Search Results (4,134)

Anthracnose, caused by Colletotrichum spp., is a major foliar disease limiting rubber tree (Hevea brasiliensis) productivity. To uncover resistance mechanisms, we compared resistant and susceptible germplasm using an integrated framework combining leaf structural analysis, physiological defense profiling, and transcriptome sequencing. Resistant germplasm exhibited lower stomatal density and more compact mesophyll, likely restricting pathogen entry and within-leaf spread. Following inoculation, resistant accessions showed stronger antioxidant responses, with higher activities of superoxide dismutase (SOD) and peroxidase (POD), and elevated phenylpropanoid-related enzymes, including polyphenol oxidase (PPO) and phenylalanine ammonia-lyase (PAL), peaking at 24–48 h post inoculation. These responses were accompanied by enhanced reactive oxygen species (ROS) accumulation (H₂O₂) but reduced lipid peroxidation (malondialdehyde), indicating efficient oxidative stress regulation. Microscopic observation revealed delayed infection progression and postponed differentiation of infection structures in resistant germplasm. Transcriptomic analysis further demonstrated that differentially expressed genes were mainly enriched in pathways related to signal transduction and secondary metabolism, particularly phenylpropanoid metabolism and related secondary metabolic pathways. Together, these results suggest that anthracnose resistance is mediated by coordinated structural barriers, redox homeostasis, and transcriptional regulation of defense networks. This study provides a mechanistic framework for resistance-oriented breeding and the utilization of resistant germplasm in rubber tree. Full article

Flower color is a key ornamental trait in Nobile-type Dendrobium, yet the molecular basis underlying purple flower formation remains poorly understood. In this study, a white-flowered paternal cultivar and its purple-flowered filial line were used to investigate the regulatory mechanism of purple floral pigmentation. Comparative phenotypic analysis showed that floral color divergence was established early during flower development, and anthocyanidin profiling of full-bloom petals revealed that purple flowers accumulated substantially higher levels of most anthocyanidins than white flowers, with delphinidin- and cyanidin-derived anthocyanidins together accounting for 80.26% and 94.56% of the total anthocyanidins in white- and purple-flowered materials, respectively. Transcriptome profiling identified a total of 21,235 differentially expressed genes (DEGs), with significant enrichment of phenylpropanoid- and flavonoid-related pathways, and MYB transcription factors prominently represented among the candidate regulators across the three comparison groups. Among them, DntMYB1 was identified as a C1 subgroup R2R3-MYB associated with floral pigmentation, and transient overexpression assays in Phalaenopsis hybrid V3 and a Nobile-type Dendrobium hybrid supported its positive role in visible purple pigmentation. By integrating RNA-seq and DAP-seq analyses, we identified 3205 candidate downstream targets of DntMYB1 and established a DntMYB1-centered regulatory module. Among these candidates, one Dnt4CL1 gene and one DntF3′H1 gene were validated as robust direct targets of DntMYB1 through yeast one-hybrid, EMSA, and dual-luciferase assays. These findings suggest that DntMYB1 is associated with purple flower formation by coordinately regulating both upstream precursor metabolism and downstream anthocyanin biosynthesis, providing new insight into the molecular regulation of flower color in Nobile-type Dendrobium and useful candidate genes for ornamental trait improvement. Full article

Heterosis utilization is an effective strategy to improve crop yield, stress resistance, and quality, and has been widely used in crop breeding. Soybean is an important oil and protein crop worldwide with heterosis, but the genetic basis of soybean heterosis remains largely unclear. Whole-transcriptome analysis provides a new technical approach to explore the molecular mechanism of heterosis. In this study, HYBSOY2, a registered soybean hybrid variety with the strongest heterosis in China, together with its female parent JLCMS47A, maintainer line JLCMS47B, and male parent JLR2, were used as experimental material. Whole-transcriptome sequencing was performed using RNA extracted from seedling leaves. After mapping high-quality reads to the soybean reference genome, 57 co-expressed differentially expressed genes (DEGs) were identified in HYBSOY2 compared with both JLCMS47B and JLR2. GO and KEGG enrichment analyses shows that these DEGs were mainly enriched in ADP binding, oxidoreductase activity, fatty acid elongation, and pyruvate metabolism. A total of 787 transcription factors were identified between HYBSOY2 and its parents, most of which shows parental expression-level dominance, with the MYB family accounting for the highest proportion. In addition, 10 differentially expressed lncRNAs were detected between HYBSOY2 and its parents. In the comparison between HYBSOY2 and JLCMS47B, 18 differentially expressed miRNAs were identified, among which up-regulated miR396d functions in promoting leaf development and enhancing drought tolerance. In the comparison between HYBSOY2 and JLR2, 20 differentially expressed miRNAs were found, including down-regulated miR172c which is involved in flowering promotion. A total of 12 DEGs were further verified by qRT-PCR, which may be closely related to soybean heterosis. This study provides a comprehensive transcriptomic profile at the seedling stage of the hybrid soybean and offers valuable information for hybrid soybean breeding. These results lay a foundation for further revealing the molecular mechanism underlying soybean heterosis. Full article

RNA-binding proteins (RBPs), specifically those containing K Homology (KH) domains, are critical for post-transcriptional regulation and abiotic stress responsiveness in plants. However, systematic characterization of the KHD gene family in potato (Solanum tuberosum L.) remains unreported. Here, we identified 83 StKHD genes unevenly distributed across 12 potato chromosomes, which clustered into five subgroups with conserved gene structures and motif compositions. Most StKHD proteins were predicted to localize to the nucleus, confirmed experimentally for StKHD-41 via transient expression in Nicotiana benthamiana. Collinearity analysis revealed 23, 22, 19, and 4 orthologous pairs with Arabidopsis, tomato, pepper, and tobacco, respectively. Promoter analysis showed distribution of hormone- and stress-responsive cis-elements, while interaction network analysis predicted 39 StKHDs interacting with 137 proteins. Tissue-specific profiling revealed broad expression of several StKHDs, and specific members displayed consistent expression changes under abiotic stresses, correlating with TC-rich repeat enrichment. RT-qPCR validated that StKHD-41 responded rapidly to JA, moderately to SA/GA, and slowly to ABA, with significant upregulation under drought and salt stress by day 2. This study provides a foundation for understanding StKHD functions and identifies targets for enhancing potato stress resistance. Full article

GRAS transcription factors are essential for plant growth and stress adaptation, yet they remain uncharacterized in the medicinal herb Coptis chinensis. To address this gap, we performed a genome-wide identification of the GRAS family and investigated its transcriptional responses to temperature and light stress, integrating comparative transcriptomics with promoter analysis to explore potential co-expression with bZIP factors. A total of 48 CcGRAS genes were identified and found to be unevenly distributed across nine chromosomes. Expression profiling revealed that CcGRAS genes are markedly more responsive to varying light intensities (476, 8340 lx) than to temperature stresses (15, 35 °C), relative to controls (2060 lx for light, 25 °C for temperature). Co-expression analysis uncovered an underground tissue-specific module in which CcbZIP16 is upregulated with four CcGRAS genes (CcGRAS11, CcGRAS12, CcGRAS43, CcGRAS48) that are coordinately upregulated specifically under low-light conditions. The promoters of these co-expressed genes are significantly enriched in canonical light-responsive cis-elements, providing correlative evidence for their coordinated transcriptional control. Together, these findings identify a tissue-specific GRAS-bZIP co-expressed gene set under light stress and suggest a candidate regulatory framework for dissecting light adaptation mechanisms. This work also provides a foundation for targeted genetic improvements in stress tolerance and alkaloid biosynthesis in this important medicinal plant. Full article

Ovarian endometriosis (OE) is a chronic, inflammatory gynecological disorder associated with sterility and an elevated risk of ovarian cancer. Despite its high prevalence, the complex molecular mechanisms governing OE pathogenesis remain poorly investigated. We conducted a comprehensive histopathological and molecular investigation of OE in a cohort of 188 Saudi women (88 patients with OE and 100 healthy controls) using histopathological, qRT-PCR, immunostaining, and Western blot techniques. Histopathological analysis confirmed significant stromal fibrosis and chronic inflammation in endometriotic lesions. Gene expression profiling revealed a pro-proliferative, anti-apoptotic signature, marked by the upregulation of PTTG1 and the downregulation of TNFRSF10D, CDK4, and CDKN1A. Interestingly, we identified a post-transcriptional regulatory paradox in the inflammatory response: while IL-6 mRNA was significantly upregulated, its corresponding protein level was downregulated, suggesting a novel, tightly controlled mechanism to limit excessive local inflammation. Besides the increased autophagic activity and decreased Ubiquitin mRNA levels, epigenetic dysregulation was prominent, characterized by the upregulation of DNA methyltransferase DNMT3B and the downregulation of the histone variant H3.1. These findings elucidate novel molecular pathways underlying OE pathogenesis as evidenced by a post-transcriptional paradox in IL-6 expression, and uncover key dysregulations spanning cell proliferation, apoptosis, inflammation, autophagy, and epigenetic regulation. Full article

Staphylococcus aureus (S. aureus) bovine mastitis is a significant public health issue. Despite enormous efforts, important gaps remain regarding host–microenvironmental factors. How intramammary reduced oxygen modulates S. aureus transcription in bovine mammary epithelial cells (MECs) remains unclear. We examined oxygen-associated transcriptional changes in a bovine-mammary adapted S. aureus clone following internalization into MECs and identified functional category enrichments under Normal-O₂ and Reduced-O₂ exposures. Bovine MAC-T monolayers were infected with a dominant bovine mastitis isolate under Normal-O₂ or Reduced-O₂ conditions. Triplicate infection experiments were performed for each oxygen condition. Each condition included matched non-reacted bacterial controls maintained under the same gas condition but without MAC-T exposure serving as the reference condition for expression calling. RNA was extracted and profiled using a high-throughput qRT-PCR platform covering genome-wide loci. Expression calls were mapped to curated BioQT roles and interpreted descriptively. Results indicated 211 loci were upregulated and 99 were downregulated under Normal-O₂ conditions, versus 53 upregulated and 35 downregulated under Reduced-O₂ conditions, relative to their non-reacted controls. Under Normal-O₂ conditions, regulated loci covered multiple functional roles, including cellular processes, transport/binding proteins, regulatory functions, and energy metabolism with downregulated loci enriched in transport/binding and cell-envelope categories. Under Reduced-O₂ conditions, upregulated loci were abundant in cellular process annotations dominated by pathogenesis/toxin-related functions, whereas downregulated loci were enriched in nucleotide biosynthetic and DNA/cell division categories. Thus, this reveals oxygen-associated shifts in the transcriptional response of intramammary S. aureus in MAC-T cells. Normal-O₂ conditions were associated with broader category representation, whereas Reduced-O₂ conditions yielded a narrower distribution enriched for selected toxin/pathogenesis- and iron/cation-associated annotations. These oxygen-linked transcriptional-shifts highlight candidate pathways for the intramammary adaptation of S. aureus, potential diagnostic markers, anti-virulence strategies, and targeted therapeutics. Full article

Transcriptome profiling has been widely used to dissect the molecular mechanisms underlying plant responses to environmental stresses, yet the extent to which RNA changes reflect functional protein levels remains unclear. Here, we performed an integrated multi-omics analysis of the transcriptome, proteome, phosphoproteome, and acetylome in rice during a drought–rewatering cycle. We first identified 5449 differentially expressed genes (DEGs) and 525 differentially expressed proteins (DEPs) under drought stress, followed by 4340 DEGs and 328 DEPs upon rewatering, which underpinned an extensive remodeling of photosynthetic and metabolic pathways. Temporal clustering of transcriptomic and proteomic data then delineated five distinct expression patterns for both transcripts and proteins, uncovering transcriptional and translational strategies ranging from rapid reversal to persistent stress adaptation. Despite the observed coherence in some expression clusters, we nonetheless uncovered widespread transcriptome–proteome discordance, with a substantial fraction of gene–protein pairs exhibiting uncorrelated abundance changes. Remarkably, the observed discordance is quantitatively associated with the dynamic nature of post-translational modifications, including phosphorylation and acetylation, which act as key post-transcriptional tuners to independently regulate protein abundance—particularly for components of photosynthesis and energy metabolism—enabling plants to dynamically balance stress tolerance with the maintenance of core physiological functions. Our research delves into the intricate and often distinct regulatory networks that span transcriptional, translational, and post-translational levels, extending beyond a singular transcriptional focus. Full article

Glutathione S-transferases (GSTs) are an important family of enzymes involved in plant detoxification, maintenance of redox homeostasis, and responses to abiotic stresses. However, the evolutionary characteristics and functional roles of the potato GST pan-gene family have not yet been systematically investigated at the pan-genome level. In this study, based on high-quality potato genomes constructed from 45 diploid accessions, GST gene family members were systematically identified, and their evolutionary features and expression patterns were analyzed. Phylogenetic analysis classified the GST family into six subgroups, among which the soft-core gene StGST7 and the near-core genes StGST8 and StGST16 were assigned to the Phi and Tau subgroups, respectively. Selection pressure analysis indicated that five StGST genes may have undergone positive selection, whereas most of the remaining genes were mainly subjected to purifying selection. Structural variation significantly affected the expression of StGST42 and the conserved domains of its encoded protein. Expression profiling revealed that GST family members exhibited clear tissue-specific expression patterns and responded differentially to drought, salt, high temperature, ABA, and IAA treatments. Co-expression network analysis revealed significant positive and negative correlations between multiple transcription factors and StGST gene expression, suggesting their potential involvement in the coordinated regulation of StGST genes. Further analyses demonstrated that StGST7 was significantly differentially expressed under multiple stress conditions, and its heterologous expression enhanced yeast tolerance to salt and drought stress. This study revealed the evolutionary characteristics and potential functions of the potato GST gene family and provides a theoretical basis for elucidating the molecular mechanisms underlying its regulation of environmental adaptation. Full article

Comparative genomics in bees has revealed correlations between transcription factor (TF) binding site (TFBS) abundance and social complexity; however, the activity of TFBS within enhancers is not experimentally examined during the caste developmental processes. In this study, we performed cap analysis of gene expression (CAGE) during worker metamorphosis in the honeybee Apis mellifera to identify TFBSs within active enhancers and to decipher the regulatory relationships between these enhancers and their target genes. We identified 17,349 transcription start sites (TSSs) and 842 candidate enhancers. Using CAGE profiles, we classified these elements into five clusters based on their expression patterns. Notably, genes associated with the canonical metamorphic regulators, Broad complex (Br-c) and E93, were found in specific clusters. By integrating correlations between enhancer and TSS activities with motif enrichment analysis, we identified 15 transcription factor–enhancer–TSS regulatory relationships. Among these, tramtrack (ttk) binding sites were identified in five enhancers associated with four target genes, including Br-c. Analysis of sequence conservation revealed that, across all target genes examined, perfect conservation of ttk binding sites was restricted to the genus Apis. These results suggest that gene regulatory relationships during worker metamorphosis are lineage-specific within the Apis genus. Full article

Oocyte maturation is a pivotal event in teleost reproduction that directly determines egg quality, fertilization success, and the developmental competence of early embryos. However, the transcriptional and post-transcriptional regulatory mechanisms operating within oocytes during maturation in marine teleosts remain poorly understood. In the present study, the orange-spotted grouper (Epinephelus coioides), an economically important marine aquaculture species, was used as a model. Oocytes at four distinct maturation stages were obtained by microscopically removing the surrounding follicular layers, followed by integrated mRNA-seq and miRNA-seq analyses to characterize the molecular regulatory landscape underlying oocyte maturation and hydration. The results showed that, as maturation progressed, oocyte diameter and wet weight increased significantly, accompanied by a marked decrease in Na⁺ content, a significant increase in K⁺ content, and the continuous accumulation of most free amino acids, indicating the gradual establishment of an osmotic basis favorable for oocyte hydration. Transcriptomic analysis further revealed extensive transcriptional remodeling during both the early and late phases of maturation. Differentially expressed genes were significantly enriched in pathways related to oocyte meiosis, cytokine signaling, lipid metabolism, DNA replication, cell cycle regulation, ribosome biogenesis, spliceosome function, oxidative phosphorylation, and mitochondrial activity, suggesting that oocyte maturation is a dynamic process characterized by a shift from basal growth maintenance to metabolic reprogramming, maternal transcript remodeling, and terminal maturation responses. miRNA profiling identified a large number of stage-specific differentially expressed miRNAs, including let-7d-5p, miR-22a-3p, and novel-miR-20/27/118, whose predicted target genes were mainly enriched in ribosome-related pathways, oxidative phosphorylation, DNA replication, transcriptional regulation, and signal transduction. Moreover, the miRNA–TF–mRNA regulatory network demonstrated that miRNAs may not only directly repress target genes, but also mediate hierarchical regulatory cascades through transcription factors, thereby coordinately participating in cell cycle progression, cytoskeletal remodeling, vesicular transport, and immune- and cell communication-related responses. Collectively, this study provides the first systematic temporal atlas of mRNA and miRNA regulation during oocyte maturation and hydration at the oocyte level in a marine teleost, thereby deepening our understanding of the molecular basis of meiotic resumption and egg quality formation, and offering valuable theoretical support for the optimization of artificial breeding and the identification of key molecular targets in grouper reproduction. Full article

Ricinus communis is the primary commercial source of ricinoleic acid (RA), a hydroxy fatty acid (HFA) synthesized by the fatty acid hydroxylase FAH12, which evolved from the Δ12-oleate desaturase FAD2. However, the evolutionary origins and diversification mechanisms of FAH12 across HFA-producing plants remain poorly understood. Here, we performed a comprehensive cross-species analysis of FAH12 and FAD2 homologs by integrating sequence analysis, structural modeling, phylogenetic reconstruction, and transcriptomic profiling. Across all currently available HFA-producing plant lineages, we found that amino acid substitutions associated with hydroxylase activity exhibit strong lineage-specific patterns rather than universal conservation, indicating multiple evolutionary solutions to catalytic divergence. Phylogenetic and synteny analyses further suggest that FAH12 arose independently from ancestral FAD2 duplications in distinct plant lineages, supporting a model of recurrent independent neofunctionalization. Transcriptomic and qRT-PCR analyses reveal that FAH12 exhibits a highly specialized endosperm-preferential expression pattern and is embedded within a regulatory network that is partially decoupled from that of FAD2. Together, these findings demonstrate that FAH12 evolution is driven by recurrent independent origins coupled with transcriptional specialization, providing a framework linking structural variation, evolutionary history, and regulatory divergence for understanding and engineering hydroxy fatty acid biosynthesis in plants. Full article

Background/Objectives: Parkinson’s disease (PD) is associated with systemic molecular alterations that extend beyond the central nervous system, including changes in peripheral blood transcriptomic profiles. While prior studies have focused predominantly on coding-gene expression, the longitudinal behavior of the peripheral blood repeatome following clinical diagnosis remains poorly characterized. Here, we investigated temporal remodeling of repetitive-element transcription over 36 months post-diagnosis by integrating repeat subfamily- and locus-specific analyses. Methods: Repeatome expression was quantified using SalmonTE and DESeq2 in peripheral blood RNA-seq data from 1560 PD and control individuals at diagnostic baseline (BL) and four follow-up visits (6, 12, 24, and 36 months). Differential expression was assessed at the subfamily level, with additional locus-specific validation in a representative subset. Results: A total of 259 repeat subfamilies were differentially expressed (padj < 0.05), of which 224 (86.5%) were already detected at baseline. Enrichment of differential expression was significantly higher at baseline than at later visits (odds ratio = 30.9, p < 2.2 × 10⁻¹⁶), with limited additional divergence over time. Longitudinal analyses revealed non-linear trajectories in selected repeat families, including Alu and SVA subfamilies. Locus-specific analysis identified 237 significantly regulated elements, demonstrating heterogeneous, site-specific transcriptional changes, including clusters of differentially expressed loci and instances within PD-relevant genomic regions (e.g., SNCA and IKZF2). Conclusions: Peripheral blood repeatome expression differs between PD and control groups, with the dominant signal established at clinical diagnosis and modest longitudinal modulation thereafter. Integration of locus-level analysis indicates that subfamily level patterns arise from discrete genomic events rather than uniform regulation. These findings support a model of systemic, immune-associated transcriptomic remodeling in circulating blood cells and position the peripheral repeatome as a dynamic framework for biomarker discovery and future mechanistic investigation. Full article

Introduction: Post-infectious bronchiolitis obliterans (PIBO) is a rare and severe chronic lung disease. Our goal was to characterize respiratory epithelium in children with PIBO, which remains unexplored, using an ex vivo model culture. Methods: Proximal bronchial biopsies from children with PIBO and reconstituted bronchial epithelium from PIBO patients (n = 3) and controls (n = 17) were analyzed using an air–liquid interface culture model. Epithelial cell composition, barrier integrity, and mediator production, including mucins, inflammatory and antiviral responses, were assessed in this pathological and functional approach. Results: Epithelial thickness was assessed in PIBO biopsies. Ex vivo reconstituted PIBO epithelia appeared to exhibit comparable cohesion and cell composition to controls. Mucin expression and secretion were likewise similar between groups. PIBO epithelial might have displayed reduced IL-33 transcript levels and decreased TSLP secretion, whereas IFN-λ1, IFN-λ2-3 and IFN-β secretion could have been elevated. No differences were detected in remodeling markers (MMP-9 and YKL-40). Conclusions: In summary, ex vivo model of PIBO epithelia suggested that the epithelium may preserve structural characteristics and mucin production, without evidence of remodeling. However, PIBO epithelial cells may have a distinct immune profile, with lower alarmin expression and higher interferon secretion. This could indicate a tendency toward enhanced antiviral response rather than structural changes. These preliminary results need to be confirmed in larger cohorts. Full article

Basic leucine zipper (bZIP) transcription factors are widely involved in plant growth, development, environmental adaptation, and secondary metabolism. However, the bZIP gene family in Taxus yunnanensis has not been systematically characterized, and its potential involvement in shading-responsive regulation of paclitaxel biosynthesis remains unclear. In this study, a genome-wide analysis was performed to identify and characterize the bZIP family in T. yunnanensis. Phylogenetic analysis, conserved motif and domain identification, promoter cis-element analysis, chromosomal localization, and expression profiling were conducted to investigate their structural features and regulatory potential. A total of 18 TyubZIP genes were identified and classified into 10 subfamilies. These genes exhibited variation in physicochemical properties but showed conserved structural features and nuclear localization. Promoter analysis revealed abundant light-responsive, hormone-related, and stress-related cis-elements. Expression profiling indicated tissue-specific expression patterns and diverse responses to shading treatment. WGCNA further identified candidate TyubZIP genes potentially associated with paclitaxel biosynthesis. Among them, TyuHY5 was selected for functional analysis. Subcellular localization and transcriptional assays demonstrated that TyuHY5 can bind to the promoter of TyuDBTNBT and positively regulate its activity. These findings provide the first genome-wide characterization of the bZIP family in T. yunnanensis and identify TyuHY5 as a shading-responsive candidate regulator of paclitaxel biosynthesis, providing insights that may inform the genetic improvement and cultivation strategies of Taxus for enhanced paclitaxel production. Full article