Search Results (2,099)

Fragaria pentaphylla, a unique wild strawberry species in China, is rich in various fruit colors and a valuable resource for studying color genes. Fruits of different colors from F. pentaphylla were selected as the experimental material. Liquid chromatography-mass spectrometry (LC-MS) and high-throughput RNA sequencing (RNA-seq) were employed to identify key genes responsible for the development of different fruit colors. Metabolite analysis revealed that 3249 metabolites were detected, including nine differential metabolites related to anthocyanin synthesis and five biological pathways. Additionally, an analysis combining transcriptome and metabolome data showed that the structural genes FpDFR, FpCHS, FpCHI, and FpUFGT were upregulated in red fruit, with significantly higher expression levels compared to pink and white fruits, actively promoting anthocyanin production in red fruit. Conversely, genes FpANR and FpLAR were upregulated in white fruit, enhancing catechin synthesis and inhibiting anthocyanin formation. The gene FpPAL was upregulated in pink fruit. Transcription factors FpbHLH18, FpMYB1, FpMYB24, and FpMYB114 collaborate with structural genes to enhance the synthesis of anthocyanins in red fruit. The findings improve our understanding of the molecular mechanisms that control anthocyanin production in F. pentaphylla. The identified key candidate genes may be utilized in the molecular breeding of strawberries. Full article

Climate change is intensifying the co-occurrence of drought and heat stresses, which substantially constrain global crop yields and threaten food security. Developing climate–resilient crop varieties requires a comprehensive understanding of the physiological and molecular mechanisms underlying combined drought–heat stress tolerance. This review systematically summarizes recent advances in integrating multi-scale remote-sensing phenomics with multi-omics approaches—genomics, transcriptomics, proteomics, and metabolomics—to elucidate stress response pathways and identify adaptive traits. High-throughput phenotyping platforms, including satellites, UAVs, and ground-based sensors, enable non-invasive assessment of key stress indicators such as canopy temperature, vegetation indices, and chlorophyll fluorescence. Concurrently, omics studies have revealed central regulatory networks, including the ABA–SnRK2 signaling cascade, HSF–HSP chaperone systems, and ROS-scavenging pathways. Emerging frameworks integrating genotype × environment × phenotype (G × E × P) interactions, powered by machine learning and deep learning algorithms, are facilitating the discovery of functional genes and predictive phenotypes. This “pixels-to-proteins” paradigm bridges field-scale phenotypes with molecular responses, offering actionable insights for breeding, precision management, and the development of digital twin systems for climate-smart agriculture. We highlight current challenges, including data standardization and cross-platform integration, and propose future research directions to accelerate the deployment of resilient crop varieties. Full article

Drought stress severely impacts the survival of Platycrater arguta, an endangered tertiary relict plant. This study investigated the mechanism by which exogenous melatonin enhances drought tolerance in P. arguta seedlings through integrated physiological, transcriptomic, and metabolomic analyses. Under 30% PEG-6000-induced drought, seedlings exhibited leaf wilting, reduced relative water content (RWC: 78.6% vs. 84.8% in controls), and elevated oxidative damage (malondialdehyde increased by 62.94%, H₂O₂ by 83.78%). Exogenous melatonin application, particularly at 100 μM (T3), significantly alleviated drought symptoms, restoring RWC to 83.7%, reducing membrane permeability (relative electrical conductivity 1.38-fold vs. CK vs. 2.55-fold in PEG), and lowering oxidative markers (MDA and H₂O₂ accumulation by 28.33% and 27.84%, respectively). T3 treatment also enhanced osmolyte synthesis, increasing proline content by 90.14% and soluble sugars by 47.25% compared to the controls. Transcriptome sequencing revealed 31,870 differentially expressed genes in T3, predominantly enriched in carbohydrate metabolism, oxidative phosphorylation, and tryptophan metabolism pathways. Metabolomic profiling demonstrated that 100 μM melatonin elevated endogenous melatonin levels 19.62-fold and modulated tryptophan-derived metabolites, including indole derivatives and benzoic acid compounds. These findings indicate that melatonin mitigates drought stress by enhancing antioxidant capacity, osmotic adjustment, and metabolic reprogramming, with 100 μM as the optimal concentration. This study provides critical insights into melatonin-mediated drought resistance mechanisms, offering a theoretical foundation for conserving and restoring P. arguta populations in arid habitats. Full article

Unsaturated fatty acids are key contributors to the nutritional and sensory quality of lamb meat. To investigate the molecular basis of intramuscular unsaturated fatty acid variation, we selected lambs with divergent fatty acid profiles and performed integrated transcriptomic and untargeted metabolomic analyses of the longissimus dorsi muscle. The high unsaturated fatty acid group exhibited distinct gene expression patterns in pathways related to lipid metabolism, mitochondrial function, and immune responses. Metabolomic profiling revealed significant enrichment of metabolites involved in both the biosynthesis and degradation of fatty acids. Among the differentially expressed genes, MYH7 was markedly upregulated in lambs with higher unsaturated fatty acid content, suggesting a potential regulatory role in energy metabolism or lipid homeostasis. These findings provide new molecular insights into the mechanisms underlying unsaturated fatty acid deposition in lamb and identify MYH7 and other candidates as potential targets for improving meat quality through breeding or nutritional strategies. Full article

This study aimed to compare the therapeutic effects of fresh (CMF) and dried (CMD) Centipeda minima against allergic rhinitis (AR), elucidate their underlying molecular mechanisms, and identify the bioactive compounds responsible for their immunomodulatory actions. An ovalbumin-induced AR mouse model was treated with CMF or CMD extracts, followed by evaluation of nasal symptoms, serum biomarkers (IgE, histamine, cytokines), and nasal mucosa histopathology. Transcriptomics and widely targeted metabolomics were integrated with network pharmacology to identify differentially expressed genes and bioactive components, which were further validated in RAW264.7 and RBL-2H3 cells. CMF and CMD exhibited distinct anti-AR mechanisms: CMF predominantly suppressed Th2 responses (reducing IgE, IL-6, and histamine while elevating IL-10), whereas CMD enhanced Th1 activity (increasing IFN-γ). Metabolomic analysis revealed CMF was rich in amino acids while CMD contained higher flavonoids, with neocnidilide and 6-gingerol identified as key bioactive compounds that modulated TNF-α, IL-6, and IL-10 via NF-κB and JAK-STAT pathways. These findings demonstrate that CMF and CMD exert complementary anti-inflammatory effects through Th2 inhibition and Th1 activation, respectively, providing a molecular basis for the traditional use of Centipeda minima and highlighting its bioactive compounds as potential therapeutics for inflammatory diseases. Full article

Traditionally considered as homogeneous innate immune cells, neutrophils are now found to exhibit phenotypic and functional heterogeneity. How to determine whether the functional changes of neutrophils are caused by activation or the result of gene reprogramming? Recent advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and spatial omics, have comprehensively explained the mechanism of neutrophil heterogeneity. At the same time, artificial intelligence, especially machine learning, has promoted the in-depth analysis of multi-omics. Here, we introduce the latest progress in the discovery of neutrophil subsets by omics research. We will further discuss the application of machine learning in analyzing the heterogeneity of neutrophils through omics methods. Our goal is to provide a comprehensive overview of how machine learning and multi-omics are reshaping our understanding of neutrophil biology and pathophysiology. Full article

Terpenoids, which are essential pharmaceutical compounds, encounter significant production challenges due to their low yields in native plants and associated ecological concerns. This review summarizes recent advances in metabolic engineering strategies applied across three complementary platforms: native medicinal plants, microbial systems, and heterologous plant hosts. We present how the “Genomic Insights to Biotechnological Applications” paradigm, supported by multi-omics technologies such as genomics, transcriptomics, metabolomics, and related disciplines, contributes to advancing research in this field. These technologies enable the systematic identification of key biosynthetic genes and regulatory networks. CRISPR-based tools, enzyme engineering, and subcellular targeting are presented as pivotal transformative strategies in advancing metabolic engineering approaches. Strategic co-expression and optimization approaches have achieved substantial improvements in product yields, as demonstrated by a 25-fold increase in paclitaxel production and a 38% enhancement in artemisinin yield. Persistent challenges, such as metabolic flux balancing, cytotoxicity, and scale-up economics, are discussed in conjunction with emerging solutions, including machine learning and photoautotrophic chassis systems. We conclude by proposing a strategic roadmap for industrial translation that highlights the essential integration of systems biology and synthetic biology approaches to accelerate the transition of terpenoid biomanufacturing from discovery to commercial-scale application. Full article

The rhizosphere microbiome, a critical determinant of plant health and productivity, exhibits structure–activity relationships influenced by plant genotype. This study investigated how three tea varieties with distinct phenotypes—Zhongcha 108 (ZC, green leaves), Huangjinya (HJY, chlorophyll-deficient yellow leaves), and Zijuan (ZJ, anthocyanin-rich purple leaves)—modulate the rhizosphere microbiome by integrated metagenomic, transcriptomic, and metabolomic analysis. Results revealed significant differences in rhizosphere bacterial diversity and composition among varieties, driven by differential abundances of Actinobacteria and Proteobacteria. HJY and ZJ exhibited higher bacterial richness and diversity compared to ZC. Root transcriptome profiling identified phenylpropanoid biosynthesis as a central pathway, with differentially expressed genes involved in flavonoid and lignin biosynthesis. Metabolite profiling highlighted varietal differences in root and rhizosphere organic acids and phenylpropanoid derivatives (e.g., hydroxycinnamyl aldehydes, sinapic acid), strongly correlating with microbial community structure. Functional metagenomics indicated that the carbohydrate and amino acid metabolism pathways in rhizosphere bacteria were influenced by root metabolites, further establishing phenylpropanoid partitioning as a keystone driver for microbial niche differentiation. These findings demonstrate that tea varieties shape rhizosphere microbiomes via genotype-specific phenylpropanoid metabolism, offering insights into targeted manipulation of plant–microbe interactions for enhancing tea plant development and tea quality. Full article

Yajiangxue cattle (XF) is three-way crossbred cattle developed specifically for producing high-quality beef in the Tibetan Plateau by introducing the bloods of Tibetan yellow cattle (HF) and Angus cattle into Tibetan yak (MF). In the present study, we mainly focused on fat deposition and metabolism changes and used RNA-seq and LC-MS/MS-based metabolomics to partially explain the meat quality improvement in Yajiangxue cattle. Differential expression analysis revealed 1762, 2949, and 2931 different expression genes in XF vs. HF, XF vs. MF, and XF vs. cattle–yak (PF), respectively, such as BMP2, WISP2, FGF1, IL1B, IL6, and WNT5B. Immune response, oxidation–reduction processes, and fatty acid metabolism were markedly enriched. Furthermore, an initial identification revealed 319 metabolites using positive ion mode and 289 metabolites using negative ion mode in bovine adipose tissue across four breeds/populations. Of these, 143 were differential metabolites in positive ion mode, while 166 were in negative ion mode. The main pathways of metabolism affected by breed/population were unsaturated fatty acid biosynthesis, tryptophan and tyrosine biosynthesis, primary bile acid biosynthesis, cholesterol metabolism, beta-alanine metabolism, etc. Similarly, both the transcriptome and the metabolome results highlighted fatty acid metabolism. These results could help elucidate the biological mechanisms involved in fat deposition and identify valuable biomarkers for specific metabolite accumulation. Full article

Sand pear is a fruit tree crop with high economic value, widely cultivated in East Asia. However, ripening fruits often suffer from high-temperature stress, which has adverse effects on the quality and yield of the fruit. In this study, we perform high-temperature treatment on mature stage ‘Housui’ pear fruits. The results showed that heat stress decreased fruit firmness and mineral elements, as well as lead to the flesh appearance of watercore. High temperature induces H₂O₂, MDA, and the antioxidant enzyme activity including SOD, APX, POD, and CAT were significantly increased. Transcriptome and metabolomic analyses revealed that heat stress up-regulated genes related to sucrose synthesis (SPS) while down-regulating those involved in sucrose degradation (SS and NI), resulting in sucrose accumulation. Moreover, the expression of sorbitol dehydrogenase (SDH) and sorbitol transporter (SOT) genes was markedly suppressed, leading to sorbitol accumulation and impaired transport, which promoted watercore development. High temperature also stimulated the expression of ethylene synthesis genes, accelerating abnormal ripening of fruits. In addition, high temperature decreased the accumulation of organic acid and bioactive compounds. Additionally, several antioxidant enzymes genes, five heat shock transcription factors (HSFs) and 34 heat shock protein (HSP) genes were significantly up-regulated. Together, these findings provided new insights into the transcriptional response and metabolomic reprogramming of sand pear response to high-temperature stress. Full article

Background: The escalating global salinization poses a significant threat to agricultural productivity, necessitating a thorough understanding of plant responses to high salinity. Pea sprouts (Pisum sativum), a nutrient-rich crop increasingly cultivated in salinized regions, serve as an ideal model for such investigations due to their rapid growth cycle and documented sensitivity to ionic stress. Methods: In order to understand the response of pea sprouts in physiological regulation, redox-metabolic adjustments, and transcriptome reprogramming under salt stress, we investigated the effects of high salt concentrations on the ascorbic acid–glutathione cycle, endogenous hormone levels, metabolite profiles, and gene expression patterns in it. Results: Our findings reveal early-phase antioxidant/hormonal adjustments, mid-phase metabolic shifts, and late-phase transcriptomic reprogramming of pea sprouts under salt conditions. In addition, a biphasic response in the ascorbic acid cycle was found, with initial increases in enzyme activities followed by a decline, suggesting a temporary enhancement of antioxidant defenses. Hormonal profiling indicated a significant increase in abscisic acid (ABA) and jasmonic acid (JA), paralleled by a decrease in indole acetic acid (IAA) and dihydrozeatin (DZ), underscoring the role of hormonal regulation in stress adaptation. Metabolomic analysis uncovered salt-induced perturbations in sugars, amino acids, and organic acids, reflecting the metabolic reconfiguration necessary for osmotic adjustment and energy reallocation. Transcriptomic analysis identified 6219 differentially expressed genes (DEGs), with a focus on photosynthesis, hormone signaling, and stress-responsive pathways, providing insights into the molecular underpinnings of salt tolerance. Conclusions: This comprehensive study offers novel insights into the complex mechanisms employed by pea sprouts to combat salinity stress, contributing to the understanding of plant salt tolerance and potentially guiding the development of salt-resistant crop varieties. Full article

Flavor formation in citrus fruit is governed by complex and dynamic changes in primary and secondary metabolism during development and ripening. Here, we integrated metabolomic, hormonal, and transcriptomic analyses to elucidate the regulatory landscape underlying soluble sugar and organic acid metabolism in ‘Kiyomi’ citrus fruit. A total of 1679 metabolites were identified, revealing stage-specific reprogramming of metabolic pathways, including a sharp decline in citric acid after 90 days after flowering (DAF) and peak accumulation of sucrose at 180 DAF. Hormonal profiling showed that abscisic acid (ABA) progressively accumulated from 120 to 210 DAF, while 1-aminocyclopropane-1-carboxylic acid (ACC) peaked at 120 DAF and declined thereafter, suggesting distinct and temporally coordinated roles in ripening regulation. Transcriptomic profiling uncovered widespread temporal shifts in gene expression, with the most pronounced changes occurring between 180 and 210 DAF. Co-expression network analysis identified gene modules associated with sugar and acid accumulation, and highlighted transcription factors from the ERF, MYB, NAC, and HSF families as candidate regulators of ripening-related metabolic transitions. These findings provide a comprehensive framework for understanding the coordinated molecular and metabolic programs underlying flavor development in non-climacteric citrus fruit and offer candidate genes for the genetic improvement of fruit quality. Full article

Passion fruit (Passiflora edulis) is an economically important fruit worldwide. However, heat stress severely threatens its production, particularly in tropical and subtropical regions. To elucidate the molecular and metabolic mechanisms underlying heat tolerance, comparative physiological, transcriptomic, and metabolomic analyses were conducted between two yellow passion fruit cultivars: heat-tolerant ‘Summer Queen’ (F2) and heat-sensitive ‘Qinmi 9’ (QM9). Physiological evaluations demonstrated that QM9 exhibited significantly lower heat tolerance than F2, manifesting as severe leaf wilting, impaired photosynthetic efficiency, and elevated reactive oxygen species (ROS) accumulation. F2 exhibited distinct metabolic and transcriptional adaptations under heat stress, particularly in purine metabolism and flavonoid biosynthesis. Metabolites such as glutamine, xanthine, luteoloside, and trifolin were enriched in F2, alongside the upregulation of genes like adenosine kinase (AK), xanthine dehydrogenase (XDH), guanine deaminase (GDA), and flavonoid 3′-hydroxylase (F3′H). Weighted gene co-expression network analysis (WGCNA) highlighted strong associations between these pathways and transcription factors (e.g., MYB, HSF, WRKY), suggesting their pivotal roles in heat adaptation. Exogenous application of xanthine and trifolin markedly enhanced heat tolerance in passion fruit. Furthermore, knockdown of PeGDA and PeXDH markedly altered the heat tolerance of F2. These findings reveal that elevated metabolites in purine metabolism and flavonoid biosynthesis enhance heat tolerance in passion fruit, offering new insights into the molecular mechanisms of heat tolerance and potential targets for breeding climate-resilient passion fruit varieties. Full article

Golden pompano (Trachinotus ovatus) is an economically important fish species along China’s southern coast. However, infections by Cryptocaryon irritans severely constrain the healthy and sustainable development of the aquaculture industry. To investigate the genetic basis of resistance to this parasite in golden pompano, this study employed transcriptomic and metabolomic analyses to compare differences between susceptible (ES) and resistant (RS) groups following C. irritans challenge. Transcriptome analysis identified 2031 differentially expressed genes (DEGs) between EST and RST groups, comprising 1004 up-regulated and 1027 down-regulated genes. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that these DEGs were primarily enriched in lipid metabolism and amino acid metabolism pathways. Untargeted metabolomics detected 461 significantly differentially abundant metabolites (295 up-regulated, 166 down-regulated), confirming pronounced metabolic differences between ES and RS groups, particularly in lipid and amino acid metabolism. Further, KEGG enrichment highlighted steroid hormone biosynthesis, α-linolenic acid metabolism, and arachidonic acid metabolism as the most significantly altered pathways upon infection. This integrated transcriptomic and metabolomic study reveals substantial differences in gene expression and metabolite profiles between susceptible and resistant golden pompano in response to C. irritans. These changes predominantly involve lipid metabolism and amino acid metabolism, suggesting that these processes are critical in determining host resistance/susceptibility. Full article