Search Results (739)

Gastrodia elata Blume is an important medicinal orchid, yet its large-scale cultivation is increasingly threatened by fungal diseases. The 4-coumarate–CoA ligase (4CL) gene family directs a key step in phenylpropanoid metabolism and plant defence, but its composition and function in G. elata have not been investigated. We mined the G. elata genome for 4CL homologues, mapped their chromosomal locations, and analysed their gene structures, conserved motifs, phylogenetic relationships, promoter cis-elements and codon usage bias. Publicly available transcriptomes were used to examine tissue-specific expression and responses to fungal infection. Subcellular localisation of selected proteins was verified by transient expression in Arabidopsis protoplasts. Fourteen Ge4CL genes were identified and grouped into three clades. Two members, Ge4CL2 and Ge4CL5, were strongly upregulated in tubers challenged with fungal pathogens. Ge4CL2 localised to the nucleus, whereas Ge4CL5 localised to both the nucleus and the cytoplasm. Codon usage analysis suggested that Escherichia coli and Oryza sativa are suitable heterologous hosts for Ge4CL expression. This study provides the first genome-wide catalogue of 4CL genes in G. elata and suggests that Ge4CL2 and Ge4CL5 may participate in antifungal defence, although functional confirmation is still required. The dataset furnishes a foundation for functional characterisation and the molecular breeding of disease-resistant G. elata cultivars. Full article

Sulfur fumigation (SF), acid dipping (HCl treatment, HAT), and their combination (SF+HAT) are common methods for long-term preservation and color protection of litchi. However, their effects on the metabolic profile of the litchi pericarp have not been investigated. SF resulted in a yellowish-green pericarp by up-regulating lightness (L*), b*, C*, and h° but down-regulating total anthocyanin content (TAC) and a*, while HAT resulted in a reddish coloration by up-regulating a*, b*, and C* but down-regulating L*, h°, and TAC. SF+HAT recovered reddish color with similar L*, C* to SF but a*, b*, h°, and TAC between SF and HAT. Differential accumulated metabolites (DAMs) detected in HAT (vs. control) were more than those in SF (vs. control), but similar to those in SF+HAT (vs. control). SF specifically down-regulated the content of cyanidin-3-O-rutinoside, sinapinaldehyde, salicylic acid, and tyrosol, but up-regulated 6 flavonoids (luteolin, kaempferol-3-O-(6″-malonyl)galactoside, hesperetin-7-O-glucoside, etc.). Five pathways (biosynthesis of phenylpropanoids, flavonoid biosynthesis, biosynthesis of secondary metabolites, glutathione metabolism, and cysteine and methionine metabolism) were commonly enriched among the three treatments, which significantly up-regulated sulfur-containing metabolites (mainly glutathione, methionine, and homocystine) and down-regulated substrates for browning (mainly procyanidin B2, C1, and coniferyl alcohol). These results provide metabolic evidence for the effect of three treatments on coloration and storability of litchi. Full article

Elodea nuttallii is a significant submerged macrophyte utilized in shrimp and crab aquaculture, yet it exhibits low thermotolerance. This study investigated the physiological responses and transcriptomic characteristics of E. nuttallii under high-temperature stress (HTS). The results indicated that HTS significantly reduced the absolute growth rate (AGR) and photosynthetic efficiency of E. nuttallii while concurrently elevating antioxidant enzyme activities, malondialdehyde (MDA) content, and concentrations of osmotic adjustment compounds. Furthermore, the apical segments of E. nuttallii demonstrated greater sensitivity to HTS compared to the middle segments. Under exposure to 35 °C and 40 °C, antioxidant enzyme activities, MDA content, and osmotic adjustment compound levels were significantly higher in the apical segments than in the middle segments. Transcriptomic analysis revealed 7526 differentially expressed genes (DEGs) in the apical segments at 35 °C, a number substantially exceeding that observed in the middle segments. Enrichment analysis of DEGs revealed significant upregulation of key metabolic regulators under HTS, including carbohydrate metabolism genes (HXK, FRK) and phenylpropanoid biosynthesis enzymes (4CL, COMT). This transcriptional reprogramming demonstrates E. nuttallii’s adaptive strategy of modulating carbon allocation and phenolic compound synthesis to mitigate thermal damage. Our findings not only elucidate novel thermotolerance mechanisms in aquatic plants but also provide candidate genetic targets (HXK, 4CL) for molecular breeding of heat-resilient cultivars through transcriptomic screening. Full article

Browning significantly impacts the commercial value of luffa (luffa cylindrica) and is primarily driven by the metabolic processes of phenolic acids. Investigating changes in phenolic acids during browning aids in understanding the physiological mechanisms underlying this process and provides a basis for improving storage, processing, variety breeding, and utilization of germplasm resources. This study compared browning-resistant (‘30’) and browning-sensitive (‘256’) luffa varieties using high-throughput sequencing and metabolomics techniques. The results revealed 55 genes involved in the phenylpropanoid biosynthesis pathway, including 8 phenylalanine ammonia-lyase (PAL) genes, 20 peroxidase (POD) genes, 2 polyphenol oxidase (PPO) genes associated with tyrosine metabolism, and 37 peroxisome-related genes. Real-time quantitative (qPCR) was employed to validate 15 browning-related genes, revealing that the expression levels of LcPOD21 and LcPOD6 were 12.5-fold and 25-fold higher in ‘30’ compared to ‘256’, while LcPAL5 and LcPAL4 were upregulated in ‘30’. Enzyme analysis showed that catalase (CAT) and phenylalanine ammonia-lyase (PAL) activities were higher in ‘30’ than in ‘256’. Conversely, superoxide dismutase (SOD) and polyphenol oxidase (PPO) activities were reduced in ‘30’, whereas CAT activity was upregulated. The concentrations of cinnamic acid, p-coumaric acid, trans-5-O-(4-coumaroyl)mangiferic acid, and caffealdehyde were lower in browning-resistant luffa ‘30’ than in browning-sensitive luffa ‘256’, suggesting that their levels influence browning in luffa. These findings elucidate the mechanisms underlying browning and inform strategies for the storage, processing, and genetic improvement of luffa. Full article

To elucidate the molecular mechanisms underlying anther abortion in celery male sterile lines, this study investigates the morphological differences of floral organs and differential gene expression patterns between two lines at the flowering stage. Using the male sterile line of celery ‘QCBU-001’ and the fertile line ‘Jinnan Shiqin’ as materials, anther structure was analyzed by paraffin sections, and related genes were detected using transcriptome sequencing and qRT-PCR. The results indicated that the anther locules were severely shrunken at maturity in the sterile lines. The callose deficiency led to abnormal development of microspores, preventing the formation of mature pollen grains and ultimately leading to complete anther abortion. The transcriptome results revealed that 3246 genes were differentially expressed in sterile and fertile lines, which were significantly enriched in pathways such as starch and sucrose metabolism and phenylpropanoid biosynthesis. Additionally, differential expression patterns of transcription factor families (MYB, bHLH, AP2, GRAS, and others) suggested their potential involvement in regulating anther abortion. Notably, the expression level of callose synthase gene AgGSL2 was significantly downregulated in sterile anthers, which might be an important cause of callose deficiency and pollen sterility. This study not only provides a theoretical basis for elucidating the molecular mechanism underlying male sterility in celery but also lays a foundation for the utilization and improvement of male sterile lines in vegetable hybrid breeding. Full article

Background: Phoebe zhennan and Phoebe chekiangensis are valuable evergreen trees recognized for their unique aromas and ecological significance, yet the organ-related distribution and functional implications of aroma-active volatiles remain insufficiently characterized. Methods: In this study, we applied an integrated GC-MS-based volatile metabolomics approach combined with a relative odor activity value (rOAV) analysis to comprehensively profile and compare the volatile metabolite landscape in the seeds and leaves of both species. Results: In total, 1666 volatile compounds were putatively identified, of which 540 were inferred as key aroma-active contributors based on the rOAV analysis. A multivariate statistical analysis revealed clear tissue-related separation: the seeds were enriched in sweet, floral, and fruity volatiles, whereas the leaves contained higher levels of green leaf volatiles and terpenoids associated with ecological defense. KEGG pathway enrichment indicated that terpenoid backbone and phenylpropanoid biosynthesis pathways played major roles in shaping these divergent profiles. A Venn diagram analysis further uncovered core and unique volatiles underlying species and tissue specificity. Conclusions: These insights provide an integrated reference for understanding tissue-divergent volatile profiles in Phoebe species and offer a basis for fragrance-oriented selection, ecological trait evaluation, and the sustainable utilization of organ-related metabolic characteristics in breeding and conservation programs. Full article

Zinc (Zn) deficiency poses a major global health challenge, and wheat grains generally contain low Zn concentrations. In this study, the wheat cultivar ‘Zhongmai 175’ was identified as zinc-efficient. Hydroponic experiments demonstrated that Zn deficiency induced the secretion of oxalic acid and malic acid in root exudates and significantly increased total root length in ‘Zhongmai 175’. To elucidate the underlying regulatory mechanisms, transcriptome profiling via RNA sequencing was conducted under Zn-deficient conditions. A total of 2287 and 1935 differentially expressed genes (DEGs) were identified in roots and shoots, respectively. Gene Ontology enrichment analysis revealed that these DEGs were primarily associated with Zn ion transport, homeostasis, transmembrane transport, and hormone signaling. Key DEGs belonged to gene families including VIT, NAS, DMAS, ZIP, tDT, HMA, and NAAT. KEGG pathway analysis indicated that phenylpropanoid biosynthesis, particularly lignin synthesis genes, was significantly downregulated in Zn-deficient roots. In shoots, cysteine and methionine metabolism, along with plant hormone signal transduction, were the most enriched pathways. Notably, most DEGs in shoots were associated with the biosynthesis of phytosiderophores (MAs, NA) and ethylene. Overall, genes involved in Zn ion transport, phytosiderophore biosynthesis, dicarboxylate transport, and ethylene biosynthesis appear to play central roles in wheat’s adaptive response to Zn deficiency. These findings provide a valuable foundation for understanding the molecular basis of Zn efficiency in wheat and for breeding Zn-enriched varieties. Full article

Powdery mildew (PM), caused by Sphaerotheca phaseoli, severely threatens mungbean (Vigna radiata) productivity and quality, yet the molecular basis of resistance remains poorly defined. This study employed transcriptome profiling to compare defense responses in a resistant genotype, SUPER5, and a susceptible variety, CN84-1, following pathogen infection. A total of 1755 differentially expressed genes (DEGs) were identified, with SUPER5 exhibiting strong upregulation of genes encoding pathogenesis-related (PR) proteins, disease resistance proteins, and key transcription factors. Notably, genes involved in phenylpropanoid and flavonoid biosynthesis, pathways associated with antimicrobial compound and lignin production, were markedly induced in SUPER5. In contrast, CN84-1 showed limited activation of defense genes and downregulation of essential regulators such as MYB14. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses highlighted the involvement of plant–pathogen interaction pathways, MAPK signaling, and reactive oxygen species (ROS) detoxification in the resistant response. Quantitative real-time PCR validated 11 candidate genes, including PAL3, PR2, GSO1, MLO12, and P21, which function in pathogen recognition, signaling, the biosynthesis of antimicrobial metabolites, the production of defense proteins, defense regulation, and the reinforcement of the cell wall. Co-expression network analysis revealed three major gene modules linked to flavonoid metabolism, chitinase activity, and responses to both abiotic and biotic stresses. These findings offer valuable molecular insights for breeding PM-resistant mungbean varieties. Full article

Functional foods like flax (Linum usitatissimum L.) are rich sources of specialized metabolites that contribute to their nutritional and health-promoting properties. Understanding the biosynthesis of these compounds is essential for improving their quality and potential applications. However, dissecting complex metabolic networks in plants remains challenging due to the dynamic nature and interconnectedness of biosynthetic pathways. In this study, we present a synergistic approach combining stable isotopic labeling (SIL), Candidate Substrate–Product Pair (CSPP) networks, and a time-course study with high temporal resolution to reveal the biosynthetic fluxes shaping phenylpropanoid metabolism in young flax seedlings. By feeding the seedlings with ¹³C₃-p-coumaric acid and isolating isotopically labeled metabolization products prior to the construction of CSPP networks, the biochemical validity of the connections in the network was supported by SIL, independent of spectral similarity or abundance correlation. This method, in combination with multistage mass spectrometry (MSⁿ), allowed confident structural proposals of lignans, neolignans, and hydroxycinnamic acid conjugates, including the presence of newly identified chicoric acid and related tartaric acid esters in flax. High-resolution time-course analyses revealed successive waves of metabolite formation, providing insights into distinct biosynthetic fluxes toward lignans and early lignification intermediates. No evidence was found here for the involvement of chlorogenic or caftaric acid intermediates in chicoric acid biosynthesis in flax, as has been described in other species. Instead, our findings suggest that in flax seedlings, chicoric acid is synthesized through successive hydroxylation steps of p-coumaroyl tartaric acid esters. This work demonstrates the power of combining SIL and CSPP strategies to uncover novel metabolic routes and highlights the nutritional potential of flax sprouts rich in chicoric acid. Full article

Background/Objectives: Sweet potato is a tropical and subtropical crop and its growth and yield are susceptible to low-temperature stress. However, the molecular mechanisms underlying the low temperature stress of sweetpotato are unknown. Methods: In this work, combined transcriptome and metabolism analysis was employed to investigate the low-temperature responses of two sweet potato cultivars, namely, the low-temperature-resistant cultivar “X33” and the low-temperature-sensitive cultivar “W7”. Results: The differentially expressed metabolites (DEMs) of X33 at different time stages clustered in five profiles, while they clustered in four profiles of W7 with significant differences. Differentially expressed genes (DEGs) in X33 and W7 at different time points clustered in five profiles. More DEGs exhibited continuous or persistent positive responses to low-temperature stress in X33 than in W7. There were 1918 continuously upregulated genes and 6410 persistent upregulated genes in X33, whereas 1781 and 5804 were found in W7, respectively. Core genes involved in Ca²⁺ signaling, MAPK cascades, the reactive oxygen species (ROS) signaling pathway, and transcription factor families (including bHLH, NAC, and WRKY) may play significant roles in response to low temperature in sweet potato. Thirty-one common differentially expressed metabolites (DEMs) were identified in the two cultivars in response to low temperature. The KEGG analysis of these common DEMs mainly belonged to isoquinoline alkaloid biosynthesis, phosphonate and phosphinate metabolism, flavonoid biosynthesis, cysteine and methionine metabolism, glycine, serine, and threonine metabolism, ABC transporters, and glycerophospholipid metabolism. Five DEMs with identified Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were selected for correlation analysis. KEGG enrichment analysis showed that the carbohydrate metabolism, phenylpropanoid metabolism, and glutathione metabolism pathways were significantly enriched and played vital roles in low-temperature resistance in sweet potato. Conclusions: These findings contribute to a deeper understanding of the molecular mechanisms underlying plant cold tolerance and offer targets for molecular breeding efforts to enhance low-temperature resistance. Full article

Seed germination and early seedling growth are pivotal stages that define crop establishment and yield potential. Conventional agrochemicals used to improve these processes often raise environmental concerns, highlighting the need for sustainable alternatives. In this study, we demonstrated that water treated with cylindrical dielectric barrier discharge (c-DBD) plasma, enriched with nitric oxide (NO) and reactive nitrogen species (RNS), markedly enhanced onion (Allium cepa) seed germination and seedling vigor. The plasma-treated water (PTW) promoted rapid imbibition, broke dormancy, and accelerated germination rates beyond 98%. Seedlings irrigated with PTW exhibited significantly increased biomass, root and shoot length, chlorophyll content, and antioxidant enzyme activities, accompanied by reduced lipid peroxidation. Transcriptomic profiling revealed that PTW orchestrated a multifaceted regulatory network by upregulating gibberellin biosynthesis genes (GA3OX1/2), suppressing abscisic acid signaling components (ABI5), and activating phenylpropanoid metabolic pathways (PAL, 4CL) and antioxidant defense genes (RBOH1, SOD). These molecular changes coincided with elevated NO₂⁻ and NO₃⁻ levels and finely tuned hydrogen peroxide dynamics, underpinning redox signaling crucial for seed activation and stress resilience. Our findings establish plasma-generated NO-enriched water as an innovative, eco-friendly technology that leverages redox and hormone crosstalk to stimulate germination and early growth, offering promising applications in sustainable agriculture. Full article

Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. Using RNA sequencing (RNA-seq), we assembled 169,652 unigenes and identified differentially expressed genes (DEGs) at each stage compared to G0, increasing from 1708 in G1 to 10,250 in G4. Functional enrichment analysis revealed upregulation of genes associated with cell wall organization, glucan metabolism, and Photosystem II assembly. Key genes involved in cell wall remodeling, including cellulose synthase (CESA), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (COMT), and peroxidase (POD) showed progressive activation during germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed dynamic regulation of phenylpropanoid and flavonoid biosynthesis, photosynthesis, carbohydrate metabolism, and hormone signaling pathways. Transcription factors such as indole-3-acetic acid (IAA), ABA-responsive element binding factor (ABF), and basic helix–loop–helix (bHLH) were upregulated, suggesting hormone-mediated regulation of dormancy release and seedling development. Physiologically, cytokinin (CTK) and IAA levels peaked in G4, antioxidant enzyme activities were highest in G2, and starch content increased toward later stages. These findings provide new insights into the molecular mechanisms underlying seed germination in C. oleifera and identify candidate genes relevant to rootstock breeding and nursery propagation. Full article

Quercus acutissima seeds exhibit high desiccation sensitivity, posing significant challenges for long-term preservation. This study investigates the physiological and metabolic responses of soluble osmoprotectants—particularly soluble proteins and proline—during the desiccation process. Seeds were sampled at three critical moisture content levels: 38.8%, 26.8%, and 14.8%, corresponding to approximately 99%, 52%, and 0% germination, respectively. We measured germination ability, soluble protein content, and proline accumulation, and we performed untargeted metabolomic profiling using LC-MS. Soluble protein levels increased early but declined later during desiccation, while proline levels continuously increased for sustained osmotic adjustment. Metabolomics analysis identified a total of 2802 metabolites, with phenylpropanoids and polyketides (31.12%) and lipids and lipid-like molecules (29.05%) being the most abundant. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that differentially expressed metabolites were mainly enriched in key pathways such as amino acid metabolism, energy metabolism, and nitrogen metabolism. Notably, most amino acids decreased in content, except for proline, which showed an increasing trend. Tricarboxylic acid cycle intermediates, especially citric acid and isocitric acid, showed significantly decreased levels, indicating energy metabolism imbalance due to uncoordinated consumption without effective replenishment. The reductions in key amino acids such as glutamic acid and aspartic acid further reflected metabolic network disruption. In summary, Q. acutissima seeds fail to establish an effective desiccation tolerance mechanism. The loss of soluble protein-based protection, limited capacity for proline-mediated osmotic regulation, and widespread metabolic disruption collectively lead to irreversible cellular damage. These findings highlight the inherent metabolic vulnerabilities of recalcitrant seeds and suggest potential preservation strategies, such as supplementing critical metabolites (e.g., TCA intermediates) during storage to delay metabolic collapse and mitigate desiccation-induced damage. Full article

The sorghum aphid (Melanaphis sacchari (Zehntner, 1897)), a globally destructive pest, severely compromises sorghum yield and quality. This study compared aphid-resistant (HX133) and aphid-susceptible (HX37) sorghum (Sorghum bicolor (L.) Moench) cultivars, revealing that HX133 significantly suppressed aphid proliferation through repellent and antibiotic effects, while aphid populations increased continuously in HX37. Transcriptome analysis identified 2802 differentially expressed genes (DEGs, 45.9% upregulated) in HX133 at 24 h post-infestation, in contrast with only 732 DEGs (21% upregulated) in HX37. Pathway enrichment highlighted shikimate-mediated phenylpropanoid/flavonoid biosynthesis and glutathione metabolism as central to HX133’s defense response, alongside photosynthesis-related pathways common to both cultivars. qRT-PCR validation confirmed activation of the shikimate pathway in HX133, driving the synthesis of dhurrin—a cyanogenic glycoside critical for aphid resistance—and other tyrosine-derived metabolites (e.g., benzyl isoquinoline alkaloids, tocopherol). These findings demonstrate that HX133 employs multi-layered metabolic regulation, particularly dhurrin accumulation, to counteract aphid infestation, whereas susceptible cultivars exhibit limited defense induction. This work provides molecular targets for enhancing aphid resistance in sorghum breeding programs. Full article

Low temperature is a major abiotic stress affecting rice productivity. Selenium (Se) treatment has been shown to enhance plant resilience to cold stress. In this study, low concentrations of selenium (ColdSe1) alleviated the adverse effects of cold stress on rice seedlings, improving fresh weight, plant height, and chlorophyll content by 36.9%, 24.3%, and 8.4%, respectively, while reducing malondialdehyde (MDA) content by 29.1%. Se treatment also increased the activities of antioxidant enzymes, including catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), by 25.2%, 42.7%, and 33.3%, respectively, and upregulated flavonoids, soluble sugars, cysteine (Cys), glutathione (GSH), and oxidized glutathione (GSSG). Transcriptome analysis revealed that ColdSe1 treatment upregulated genes associated with amino and nucleotide sugar metabolism, glutathione metabolism, and fructose and mannose metabolism. It also alleviated cold stress by modulating the MAPK signaling pathway, phytohormone signaling, and photosynthesis-related pathways, enriching genes and transcription factors linked to antioxidant metabolism and photosynthesis. Metabolomic analyses showed that ColdSe1 positively influenced amino acid glucose metabolism, glycerolipid metabolism, hormonal pathways, and alanine/glutamate pathways under cold stress, while also upregulating metabolites associated with plant secondary metabolites (e.g., flavonoids, phenolic compounds) and antioxidant metabolism (e.g., α-linolenic acid metabolism). In contrast, high selenium concentrations (ColdSe2) disrupted phenylpropanoid biosynthesis, α-linolenic acid metabolism, and ABC transporter function, exacerbating cold-stress injury. This study highlights the critical role of Se in mitigating cold stress in rice, offering a theoretical basis for its application as an agricultural stress reliever. Full article