibited increased anthracnose resistance. Furthermore, the transgenic plants had higher salicylic acid content. These findings offer potential insights into the pivotal role of CoDFR involved in flavonoid-mediated defense mechanisms during anthracnose invasion in resistant C. oleifera.

The gastrodin biosynthetic pathway in Pholidota chinensis Lindl. revealed by transcriptome and metabolome profiling

Pholidota chinensis Lindl. is an epiphytic or lithophytic perennial herb of Orchidaceae family used as a garden flower or medicinal plant to treat high blood pressure, dizziness and headache in traditional Chinese medicine. Gastrodin (GAS) is considered as a main bioactive ingredient of this herb but the biosynthetic pathway remains unclear in P. chinensis. To elucidate the GAS biosynthesis and identify the related genes in P. chinensis, a comprehensive analysis of transcriptome and metabolome of roots, rhizomes, pseudobulbs and leaves were performed by using PacBio SMART, Illumina Hiseq and Ultra Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS). A total of 1,156 metabolites were identified by UPLC-MS/MS, of which 345 differential metabolites were mainly enriched in phenylpropanoid/phenylalanine, flavone and flavonol biosynthesis. The pseudobulbs make up nearly half of the fresh weight of the whole plant, and the GAS content in the pseudobulbs was also the highest in four tissues. Up to 23,105 Unigenes were obtained and 22,029 transcripts were annotated in the transcriptome analysis. Compared to roots, 7,787, 8,376 and 9,146 differentially expressed genes (DEGs) were identified in rhizomes, pseudobulbs and leaves, respectively. And in total, 80 Unigenes encoding eight key enzymes for GAS biosynthesis, were identified. Particularly, glycosyltransferase, the key enzyme of the last step in the GAS biosynthetic pathway had 39 Unigenes candidates, of which, transcript28360/f2p0/1592, was putatively identified as the most likely candidate based on analysis of co-expression, phylogenetic analysis, and homologous searching. The metabolomics and transcriptomics of pseudobulbs versus roots showed that 8,376 DEGs and 345 DEMs had a substantial association based on the Pearson's correlation. This study notably enriched the metabolomic and transcriptomic data of P. chinensis, and it provides valuable information for GAS biosynthesis in the plant.

Integrated metabolome and transcriptome analysis reveals salicylic acid and flavonoid pathways' key roles in cabbage's defense responses to Xanthomonas campestris pv. campestris

Xanthomonas campestris pv. campestris (Xcc) is a vascular bacteria pathogen causing black rot in cabbage. Here, the resistance mechanisms of cabbage against Xcc infection were explored by integrated metabolome and transcriptome analysis. Pathogen perception, hormone metabolisms, sugar metabolisms, and phenylpropanoid metabolisms in cabbage were systemically re-programmed at both transcriptional and metabolic levels after Xcc infection. Notably, the salicylic acid (SA) metabolism pathway was highly enriched in resistant lines following Xcc infection, indicating that the SA metabolism pathway may positively regulate the resistance of Xcc. Moreover, we also validated our hypothesis by showing that the flavonoid pathway metabolites chlorogenic acid and caffeic acid could effectively inhibit the growth of Xcc. These findings provide valuable insights and resource datasets for further exploring Xcc-cabbage interactions and help uncover molecular breeding targets for black rot-resistant varieties in cabbage.

Analysis of terpenoids and their gene regulatory networks on the basis of the transcriptome and metabolome of Opisthopappus longilobus

Opisthopappus longilobus, which is a unique wild plant resource in China, produces leaves and flowers with distinct aromas. However, there have been relatively few molecular studies on its floral aroma, which has hindered the research on this plant species at the molecular level and the breeding of novel varieties. In this study, transcriptome and metabolome analyses were performed using O. longilobus leaves, buds, and inflorescences at the exposure, initial opening, and blooming stages. Using high-quality reads and assembly software, a total of 45,674 unigenes were annotated according to the Nr, Swiss-Prot, KOG, and KEGG databases. Additionally, a GC-MS system and a self-built database were used to detect 1,371 metabolites in the leaves, buds, and inflorescences. Terpene metabolites were the most common compounds (308 in total). We analyzed the gene network regulating terpenoid accumulation in O. longilobus and identified 56 candidate genes related to terpenoid synthesis. The expression of OlPMK2, OlMVK1, OlTPS1, and OlTPS3 may lead to the accumulation of 11 different terpenoids specifically in the inflorescences at the exposure, initial opening, and blooming stages. The generated data may be useful for future research on O. longilobus genetic resources and the molecular mechanism regulating aroma formation in this plant species. The findings of this study may be used to accelerate the breeding of new O. longilobus varieties with enhanced aromatic traits.

Combined transcriptome and metabolome reveal glutathione metabolism plays a critical role in resistance to salinity in rice landraces HD961

Rice (Oryza sativa) is one of the most important food crops around the world, which is sensitive to salt stress, especially in the seedling and booting stage. HD961 is a salt-tolerant rice landrace that grows along coastal beaches and has disease and insect pest resistance, salt tolerance, and vigorous growth characteristics. We performed a combined transcriptome and metabolome analysis to clarify salinity resistance mechanisms in cultivar HD961, which has adapted to salinity soil at the early seedling stage. The results showed that the growth and antioxidant capacity of HD961 were stronger than 9311 under salt stress (SS). Transcriptomic analysis showed that a total of 6,145, 3,309, 1,819, and 1,296 differentially expressed genes (DEGs) were identified in the groups of TH60 (control group vs. 60 mM group of HD961 for transcriptome), TH120 (control group vs. 120 mM group of HD961 for transcriptome), T60 (control group vs. 60 mM group of 9311 for transcriptome), and T120 (control group vs. 120 mM group of 9311 for transcriptome), respectively. Starch and sucrose metabolism and phenylpropanoid biosynthesis were shared in the four treatment groups based on a KEGG enrichment analysis of DEGs. In addition, alpha-linolenic acid metabolism, plant hormone signal transduction, plant-pathogen interaction, and fatty acid elongation were specific and significantly different in HD961. A total of 92, 158, 151, and 179 significantly regulated metabolites (SRMs) responded to SS in MH60 (control group vs. 60 mM group of HD961 for metabolome), MH120 (control group vs. 120 mM group of HD961 for metabolome), M60 (control group vs. 60 mM group of 9311 for metabolome), and M120 (control group vs. 120 mM group of 9311 for metabolome), respectively. The KEGG analysis showed that eight common metabolic pathways were identified in the four treatment groups, of which biosynthesis of amino acids was the most significant. Three specific metabolic pathways were identified in the HD961, including glutathione metabolism, ascorbate and aldarate metabolism, and pantothenate and CoA biosynthesis. Integrative analysis between the transcriptome and metabolome showed that glutathione metabolism was specific and significantly affected under SS in HD961. A total of seven SRMs and 48 DEGs and four SRMs and 15 DEGs were identified in the glutathione metabolism pathway in HD961 and 9311, respectively. The Pearson correlation analysis showed a significant correlation between reduced glutathione and 16 genes (12 upregulated and four downregulated genes), suggesting these genes could be candidates as salt-tolerance regulation genes. Collectively, our data show that glutathione metabolism plays a critical role in response to SS in rice. Moreover, the stronger regulative ability of related common genes and metabolites might contribute to salt resistance in HD961.

Physiological and transcriptome analyses reveal the photosynthetic response to drought stress in drought-sensitive (Fengjiao) and drought-tolerant (Hanjiao) Zanthoxylum bungeanum cultivars

As an important economical plant, Zanthoxylum bungeanum is widely cultivated in arid and semi-arid areas. The studies associated with photosynthesis under drought stress were widely carried out, but not yet in Z. bungeanum. Here, the photosynthesis of two Z. bungeanum cultivars (FJ, Z. bungeanum cv. "Fengjiao"; HJ, Z. bungeanum cv. "Hanjiao") was analyzed under drought stress using physiological indicators and transcriptome data. Drought decreased stomatal aperture and stomatal conductance (Gsw), reduced transpiration rate (E) and sub-stomatal CO₂ concentration (Ci), and lowered chlorophyll and carotenoid content, which reduced the net photosynthetic rate (Pn) of Z. bungeanum. The higher photosynthetic rate in HJ stemmed from its higher chlorophyll content, larger stomatal aperture and Gsw, and higher Ci. Weighted gene co-expression network analysis (WGCNA) identified several ABA signal transduction genes (PYL4, PYL9, and PYR1), LCH-encoding genes (LHCB4.3), and chlorophyll metabolism genes (CRD1, PORA, and CHLH). Additionally, seven transcription factor genes were identified as important factors regulating photosynthesis under drought conditions. In general, a photosynthetic response model under drought stress was built firstly in Z. bungeanum, and the key genes involved in photosynthesis under drought stress were identified. Therefore, the results in our research provide important information for photosynthesis under drought and provided key clues for future molecular breeding in Z. bungeanum.

Biosynthetic mechanisms of isoflavone accumulation affected by different growth patterns in Astragalus mongholicus products

BACKGROUND

At present, Astragalus mongholicus products on the market represent two growth patterns: imitative wild A. mongholicus (WAM) and cultivated A. mongholicus (CAM). The 6-year-old WAM (A6) and 2-year-old CAM (B2) products are often sold as commodities. This study aimed to explore the effects of the abovementioned growth patterns on the biosynthetic mechanisms of isoflavone accumulation in A. mongholicus products.

RESULTS

In this paper, the content of calycosin-7-O-β-D-glucoside in 6-year-old WAM (A6) was significantly higher than that in 2-year-old CAM (B2) based on high-performance liquid chromatography. Tissue anatomy indicated that A6 has developed phloem fibers, thickened secondary walls, and a more well-developed vascular system than B2. Thirteen differentially accumulated metabolites were found in A6 and B2 by UHPLC-ESI-Q-TOF-MS/MS, of which isoflavones were highly and significantly enriched in A6. By combining transcriptomics and metabolomics analysis, we found that the metabolomics profile was the same as the transcriptomics profile in both A6 and B2. In total, 11 novel isoflavone-related genes were isolated using BLAST and functional annotation through RNA-Seq and Iso-Seq. The results of integrated analysis, Short Time-series Expression Miner analysis, and Pearson correlation analysis showed that the regulation of four key enzymes, cinnamate 4-hydroxylase, 6-deoxychalcone synthase, chalcone reductase, and chalcone isomerase, led to the high accumulation of isoflavones in A6. In addition, AmUFGT (c778119) and AmUCGT (c303354) were predicted to be 7-O-glycosyltransferases by phylogenetic analysis; these genes catalyze formononetin and calycosin, respectively.

CONCLUSIONS

The findings of this work will clarify the differences in the biosynthetic mechanism of isoflavone accumulation between A6 and B2, which will guide the cultivation of A. mongholicus.

Transcriptomic and metabolomic investigation of metabolic disruption in Vigna unguiculata L. triggered by acetamiprid and cyromazine

A variety of pesticides are often used in agricultural management to control target pests but may trigger disruptions in the metabolism of nontarget organisms, ultimately affecting crop quality. Acetamiprid (ACE) and cyromazine (CYR) are two frequently used insecticides on cowpea, so it is critical to understand whether these two insecticides cause metabolic disorders in cowpea quality changes and the mechanism by which they do so. Here, we used metabolomic and transcriptomic methods to explore the mechanisms of the effects of ACE, CYR, and their mixture (MIX) on cowpea. In this study, ACE, CYR and MIX had no significant effects on plant biomass or growth status but decreased the contents of starch, soluble protein, and total flavonoids. All treatments reduced the total flavonoid content, but MIX showed the largest reduction of 10.02%. Metabolomic and transcriptomic analyses revealed that ACE markedly affected amino acid metabolism, and CYR and MIX affected sugar metabolism and flavonoid synthesis pathways. ACE and CYR reduced the levels of alanine, glutamic acid, isoleucine and phenylalanine and the expression of amino acid-related genes in cowpea, while MIX significantly increased the levels of most amino acids. All pesticide treatments reduced saccharide levels and related genes, with the most pronounced reduction in the MIX treatment. Exposure to ACE decreased the content of naringenin chalcone and quercetin and increased the content of anthocyanins in cowpeas, while MIX caused a significant decrease in the contents of quercetin and anthocyanins. According to the current study, single and mixed pesticides had different effects on the active ingredients of cowpea, with MIX causing the most significant decrease in the metabolite content of cowpea. These results provide important insights from a molecular perspective on how neonicotinoids and triazine insecticides affect cowpea metabolism.

Metabolomics Study on the Resistance of Walnut Peel to Colletotrichum gloeosporioides under Prochloraz Treatment

Anthracnose, caused by Colletotrichum gloeosporioides, is highly harmful for walnut production in the world. To better control this disease, the inhibitory effects of 3 fungicides against Colletotrichum gloeosporioides were determined, and the results showed that prochloraz had better inhibitory activity. Through comparative metabolomics analysis, 311 metabolites might be associated with the walnut peel response to Colletotrichum gloeosporioides under prochloraz treatment. Furthermore, we supposed that the phenylpropanoid pathway might be induced by prochloraz to resist Colletotrichum gloeosporioides infection. In conclusion, the upregulated metabolites in the phenylpropanoid pathway might be related to synthesize lignin to further form a cell wall against Colletotrichum gloeosporioides infection.