Search Results (691)

High temperature (HT) is a crucial environmental factor influencing floral pigmentation and ornamental quality in chrysanthemum (Chrysanthemum morifolium) by modulating anthocyanin biosynthesis. In this study, comparative transcriptome profiling was performed in two F₁ chrysanthemum lines (RO72 and RO99) under high-temperature stress to elucidate the molecular mechanisms behind heat-induced floral color fading. Analysis revealed extensive transcriptional reprogramming of genes associated with anthocyanin metabolism, hormonal signaling, and oxidative stress responses. While structural genes in the anthocyanin biosynthetic pathway (CHS, DFR, ANS, 3MAT and LDOX) were significantly downregulated, key glycosylation-related genes such as UFGT were upregulated, suggesting a compensatory mechanism that enhances pigment stabilization rather than de novo synthesis. This study identified a shift in the MYB–bHLH–WD40 regulatory complex, specifically the upregulation of transcriptional repressors (MYB62, MYB15) and downregulation of activators (MYB106, bHLH49), suggesting a suppressed anthocyanin accumulation. Simultaneously, genes associated with several signaling cascades such as ROS, ABA, and auxin–jasmonate signaling pathways were differentially expressed, suggesting that these alterations may contribute to the repression of pigment biosynthesis and color fading. Collectively, these results hypothesize that high temperature suppresses anthocyanin accumulation through a dual mechanism of transcriptional inhibition and hormonal modulation, while simultaneously promoting pigment stabilization via glycosylation. This study therefore provides fundamental insights into thermal regulation of floral pigmentation and identifies candidate genes and pathways potentially involved in heat-induced floral color fading in chrysanthemum. Full article

Rind color is an important quality trait in zucchini (Cucurbita pepo). As a core transcription factor in plant pigment biosynthesis, APRR2 plays a conserved yet mechanistically diverse regulatory role in the formation of rind color in various vegetables. However, the APRR2 transcription factor regulates rind color but has not been systematically identified in C. pepo. In this study, 50 APRR2 genes were defined by the presence of the conserved REC domain verified. These genes were identified and found to be unevenly distributed across the 20 chromosomes, primarily expanded through tandem duplication events. Phylogenetic and structural analysis classified these genes into three distinct subgroups, all featuring the conserved REC domain essential for pigment regulation but exhibiting variations in motifs and intron–exon structures. Promoter analysis revealed abundant light-responsive, hormone-responsive and stress-responsive elements that may contribute to environmental adaptation and photomorphogenesis. Crucially, transcriptome analysis during rind development (0 and 10 days after pollination) in green (GR) and white (WR) rind lines demonstrated profound functional divergence. Expression clusters indicated temporal shifts in metabolism and enriched “circadian rhythm-plant” and “photosynthesis” pathways in WR at 0 DAP. Specific APRR2 genes were tightly correlated with rind color. qPCR validation of the 24 selected APRR2 genes classified them into four trend groups based on the direction of expression change at 10 DAP. In total, 14 genes were upregulated in both GR and WR, 6 were downregulated in both lines, 1 was upregulated in GR but downregulated in WR, and 3 were downregulated in GR but upregulated in WR. Furthermore, protein–protein interaction prediction and yeast two-hybrid (Y2H) assays detected a physical interaction in yeast between a core APRR2 protein and a bHLH62 transcription factor, suggesting a potential interaction that may be involved in rind color regulation, pending in planta validation. The study first identified the members of the APRR2 gene family in C. pepo and conducted a bioinformatics analysis on them. The study establishes the molecular basis of APRR2 function and offers valuable resources for breeding improved C. pepo varieties. Full article

High-temperature stress impairs plant growth and alters secondary metabolism. Polymethoxyflavones (PMFs) are citrus-specific flavonoids with important nutritional benefits; however, their transcriptional responses to heat stress remain poorly understood. Here, five-month-old ‘Ponkan’ citrus seedlings were exposed to 40 °C for 6, 11, and 21 days. HPLC analysis showed that the accumulation of four major PMFs (sinensetin, nobiletin, tangeretin, and 5-demethylnobiletin) was significantly reduced in leaves under heat stress. RNA-seq identified 3424 differentially expressed genes shared across all three time points, which were enriched in pathways associated with microtubule cytoskeleton organization, cell cycle regulation, and glyoxylate and dicarboxylate metabolism. Further analysis of the PMF biosynthetic pathway revealed that 14 of 18 key structural genes, including CHS, CHI, FNSII, and OMT family members, were downregulated by heat treatment. In addition, several bHLH, AP2/EREBP, and MYB transcription factors, known regulators of flavonoid biosynthesis, exhibited expression patterns closely associated with PMF accumulation. RT-qPCR analysis validated the transcriptome results. Collectively, these findings suggest that heat stress suppresses PMF accumulation through coordinated repression of PMF biosynthetic genes and their potential regulators. This study provides new insights into the molecular basis of heat-responsive PMF metabolism and offers potential targets for maintaining citrus nutritional quality under elevated temperatures. Full article

Green tea quality is largely determined by the metabolite profile of fresh leaves. However, the time-of-day-dependent dynamics of these metabolites remain largely unknown in Xinyang Maojian (XYMJ), a premium Chinese green tea. In this study, we performed the first integrative transcriptomic and metabolomic analysis of Camellia sinensis cv. Xinyang 10 shoots (one bud and one leaf) sampled at 7:00, 13:00, and 18:00 under field conditions with light intensities of 19.2, 113, and 5.4 klx, respectively. We identified 525 differentially accumulated metabolites and 19,767 differentially expressed genes exhibiting distinct time-of-day-dependent patterns. Physiological measurements confirmed significant fluctuations in starch, soluble sugars, chlorophyll, relative water content, and polyphenols throughout the daytime. A key finding was a daytime carbon allocation trade-off: primary metabolism (starch biosynthesis, glycolysis, TCA cycle) peaked at 13:00, whereas secondary metabolism (flavonoids, theaflavins, phenolic acids, anthocyanins) dominated at 18:00, supported by strong negative correlations between primary and secondary metabolic modules. Chlorophyll and oligomeric catechins peaked at 7:00; theaflavins at 13:00; and starch, soluble sugars, theanine, and organic acids at 18:00. Light-responsive transcription factors (bZIP, NF-Y, HD-Zip, SPL, ARF, MADS) and other regulators (MYB, AP2/ERF, WRKY, NAC, GRAS, bHLH) exhibited time-specific expression, sequentially modulating flavonoid, caffeine, and theanine biosynthesis, along with specific gene modules including SS3/SS4 (starch synthesis), BAM3 (starch degradation), FBA1 (carbon fixation), CYP72A219 (terpenoid metabolism), and L7A (theaflavin biosynthesis). Evening-harvested leaves accumulated higher levels of theanine (umami) and soluble sugars (sweetness), whereas morning leaves were enriched in astringent catechins and flavonols. This multi-omics dissection of time-of-day-dependent metabolism in XYMJ tea provides a scientific basis for time-of-day harvesting strategies and graded processing of tea products. Full article

The microphthalmia-associated transcription factor (Mitf) family is central to melanocyte biology. Teleosts possess two mitf paralogs, mitfa and mitfb, yet their functional divergence remains incompletely understood. Here, we characterized the coding sequences, phylogeny, tissue distribution, developmental expression, cellular localization, and stress responsiveness of mitfa and mitfb in Congjiang natural mutant crucian carp (NMCC). Both genes encoded proteins containing the characteristic bHLH-ZIP domain. Phylogenetic analysis revealed that teleost mitfb clustered with the tetrapod mitf clade, indicating closer evolutionary affinity than mitfa. mitfa was predominantly expressed in skin and eyes, whereas mitfb showed broad tissue distribution. Both paralogs were constitutively expressed in skin across developmental stages; mitfa levels remained consistently lower than mitfb. Both transcripts were localized to melanocyte-containing regions of the skin. Transcriptomic analysis following high temperature (34 °C), UV radiation, and combined stress (48 h) revealed that mitfa was significantly upregulated by thermal stress, while mitfb showed no significant changes. Profiling of DNA damage response pathways uncovered extensive, stress-specific transcriptional remodeling. High temperature broadly suppressed apoptotic genes while upregulating tsc2, gadd45b, and cdip1; UV triggered widespread apoptotic gene activation. Combined stress elicited a hybrid signature. Notably, robust DNA Damage Response pathway remodeling contrasted with muted mitf responses, suggesting that DNA Damage Response-to-pigmentation signaling may operate predominantly at post-transcriptional levels. These findings reveal a substantial regulatory divergence between mitfa and mitfb, with mitfa maintaining a conserved melanogenic role while mitfb has been co-opted for broader functions in non-pigmentary tissues. The differential stress responses of the two paralogs further provide new insights into tissue-specific genotoxic stress signaling and melanogenic regulation in teleosts. Full article

Anther development is a complex and highly regulated process essential for pollen formation and reproductive development. However, systematic identification of genes exhibiting anther-preferential expression patterns through multi-tissue transcriptomic comparisons remains limited in cotton. In this study, comparative transcriptome analysis was performed using root, stem, leaf, and anther tissues of the cotton D8R line to identify candidate genes associated with anther development. Transcriptomic comparisons revealed extensive transcriptional differences between anthers and vegetative tissues, with 11,255 differentially expressed genes commonly identified among the three pairwise comparisons. Through stringent expression filtering, 843 putative anther-preferentially expressed candidate genes were identified, showing predominant expression in anthers and minimal expression in vegetative tissues. Nine representative genes, including GhGDSL_A08, GhGDSL_D08 esterase/lipase, GhPRX (class III peroxidase), GhAGL (MADS-box transcription factor), and GhTKPR1-like reductase genes, were further validated by qRT-PCR, confirming their anther-preferential expression patterns. Promoter analysis of the nine validated genes identified three recurrent sequence motifs among seven selected promoters, including CG-rich and G-rich sequences, which showed similarity to reported binding motifs of CAMTA, bHLH, and TCP transcription factors. Collectively, this study provides a valuable transcriptomic resource of anther-preferentially expressed candidate genes and potential cis-regulatory features, offering genetic resources for further investigation of cotton anther development and related reproductive processes. Full article

Syringa oblata is a renowned flowering shrub, yet the functional studies on the regulatory factors governing its flower color formation remain limited. In this study, a new MYB transcription factor, named SoMYB1, was isolated from the petals of Syringa oblata by the homologous cloning technique. The open reading frames of SoMYB1 was 705 bp in length. Amino acid sequence analysis showed that SoMYB1 contained the highly conserved R2 and R3 MYB domains. A quantitative real-time PCR analysis revealed that SoMYB1 was expressed tissue specifically in flowers. Ectopic expression of SoMYB1 induced anthocyanins accumulation in both vegetative and reproductive tissues of transgenic tobacco lines. Overexpression of SoMYB1 in tobacco enhanced the expression of NtAN2 (MYB) and NtAN1b (bHLH), and the expression of structural genes NtCHS, NtCHI, NtF3H, NtF3′H, NtDFR, NtANS, NtUFGT, and Nt3RT increased remarkably. The UPLC-MS/MS analysis of transgenic tobacco leaves showed that the heterologous expression of SoMYB1 significantly promoted the accumulation of anthocyanin metabolites, especially cyanidin, which accounted for more than 50% of the total anthocyanins in the transgenic tobacco lines. This study elucidates the molecular mechanism by which SoMYB1 positively regulates anthocyanin biosynthesis in S. oblata, providing theoretical and technical support for developing plant resources rich in cyanidin. Full article

Indole alkaloids are major bioactive compounds in Strobilanthes cusia. Although methyl jasmonate treatment can promote the accumulation of indole alkaloids in S. cusia, the transcriptional regulation remains unclear. In this study, the jasmonic acid responsive bHLH transcription factor ScMYC2 was cloned and characterized. It encodes a protein containing 477 amino acids, which features typical bHLH-MYC_N and HLH domains. ScMYC2 localized in the nucleus, showed tissue specific expression consistent with indole alkaloid accumulation, and was significantly induced by methyl jasmonate. Furthermore, the coding sequence of ScMYC2 was cloned into an expression vector and overexpressed in Arabidopsis thaliana via Agrobacterium-mediated transformation technology. Alkaloid metabolic analysis was performed on three homozygous A. thaliana lines (ScMYC2-OE1, OE2, OE3) stably transformed using UPLC-MS/MS. The results indicated that, compared with wild-type, 14 differential metabolites were detected in the A. thaliana lines overexpressing ScMYC2. Among them, the content of indole increased to 2.83-fold that of the wild-type, while the indole glycoside component indole-3-cyano-6-O-glucoside increased to 2.35-fold. Yeast two-hybrid screening identified 35 ScMYC2-interacting proteins, including UDP-glycosyltransferase, TOPLESS-related proteins, and E3 ubiquitin-protein ligase. BiFC assays further confirmed the in vivo interaction between ScMYC2 and ScUGT1. These findings suggest that ScMYC2 is associated with methyl jasmonate-responsive regulation of indole alkaloid biosynthesis and provides genetic resources for the cultivation of S. cusia with high medicinal value. Full article

Plant diseases impose major constraints on global crop productivity and pose a major threat to food security. Here, we review transcription factors (TFs) as central orchestrators of plant defense, consolidating recent advances in how these regulators connect pathogen perception to immune signaling, transcriptional reprogramming, and durable defense responses. Initially, we combined a literature-based synthesis with a natural language processing (NLP) analysis of 1647 PubMed abstracts published between 2021 and 2026 to map dominant and underexplored TF families associated with plant immunity. WRKY, MYB, AP2/ERF, bHLH/MYC, and NAC dominated the recent literature, whereas families such as NF-Y, Trihelix, PLATZ, TCP, and GRAS represent emerging regulatory actors. Across these and other families, TFs integrate pattern- and effector-triggered immunity, hormone crosstalk, chromatin dynamics, non-coding RNA regulation, post-translational modifications, and metabolic remodeling, in addition to cell-type-specific expression. Further evidence indicates that pathogens frequently manipulate TFs to weaken host defense, underscoring their central position in plant molecular physiology and plant-pathogen coevolution. The data emphasize that TF function is context-dependent and influenced by multilayered regulation, cell type, pathogen lifestyle, and host genetic background. This review provides a framework for understanding TFs in plant immune control and highlights TF-centered strategies for engineering durable crop resistance, along with future challenges. Full article

Vegetative propagation of recalcitrant woody species is a challenging task that limits biotechnological exploitation of economically relevant trees. In the case of chestnut, a severe decline in its ability to form adventitious roots is imposed during maturation. In previous reports, both juvenile-like and mature microshoots were subject to different hormonal treatments to gain deeper insights into the molecular processes driving the formation of adventitious roots while allowing us to increase our understanding of failed treatments. In the present work, RNAseq libraries from those treatments were used to develop a Weighted Gene Co-expression Network Analysis in order to identify gene modules correlated with the formation of adventitious roots. Hub genes within relevant modules were then used for promoter region analysis to identify transcription factor families that may play a role in the process by controlling the expression of the genes within those modules. bZIP and bHLH families in juvenile-like microshoots and WRKY and SBP families in mature microshoots were found to be particularly relevant for this developmental process. Specific transcription factors, like CsbHLH30 and CsbZIP44, seem to play key roles in the rooting process, while the activity of CsWRKY75 is putatively related to recalcitrant responses in mature shoots. Full article

Low-temperature stress severely restricts the growth, development, and ornamental value of Osmanthus fragrans Lour. However, the molecular mechanisms by which brassinolide (BR) and melatonin (MT) alleviate low-temperature-induced damage remain unclear. Here, O. fragrans branches were exposed to low-temperature stress (5, 0, −5, −10, −15, and −20 °C for 12 h) and treated with exogenous MT (50, 100, and 200 μM) or BR (0.5, 1, and 2 μM). An integrated approach combining phenotypic observation, physiological measurements, transcriptomics, and metabolomics was employed to elucidate the regulatory mechanisms underlying BR- and MT-mediated cold tolerance. The results showed that low-temperature stress significantly increased electrolyte leakage (EL), malondialdehyde (MDA), and hydrogen peroxide (H₂O₂) accumulation, while reducing superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Compared with the control, BR and MT treatments alleviated leaf chlorosis and wilting, reduced oxidative damage, and enhanced antioxidant enzyme activities. Integrated transcriptome–metabolome analyses demonstrated that BR and MT commonly activated phenylpropanoid and flavonoid biosynthesis, thereby promoting antioxidant metabolite accumulation, while suppressing α-linolenic acid and linoleic acid metabolism associated with stress-induced lipid remodeling. Network-based transcriptomic analyses identified transcription factors, including ARF, EIL, bHLH, and GRAS, as potential regulators of cold-responsive pathways. Furthermore, BR primarily regulated hormone-responsive networks, whereas MT mainly maintained redox homeostasis and metabolic reprogramming. These findings reveal the coordinated regulatory mechanisms underlying BR- and MT-mediated cold tolerance, providing potential targets for improving cold resilience in O. fragrans. Full article

Huperzine A (HupA) is a natural Lycopodium alkaloid known for its potent neuroprotective properties through the inhibition of acetylcholinesterase. Nevertheless, the limited understanding of its biosynthesis restricts its broader application. This study integrates full-length and second-generation transcriptomes with the quantification of HupA and its precursor, huperzine B, across various tissues of Huperzia serrata, the primary source plant. By employing phylogenetic clustering, expression profiling, and correlation analysis between gene expression and metabolite abundance, we identified 71 candidate genes from seven enzyme families potentially involved in the synthesis of the HupA backbone, including lysine/ornithine decarboxylases, copper amine oxidases (CAOs), chalcone synthases, and cytochrome P450 monooxygenases. Additionally, 28 genes from two families were identified for modification reactions, specifically 2-oxoglutarate/Fe(II)-dependent dioxygenases and caffeoyl shikimate esterases. Comparative analysis between young and mature leaves revealed 3801 genes with higher expression in young leaves, with 84 showing a high correlation with HupA content across seven families. Protein–protein interaction network analysis indicated possible interactions with transcription factors from the MYB, NF-YC, GRAS, ERF, BHLH, and SAP families. Functional validation of two candidate CAOs in planta confirmed their catalytic roles in amine/alkaloid metabolism. This study provides a theoretical foundation and a set of candidate genes for elucidating the biosynthetic pathway of HupA and related alkaloids in H. serrata. Full article

Plant specialized metabolites connect genetic programs and environmental responses with ecologically and economically valuable natural products. Their accumulation is rarely constitutive, varying instead with tissue identity, developmental stage, stress exposure, hormone signaling, and cellular storage capacity. This review examines basic helix-loop-helix (bHLH) transcription factors as regulatory switch points in plant specialized metabolism, with emphasis on the jasmonate-JAZ-MYC module. In resting tissues, JAZ repressors constrain MYC/bHLH activity; after wounding, herbivory, pathogen challenge, or elicitation, jasmonoyl-isoleucine triggers COI1-dependent JAZ turnover, releasing MYC factors to bind E-box/G-box motifs, recruit coregulators such as MED25, and activate biosynthetic genes or downstream transcription-factor cascades. Plant lineages have repeatedly adapted this regulatory logic to control terpenoids, alkaloids, phenylpropanoids, flavonoids, glucosinolates, phytoalexins, and related metabolites. Comparative examples include Arabidopsis sesquiterpenes and glucosinolates, Taxus taxanes, Artemisia artemisinin, Catharanthus terpenoid indole alkaloids, Salvia phenolic acids and tanshinones, Ginkgo terpene trilactones, rice diterpenoid phytoalexins, and cotton gossypol. Across these systems, bHLH output depends on dimer choice, promoter grammar, chromatin accessibility, hormone crosstalk, partner transcription factors, and cell-type competence. Six shared principles emerge: signal gating, topology matched to pathway architecture, partner-dependent promoter decoding, spatial competence, feedback rheostats, and evidence-dependent transferability. We further discuss evidence standards, multi-omics-guided factor discovery, miRNA-mediated post-transcriptional control, and engineering strategies for crop defense, food quality, medicinal-metabolite production, and synthetic biology. Unlike pathway- or MYC2-centered surveys, this review organizes the literature within a direct–cascade–hybrid framework that integrates promoter grammar, spatial competence, storage anatomy, and an explicit evidence hierarchy. Full article

Drought stress significantly limits agricultural productivity and threatens food security. The identification of drought tolerance genes and the dissection of their regulatory networks in crops are crucial for ensuring future food production. The BRI1-EMS1 suppressor (BES1)/brassinazole-resistant 1 (BZR1) family is a kind of plant-specific transcription factor that regulates growth, development, and stress responses in plants. Here, the maize ZmBES1/BZR1-7 gene was cloned and transformed into Arabidopsis and rice to characterize plant phenotypes under drought stress conditions. Sequence analysis revealed that the ZmBES1/BZR1-7 protein contains a conserved basic helix-loop-helix (bHLH) domain, localizes to the nucleus, and exhibits transcriptional activation activity. Expression profiling revealed that ZmBES1/BZR1-7 is induced by drought stress in maize. Overexpression of ZmBES1/BZR1-7 significantly enhanced drought tolerance in both transgenic Arabidopsis and rice. Under drought stress conditions, all transgenic lines showed higher survival rates and relative water content (RWC), increased root length, reduced relative electrolyte leakage (REL) and malondialdehyde (MDA) content, as well as higher yield of transgenic rice than the wild type. Integrated analyses of RNA-seq and qRT-PCR assays demonstrated that ZmBES1/BZR1-7 modulates transcription of stress-responsive genes to enhance drought tolerance. Collectively, the study provides insights into the molecular mechanisms by which ZmBES1/BZR1-7 mediated drought stress response in maize. Full article

Background/Objectives: Whole-genome duplication (WGD) and transposed duplication (TRD) are two principal evolutionary drivers of plant genome expansion, yet the molecular mechanisms underlying their divergent co-expression patterns remain poorly characterized. Methods: In this study, based on the reference genome of tea plant (Camellia sinensis ‘Yunkang 10’, YK10), we integrated publicly available transcriptomic, ATAC-seq, H3K27ac ChIP-seq, whole-genome bisulfite sequencing (WGBS), and SNP data from eight tissues and performed a multi-layered analysis of co-expression divergence across 4071 WGD and 10,174 TRD gene pairs. Results: WGD gene pairs exhibited significantly higher co-expression rates (44.3%) than TRD pairs (33.0%), with gene length and sequence similarity jointly promoting co-expression. Chromatin accessibility and H3K27ac modification were each positively correlated with expression and co-expression; however, under equivalent chromatin accessibility conditions, TRD gene expression remained systematically attenuated, and this reduced expression state was significantly associated with elevated levels of CG, CHG, and CHH methylation, suggesting that these epigenetic marks may collectively participate in the transcriptional repression of TRD genes. Promoter-proximal SNPs exerted disproportionately deleterious effects on TRD co-expression, demonstrating that the combined effects of genetic variation and epigenetic modifications are associated with enhanced transcriptional divergence. Weighted gene co-expression network analysis (WGCNA) revealed that WGD modules showed significant associations with EC, GC, and EGC accumulation, whereas WRKY and bHLH transcription factors in the TRD MEblue module exhibited strong associations with EGCG and ECG. Conclusions: This study systematically characterizes multi-omics association patterns related to duplicate gene co-expression divergence, providing insights into potential hierarchical regulation. It offers mechanistic clues for catechin metabolic regulation and provides candidate targets for metabolite-directed breeding. Full article