Search Results (3,466)

Valsa canker, caused by Valsa mali (Cytospora mali) or V. pyri, is a destructive fungal disease affecting apple and pear production. NAC transcription factors have been shown to participate in multiple immune signaling pathways. However, the key members of this family involved in Valsa canker resistance remain largely unknown. In this study, we demonstrate that PbeNAC72, an NAC transcription factor responsive to Valsa canker signals in Pyrus betulifolia, positively regulates resistance in apple and pear fruits. In ‘Duli-G03’ (P. betulifolia) suspension cells, overexpression of PbeNAC72 significantly enhanced resistance to Valsa canker and induced reactive oxygen species bursts, as well as the expression of salicylic acid and jasmonic acid-related genes. Subsequent weighted gene co-expression network analysis revealed that PbeNAC72 is primarily linked to genes associated with “DNA replication” and “microtubule-based movement.” We therefore suggest that PbeNAC72 activates genes related to core signaling pathways and fundamental cellular processes, which further contribute to the positive regulation of Valsa canker resistance. Our results provide novel insights into the resistance mechanism and identify a candidate gene for future molecular breeding efforts. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) exhibits poor clinical response to gemcitabine, largely due to intrinsic and acquired mechanisms of chemoresistance. Identifying agents capable of enhancing gemcitabine efficacy without increasing cytotoxicity remains an unmet therapeutic need. Here, we characterise a small drug sensitiser molecule, B12, and evaluate its potential to sensitise PDAC cells to gemcitabine. Methods: Gemcitabine’s dose–response was assessed by MTT assay to determine IC₅₀ values and dose-modifying factor (DMF). Phenotypic consequences of co-treatment were examined using colony formation and wound scratch assays. Mitochondrial membrane potential (JC-1) and apoptosis (Annexin V/PI) were measured using flow cytometry. Transcriptomic profiling was performed using mRNA-seq with differential expression analysis and pathway enrichment (KEGG/GSEA). NF-κB activity was assessed by nuclear and cytoplasmic fractionation of p65, and RT-qPCR validation of NF-κB associated target genes. Results: B12 alone displayed minimal cytotoxicity in the PANC-1 cell line and normal pancreatic ductal HPDE cells, yet shifted the gemcitabine dose–response curve in PANC-1 cells, reducing the IC₅₀ and yielding a dose-modifying factor of 1.39. Functionally, B12 enhanced gemcitabine-induced suppression of colony formation and reduced wound closure relative to gemcitabine alone. The co-treatment also increased both mitochondrial depolarisation and apoptotic cell populations, with increased cell proliferation inhibition over time. Transcriptomic profiling identified a set of B12-associated genes downregulated both in B12-treated and B12 + gemcitabine conditions, including factors linked to growth, survival, inflammation, metabolism, and drug inactivation. Gene set enrichment analysis revealed negative enrichment of NF-κB associated pathways during B12 co-treatment. Consistently, nuclear-cytoplasmic fractionation showed that B12 reduced gemcitabine-induced nuclear accumulation of p65, accompanied by decreased expression of NF-κB associated targets such as BCL2L1, CCL20, SLC2A1, and MAP3K14. Conclusions: In PDAC cell models, B12 enhances gemcitabine cytotoxic response while displaying minimal intrinsic toxicity under the conditions tested. The sensitising phenotype is accompanied by increased apoptotic susceptibility and is associated with reduced NF-κB signalling at the pathway, transcript, and p65 nuclear localisation levels. However, to establish causality, the lack of sensitisation in HPDE cells will require further validation. Full article

Background/Objectives: SLC13A5 encodes a sodium–citrate cotransporter implicated in early-onset epileptic encephalopathy and metabolic brain dysfunction, yet its developmental regulation and molecular context in the human brain remain incompletely defined. Methods: Leveraging human developmental transcriptomes from the Evo-Devo resource, we delineated tissue trajectories and network context for SLC13A5 across the fetal–postnatal life. Results: In the cerebrum, SLC13A5 expression rises from late fetal stages to peak in the first postnatal year and then declines into adulthood, while cerebellar levels increase across the lifespan; liver shows a fetal decrease followed by sustained postnatal upregulation. A transcriptome-wide scan identified extensive positive and negative associations with SLC13A5, and a signed weighted gene co-expression network analysis (WGCNA) built on biweight midcorrelation placed SLC13A5 in a large module. The module eigengene tracked brain maturation (Spearman rho = 0.802, p = 8.62 × 10⁻⁶) and closely matched SLC13A5 abundance (rho = 0.884, p = 2.73 × 10⁻⁶), with a significant partial association after adjusting for developmental rank (rho = 0.672, p = 6.17 × 10⁻⁴). Functional enrichment converged on oxidative phosphorylation and mitochondria. A force-directed subnetwork of the top intramodular members (|bicor| > 0.6) positioned SLC13A5 adjacent to a densely connected nucleus including CYP46A1, ITM2B, NRGN, GABRD, FBXO2, CHCHD10, CYSTM1, and MFSD4A. Conclusions: Together, these results define a developmentally tuned, mitochondria-centered program that co-varies with SLC13A5 in the human brain across the lifespan. It may provide insights to interrogate age-dependent phenotypes and therapeutic avenues for disorders involving citrate metabolism. Full article

Acute lung injury (ALI) pathogenesis is intricately linked to microvascular permeability. Soluble guanylate cyclase (sGC) is prominently expressed in the vascular system, playing a central role in vascular function. In contrast, its expression and function diminish notably during the progression of ALI, indicating sGC’s potential significance as a pivotal modulator in the pathological processes of ALI. Nonetheless, the precise localization of sGC within lung tissue and its distinct mechanism in maintaining vascular homeostasis remain unclear. Furthermore, there is a necessity for a pharmacological agent capable of consistently activating sGC for the treatment of ALI. A novel sGC stimulator, sGC003, was engineered through structural modification of Riociguat. In a mouse model of ALI, sGC003 exhibited superior sGC activation and more potent anti-inflammatory effects relative to Riociguat. It also exhibited superior efficacy in improving respiratory function and reducing pulmonary edema. Through single-cell RNA sequencing and immunofluorescence co-localization analysis, we confirmed predominant expression of soluble guanylate cyclase in pericytes. The sGC stimulators were found to modulate the LPS-induced pericyte transcriptome reprogramming via the nitric oxide (NO)-sGC-cyclic guanosine monophosphate (cGMP) pathway. Differential gene expression analysis categorized pericytes into nine distinct subgroups, which were sequentially activated during vascular development, inflammation, and myofibrosis. Pseudotime analysis revealed that sGC003 more effectively suppressed the myofibroblast differentiation of pericytes compared to Riociguat. In conclusion, sGC003 mitigates ALI-induced pulmonary inflammation by modulating pericyte differentiation, particularly in preserving microvascular integrity outstanding performance. Its exceptional efficacy suggests that it could potentially serve as a safer and more efficient option as a novel sGC stimulant in the future. Full article

Innovative developments of GC-MS over the last two decades made this methodology a powerful tool for profiling a broad range of volatile metabolites and non-volatile ones of non-polar, semi-polar and even polar nature after appropriate derivatization. Indeed, the high potential of GC-MS in the analysis of low molecular weight metabolites involved in essential cellular functions (energy production, metabolic adjustment, signaling) made it the method of choice for the life and plant scientists. However, despite these advances, due to their intrinsic thermal lability, multiple classes of hydrophilic low-molecule weight metabolites (like nucleotides, sugar phosphates, cofactors, CoA esters) are unsuitable under the high-temperature conditions of the split–splitless (SSL) injection and GC separation, which makes the analysis of such compounds by GC-MS challenging. Therefore, to ensure comprehensive coverage of the plant metabolome, the GC-MS-based metabolomics platform needs to be efficiently combined with other metabolomics techniques and instrumental strategies. Moreover, to get a deeper insight into dynamics of plant cell metabolism in response to endogenic and exogenic clues, integration of the metabolomics data with the output obtained from other post-genomics techniques is desired. Therefore, here, we overview different strategies for the integration of the GC-MS-based metabolite profiling output with the data, acquired by other metabolomics techniques in terms of the multi-platform metabolomics approach. Further, we comprehensively discuss the implementation of the GC-MS-based metabolomics in multi-omics strategies and the data integration strategies behind this. This approach is the promising strategy, as it gives deep and multi-level insight into physiological processes in plants in the systems biology context, with consideration of all levels of gene expression. However, multiple challenges may arise in the way of integrating data from different omics technologies, which are comprehensively discussed in this review. Full article

Crassulacean acid metabolism (CAM) is a specialized photosynthetic pathway that enhances water-use efficiency by temporally separating nocturnal CO₂ uptake from daytime decarboxylation and carbon fixation. To uncover the regulatory mechanisms coordinating these temporal dynamics, we generated high-resolution, 48 h time-course transcriptomes for the CAM model Kalanchoe fedtschenkoi under both 12 h/12 h light/dark (LD) cycles and continuous light (LL). A rhythmicity analysis revealed that diel light cues are the dominant driver of transcript oscillations: 16,810 genes (54.3% of annotated genes) exhibited rhythmic expression only under LD, whereas just 399 genes (1.3%) remained rhythmic under LL. A smaller set of 3009 genes (9.7%) oscillated in both conditions, indicating that the intrinsic circadian clock sustains rhythmicity for a limited subset of the transcriptome. A gene co-expression network analysis revealed extensive integration between circadian clock components, core CAM pathway enzymes, and stomatal regulators, defining regulatory modules that coordinate metabolic and physiological timing. Notably, key hub genes associated with post-translational and post-transcriptional regulation, including the E3 ubiquitin ligase HUB2 and several pentatricopeptide repeat (PPR) proteins, act as central nodes in CAM-associated networks. This discovery implicates epigenetic and organellar regulation as previously unrecognized critical tiers of control in CAM. Together, our results support a regulatory model in which CAM rhythmicity is governed by both external light/dark cues and the endogenous circadian clock through multi-level control spanning transcriptional and protein-level regulation. To support community exploration, we also provide an interactive eFP (electronic Fluorescent Pictograph) browser for visualizing time-resolved gene expression profiles. Full article

Background: Barnacles are important marine fouling organisms, and their complex life cycle involves key metamorphic nodes from nauplius to cyprid larvae and then to sessile adults. However, the molecular mechanisms underlying their larval development remain poorly understood. Metabolomics and transcriptomics are powerful tools for exploring biological development pathways and regulatory networks. Methods: We employed non-targeted metabolomics and transcriptomics to analyze three key developmental stages of embryonic stage, nauplius stage, and cyprid stage. Differential metabolites were screened using fold change (FC), p-value, and variable importance in projection (VIP) values, while DEGs were identified with adjusted p-value and |log₂(fold change)| criteria. WGCNA was used to construct gene co-expression networks, and qRT-PCR validated RNA-seq results. Results: A total of 3683 metabolites were identified, with the bile secretion pathway serving as a core regulatory pathway throughout early development. Transcriptomic analysis identified 7234 DEGs, which were clustered into four modules corresponding to different developmental stages. Key pathways such as chitin metabolism, and linoleic acid metabolism were significantly enriched, and qRT-PCR confirmed the reliability of RNA-seq data. Conclusions: This study reveals the metabolic and molecular regulatory mechanisms underlying the early development of M. volcano, highlighting stage-specific metabolic characteristics and core gene modules. The findings provide a theoretical basis for understanding barnacle developmental adaptation strategies and offer potential targets for the development of novel antifouling agents. Full article

Background: Adipose tissue surrounds organs and tissues in the body and can alter their function. It could secrete diverse biological molecules, including lipids, cytokines, hormones, and metabolites. In light of all this information, obesity can influence many tissues and organs in the body, and this situation makes obesity a central contributor to multiple disorders. It is very important to investigate the crosstalk between tissues and organs in the body to clarify the key mechanisms of obesity. Methods: In this study, we analyzed the gene expression profiles of the liver, skeletal muscle, blood, visceral, and subcutaneous adipose tissue. Differentially expressed genes (DEGs) were identified for each tissue, and functional enrichment and protein–protein interaction network analyses were performed on genes commonly identified across tissues. Priority candidate genes were identified using network-based centrality measures, and potential molecular intersection points were explored through host-pathogen interaction network analysis. This study provides an integrative framework for characterizing inter-tissue molecular patterns associated with obesity at the network level. Results: The muscle, subcutaneous adipose tissue, and blood have the highest number of DEGs. The subcutaneous adipose tissue and blood stand out due to the number of DEGs they possess, although liver and visceral adipose tissue have lower amounts. Cancer ranks first in terms of diseases associated with obesity, and this association is accompanied by leukemia, lymphoma, and gastric cancer. RPL15 and RBM39 are the top genes in both degree and betweenness metrics. The host–pathogen interaction network consists of 13 unique-host proteins, 54 unique-pathogen proteins, and 27 unique-pathogen organisms, and the Influenza A virus had the highest interaction. There were a small number of common metabolites in all tissues: 2-Oxoglutarate, Adenosine, Succinate, and D-mannose. Conclusions: In this study, we aimed to identify candidate molecules for obesity using an integrative approach, examining the gene profiles of different organs and tissues. The findings of this study suggest a possible link between obesity and immune-related biological processes. The network obtained from the host-pathogen interaction analysis, and especially the pathways associated with viral infections that stand out in the functional enrichment analysis, may overlap with molecular signatures linked to obesity. Furthermore, the co-occurrence of cytokine signaling, insulin, and glucose metabolism pathways in the enrichment results indicates that the response of cells to insulin may be affected in obese individuals, suggesting a potential interaction between immune and metabolic processes; however, further experimental validation is needed to reveal the direct functional effects of these relationships. Full article

Liver cirrhosis (LC) is a complex pathological condition characterized by extensive transcriptomic reprogramming, yet the regulatory role of non-coding RNAs in disease progression remains poorly understood. This study aimed to systematically investigate long non-coding RNA (lncRNA)-messenger RNA (mRNA) interaction networks in LC through weighted gene co-expression network analysis (WGCNA). Gene expression profiles from datasets GSE197406, GSE107170, and GSE17548 were retrieved from the Gene Expression Omnibus (GEO) database, and differentially expressed lncRNAs and mRNAs were identified. Co-expression modules were constructed using WGCNA. Furthermore, functional enrichment analyses were conducted and drug repurposing opportunities were evaluated. Additionally, lncRNA-mRNA co-expression networks and lncRNA-mRNA-pathway networks were constructed to identify key regulatory relationships. Molecular docking simulations were subsequently performed to validate potential drug–target interactions. The results revealed several co-expression modules significantly associated with LC, particularly the turquoise module (r = 0.81). Genes within this module were enriched in several biological pathways, including the PI3K-Akt signaling pathway, NF-κB signaling pathway, and chemokine signaling pathway. The hub lncRNA in the turquoise module, NONHSAT134945.2, was found to be co-expressed with mRNAs involved in inflammasome-mediated pyroptosis and hepatocyte activation, such as CSF1R, HCK, and CASP1. Based on this hub gene signature, AB-1010, GW768505A, and Dasatinib were identified as potential therapeutic candidates. Molecular docking analysis confirmed that these compounds exhibit high binding affinity to CSF1R and HCK, with all interatomic distances maintained below 3.5 Å. These findings provide new insights into the molecular mechanisms underlying LC and suggest that the NONHSAT134945.2–CSF1R/HCK axis may serve as a valuable target for future translational research and therapeutic development. Full article

Exaggerated immune responses to respiratory viruses may contribute to increased morbidity in older adults. To investigate virus-specific immune activation in this population, we developed an ex vivo whole blood stimulation model using samples from 30 healthy individuals aged ≥65 years. Whole blood was stimulated with UV-inactivated influenza A virus (IAV), respiratory syncytial virus (RSV), and SARS-CoV-2, and the expression of 22 immune-related genes was assessed by quantitative RT-PCR array. All three viruses elicited responses with marked variability across individuals, as well as differences in the magnitude and distribution of cytokine expression across stimuli. RSV stimulation was associated with relatively higher expression of inflammatory mediators, while IAV and SARS-CoV-2 induced greater expression of Type I interferon. SARS-CoV-2 also led to an increased expression of regulatory cytokines. Although individual responses varied, correlation analysis indicated coordinated gene expression within functional categories, and Uniform Manifold Approximation and Projection (UMAP) showed distinct grouping of cytokine responses by virus and function. These findings describe differential immune mRNA expression profiles in response to viral stimuli in older adults and may support future studies aimed at understanding age-related differences in host–virus interactions. Full article

As a critically important global food crop, wheat has been increasingly threatened by the frequent occurrence of extreme high-temperature events, which impairs its growth and development, resulting in reduced seed-setting rate, compromised grain quality and diminished yield. Therefore, identifying heat-tolerant genes and enhancing thermotolerance through molecular breeding are essential strategies for wheat improvement. In this study, we retrieved spatial transcriptomic data from the public database PRJNA427246, which captured gene expression profiles in flag leaves and grains of the heat-sensitive wheat cultivar Chinese Spring (CS) under 37 °C heat stress at time points of 0 min, 5 min, 10 min, 30 min, 1 h, and 4 h. Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct co-expression networks for flag leaf and grain transcriptomes. One highly significant module was identified in each tissue, along with 35 hub genes that showed a strong temporal association with heat stress progression. Notably, both modules contained the previously characterized thermotolerance gene TaMBF1c, suggesting that additional heat-responsive genes may be present within these modules. Simultaneous analysis of the expression data from four groups (encompassing different tissues and high-temperature treatments) for the 35 core genes revealed that genes from the TaHSP20 family, TaMBF1c family, and other related genes exhibit coordinated expression patterns in terms of the temporal dynamics and tissue distribution of stress responses. Additionally, 27 genes of the small heat shock protein (HSP20) family are predicted to be involved in the endoplasmic reticulum-associated degradation (ERAD) pathway. They assist in clearing misfolded proteins induced by stress, thereby helping to maintain endoplasmic reticulum homeostasis and cellular functions under stress conditions. Finally, the expression levels of three core genes, TaHSP20-1, TaPCDP4, and TaMBF1c-D, were validated by qRT-PCR in two wheat cultivars with distinct thermotolerance: S116 (Zhehuamai 2008) and S128 (Yangmai 33). These findings provide new insights into the molecular mechanisms underlying heat tolerance in wheat and offer valuable genetic resources for breeding thermotolerant varieties. Full article

Background: Hydroxycinnamoyl-CoA quinate hydroxycinnamoyl-transferase (HQT) is an essential enzyme for chlorogenic acid (CGA) biosynthesis in plants. Multiple HQT-encoding genes potentially involved in CGA synthesis in sweet potato (Ipomoea batatas) have been predicted. However, the functions of these genes have not been verified. Methods: In this study, the gene IbHQT1 was isolated from the sweet potato cultivar ‘Nanshu-88’ and functionally characterized using transgenic technology. Results: IbHQT1 encodes a protein comprising 431 amino acids, with conserved HXXXD and DFGWG motifs characteristic of BAHD acyltransferase family members. A phylogenetic analysis indicated that IbHQT1 has a close evolutionary relationship with StHQT in Solanum tuberosum. According to qPCR data, IbHQT1 is highly expressed in young leaves, and its expression is affected by exogenous MeJA (100 µM), ABA (100 µM), GA₃ (50 µM), and SA (100 µM). Analyses of cis-acting regulatory elements indicated that the IbHQT1 promoter contains multiple elements responsive to MeJA, ABA, SA, GA₃, and light. In plants overexpressing IbHQT1, CGA contents in mature leaves and storage roots increased 1.30- to 1.44-fold and 1.28- to 1.43-fold, respectively. Conversely, in IbHQT1-RNAi lines, CGA contents in mature leaves and storage roots decreased by 16–38% and 18–40%, respectively. Conclusions: These findings indicate that IbHQT1 positively regulates CGA biosynthesis in sweet potato plants. Full article

Flammulina filiformis is the key industrial edible fungus that requires elevated CO₂ to promote the growth of long stipe and small pileus fruiting bodies. Heat shock transcription factors (HSFs) play vital roles in stress response and development regulation; yet the HSF gene family and its expression dynamics during fruiting body development in F. filiformis remain uncharacterized. This study aims to identify and characterize the HSF gene family in F. filiformis and to investigate their expression patterns during fruiting body development and in response to CO₂ treatments. In this study, 7 FfHSFs were identified, and their structures, sequence features, and phylogenetics were further analyzed. Expression patterns under CO₂ regulation were examined via qRT-PCR. The FfHSFs exhibited CDS lengths of 618–2298 bp, encoding 301–765 hydrophilic amino acids, with molecular weights ranging from 23.4 to 83.8 kDa and theoretical pI values between 4.75 and 9.15. All were predicted to be nuclear-localized. Cis-element analysis revealed motifs associated with growth regulation and stress responses such as low temperature, drought, and hypoxia. Phylogenetically, fungal HSFs were grouped into five clusters, with FfHSFs distributed across four. In this study, we examined the expression levels at four time points (0 h, 2 h, 12 h, and 36 h), under three different carbon dioxide concentrations (0.1%, 5%, and 20%) and in two types of tissues (pileus and stipe) for each six biological replicates. CO₂ treatments showed that 5% CO₂ significantly suppressed pileus expansion but not stipe elongation, while 20% CO₂ inhibited both. Under 20% CO₂ treatment, the pileus diameter decreased by approximately 40%, and simultaneously, the expression level of FfHSF1 decreased by about 70%. qRT-PCR indicated that FfHSF1 decreased with pileus expansion, whereas FfHSF4 increased. All FfHSFs were highly expressed in the stipe elongation zone. Elevated CO₂ down-regulated FfHSF1 in pileus and FfHSF6 in stipes. Based on these findings, it could be proposed that FfHSF1 and FfHSF6 might be candidate regulators in CO₂-mediated morphogenesis, providing insights into hormonal and environmental control of fruiting body development in F. filiformis. Full article

Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root responses to P. indica colonization at 10 days after inoculation (dais; early stage) and 20 dais (late stage) during symbiosis establishment. Colonization was confirmed by phenotypic and physiological assessments, with inoculated plants showing enhanced root growth; colonized roots exhibited higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), along with increased indole-3-acetic acid (IAA) levels, whereas malondialdehyde (MDA), jasmonic acid (JA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were reduced. Transcriptome and metabolomic profiling identified 1884 and 1077 differentially expressed genes (DEGs) and 2098 and 1509 differentially accumulated metabolites (DAMs) at 10 dais (Pi10d vs. CK10d) and 20 dais (Pi20d vs. CK20d), respectively, and 3355 DEGs and 2314 DAMs between stages (Pi20d vs. Pi10d). Functional enrichment highlighted key pathways related to secondary metabolism, carbohydrate metabolism, and lipid biosynthesis. Differentially expressed transcription factors spanned multiple families, including MYB, AP2/ERF, MADS-box, and bZIP, consistent with broad transcriptional reprogramming during symbiosis establishment. Integrative multi-omics analysis further highlighted phenylpropanoid biosynthesis and α-linolenic acid metabolism as consistently co-enriched pathways, suggesting coordinated shifts in gene expression and metabolite accumulation across colonization stages. Collectively, these results provide a multi-layered resource and a framework for mechanistic dissection of the P. indica–B. decumbens interaction. Full article

Background/Objectives: The arrangement and positioning of genes on chromosomes are non-random in plant genomes. Adjacent gene pairs often exhibit similar co-expression patterns and regulatory mechanisms. However, the genomic and epigenetic features influencing such co-expression, particularly in perennial crops like tea (Camellia sinensis), remain largely uncharacterized. Methods: Firstly, we identified 771 specific neighboring gene pairs (SNGs) in C. sinensis (YK10) and investigated the contributions of intergenic distance and gene length to SNGs’ co-expression. Secondly, we integrated multi-omics data including transcriptome, ATAC-seq, Hi-C and histone modification data to explore the factors influencing their co-expression. Thirdly, we employed logistic regression models to individually assess the contributions of nine factors—ATAC-seq, H3K27ac, Hi-C, GO, distance, length, promoter, enhancer, and expression level—to the co-expression of SNGs. Finally, by integrating co-expression networks with metabolic profiles, several transcription factors potentially involved in the regulation of catechin metabolic pathways were identified. Results: Intergenic distance was significantly negatively correlated with co-expression strength, while gene length showed a positive correlation. Furthermore, these two features exerted synergistic effects with threshold characteristics and functional significance. SNGs marked by either ATAC-seq or H3K27ac peaks displayed significantly higher expression levels, suggesting that epigenetic regulation promotes co-expression. In addition, correlation analysis revealed that the expression of certain SNGs was closely associated with catechin accumulation, particularly epicatechin gallate (EGC) and epigallocatechin gallate (EGCG), highlighting their potential role in modulating tissue-specific catechin levels. Conclusions: Collectively, this study reveals a multilayered regulatory framework governing SNG co-expression and provides theoretical insights and candidate regulators for understanding metabolic regulation in tea plants. Full article