Search Results (15,421)

Alternative splicing (AS) is a significant post-transcriptional regulatory mechanism that facilitates environmental adaptation in fungi. However, the conservation of this mechanism and its host specificity during the infection of various hosts by B. cinerea remain ambiguous. This study utilized strand-specific RNA sequencing to perform a comparative analysis of genome-wide AS patterns during the infection of tomato and strawberry by B. cinerea. A comparative analysis identified a total of 1714 AS events and 1130 associated genes across the two hosts, alongside a significant number of host-specific events. Common alternatively spliced genes were predominantly enriched in processes related to gene expression regulation and signal transduction, whereas host-specific genes displayed distinct functional enrichment characteristics and temporal dynamics in their Percent Spliced In (PSI) patterns. Notably, introns linked to AS were generally longer than those associated with constitutive splicing and predominantly featured canonical GT-AG splice boundaries. Furthermore, the magnitude of PSI changes in host-specific events was greater than that observed in common events. This study reveals that B. cinerea exhibits both conserved and host-dependent AS regulatory programs, providing new insights into its post-transcriptional regulatory plasticity during the infection of various plant hosts. Full article

Philadelphia chromosome-positive (Ph+) B-cell acute lymphoblastic leukemia (ALL), driven by the BCR-ABL1 fusion, remains highly aggressive, with poor prognosis despite tyrosine kinase inhibitor (TKI) therapy. Aberrant PI3K/Akt/mTOR pathway activation contributes to resistance, warranting identification of predictive kinase biomarkers. To identify and validate critical phospho-kinase markers within the PI3K/Akt/mTOR axis as candidate adaptive signaling nodes and exploratory prognostic markers in Ph+ B-ALL. Network pharmacology using STRING and Cytoscape mapped the protein–protein interactions, identifying high-centrality nodes. Functional enrichment analyses (GO/KEGG) were then performed via ShinyGO. Experimentally, phospho-kinase arrays profiled 39 kinase phosphorylation sites in Ph+ B-ALL cells (SUPB-15) treated with PI3K/Akt/mTOR inhibitors (Rapamycin, GDC-0941, GSK690693, Perifosine). Gene expression was validated by RT-qPCR in 100 Ph+ B-ALL patients and protein validation employed Western blot in 50 patient samples with 15 and five healthy controls, respectively. Network analysis identified CREB1 and GSK3 isoforms as central hub regulators. Phospho-kinase profiling revealed p-CREB (Ser133) phosphorylation upregulation following Perifosine, GDC-0941, and Rapamycin treatment, with no statistically significant change after GSK690693. p-GSK3α/β (Ser21/9) phosphorylation showed a statistically significant increase after Perifosine, with non-significant trends after GDC-0941, and a significant reduction following Rapamycin. Hierarchical clustering then divided proteins into four distinct clusters positioning CREB1 in cluster 3 and GSK3α/β in cluster 2 as candidate adaptive response markers based on their phosphorylation profiles. RT-qPCR demonstrated marked downregulation of GSK3α (approximately 71%), GSK3β (63%), and CREB1 (65%) transcripts in patients versus controls, with even greater suppression seen in cell lines. Conversely, Western blot revealed a significant 2.49 fold elevated p-CREB (Ser133) (β = 1.317, p = 0.000347) and a phospho-GSK3α/β (Ser21/9) level that did not differ significantly between patients and controls (β = 0.467, p = 0.466), revealing mRNA–protein discordance indicative of compensatory post-transcriptional and post-translational regulation. These findings represent treatment-associated and disease-state associations between altered phosphorylation states and the Ph+ B-ALL context; functional validation remains an essential next step. mRNA–protein discordance with transcriptional downregulation (63–71%) contrasting with elevated p-CREB levels (2.49-fold, p = 0.000347) suggests post-translational compensatory mechanisms under therapeutic pressure. CREB1 and GSK3 isoforms emerge as central network nodes that might potentially mediate adaptive resistance, although functional validation is required. It should be noted that the evidence presented is associative rather than causal and a direct link between the observed phosphorylation changes and clinical drug resistance has not been established in this study. Sustained CREB phosphorylation despite PI3K/Akt/mTOR inhibition implicates alternative kinase pathways (MAPK/ERK, CaMK), supporting rational combination therapy strategies. These findings position p-CREB and p-GSK-3α/β as candidate biomarkers, highlighting the value of phospho-proteomics over transcriptomics alone in capturing pathway activation. Multi-omics integration may prove essential for overcoming adaptive resistance in ALL patients. Full article

Tocopherols are essential lipid-soluble antioxidants that play important roles in plant protection against oxidative stress and are closely connected with isoprenoid metabolism. To the best of our knowledge, this is the first report of stable constitutive expression of Arabidopsis thaliana VTE2 (AtVTE2) in flax (Linum usitatissimum L.) and its effects on plant metabolism and development. As a dual-purpose oil and fibre crop, flax combines PUFA-rich seeds with industrially important fibre-rich stems, providing a useful system for assessing the broader consequences of antioxidant-pathway engineering. Three independent transgenic lines were characterized by RT-qPCR analysis of genes associated with tocopherol, MEP, MVA, and carotenoid biosynthesis, targeted metabolite profiling, antioxidant-capacity assays, field phenotyping, and biochemical and spectroscopic analyses of mature straw. Three independent transgenic lines were characterized using gene-expression analyses, metabolic profiling, antioxidant assays, phenotypic evaluation, and biochemical analyses of mature stems. Constitutive AtVTE2 expression was associated with α-tocopherol accumulation and was accompanied by coordinated transcriptional changes in genes associated with the plastidial methylerythritol phosphate and cytosolic mevalonate pathways. These changes were associated with modifications in isoprenoid and phenylpropanoid metabolism, enhanced antioxidant capacity in selected transgenic lines, and altered plant architecture under field conditions. In mature straw, transgenic plants exhibited changes in phytosterol composition, lignin accumulation, and pectin distribution, whereas cellulose content remained unchanged. FT-IR spectra retained the same principal bands but showed differences in the relative intensities of selected cell-wall-associated bands. Collectively, these findings demonstrate that constitutive AtVTE2 expression is associated with tissue-dependent metabolic responses extending beyond vitamin E accumulation and affecting interconnected pathways involved in secondary metabolism, antioxidant capacity, and cell-wall organization. Full article

Skin pigmentation in teleosts is a complex process governed by molecular and cellular mechanisms during development. In this study, we investigated the pigmentation process in the tomato clownfish (Amphiprion frenatus) using an integrated approach combining histological analysis and transcriptomics (RNA-Seq and Ribo-Seq). Histological examination revealed the stepwise differentiation of chromatophores during post-embryonic development. Transcriptomic profiling at 14 days post-hatching (dph) identified extensive changes in transcript abundance, with 2063 of 2667 differentially expressed unigenes (DEUs) upregulated relative to hatching. These genes predominantly governed innate defense, digestion, and early pigmentary development, driven by the enrichment of Gene Ontology (GO) terms including inflammatory response, digestion, and developmental pigmentation. Integration of transcriptomic and Ribo-Seq datasets identified widespread discordance between transcript abundance and ribosome-protected fragment (RPF) abundance. These discordant expression patterns suggest candidate post-transcriptional regulatory events during skin pigmentation development. Quantitative PCR analysis at 23 and 45 dph confirmed the dynamic upregulation of genes involved in cell proliferation (myc, pcna), pigment transport (myo5a, rab38), and pigment cell signaling (mchr1). These findings suggest that skin pigmentation is associated with the selected transcript-abundance differences in A. frenatus. This study offers new insights into the molecular basis of chromatophore development and pigment pattern formation in coral reef fish species. Full article

Apple is notoriously difficult to propagate by cuttings, which severely restricts the large-scale production of own-rooted dwarfing rootstocks. ‘Y-1’ is a promising apple dwarfing rootstock that has been newly bred in China, but its recalcitrant rooting limits its application as an own-rooted stock. In this study, three-year-old ‘Y-1’ stock plants were subjected to three shading rates (40%, 60% and 80%) for 7, 14 and 21 days before cutting collection, and the rooting performance, endogenous hormone and phenolic profiles, antioxidant enzyme activities, and transcriptomic responses of the shoots and cuttings were systematically investigated. Shading of stock plants significantly promoted adventitious rooting, with the combination of 60% shading for 14 days giving the highest rooting rate (39.74%), compared with 5.13% in the unshaded control at the same stage. During shading, leaf chlorophyll content increased with shading intensity and peaked at day 14; phloem indole-3-acetic acid (IAA) and gibberellin (GA₃) contents remained higher than the control, whereas abscisic acid (ABA) and major phenolics (phloridzin, chlorogenic acid, quercitrin and rutin) declined. Transcriptome analysis of the phloem (full light vs. 60% shading at days 7 and 14) identified up to 10,944 differentially expressed genes (DEGs), which were significantly enriched in plant hormone signal transduction, MAPK signaling and plant–pathogen interaction pathways. Shading up-regulated auxin biosynthesis and transport genes (YUCCA6, ARG7, LAX2/LAX3, PIN2) and SAUR genes (SAUR20/50/72/78) while down-regulating auxin signaling repressors and receptors (IAA3/13/14/16/17/26/29/30, TIR1, AFB2, ARF5/6/17/19, PIN3) and the ABA-responsive factor DPBF3. During subsequent rooting, shaded cuttings exhibited four rooting phases (callus formation, root primordium induction, root emergence and elongation); higher IAA and GA₃ and lower ABA and total phenols, together with earlier peaks of POD, PPO, and IAAO activities, characterized the shaded, easy-to-root cuttings. These results indicate that pre-cutting shading creates a “rooting-competent” physiological and transcriptional state in stock-plant shoots that is inherited by the cuttings, providing a practical protocol for ‘Y-1’ cutting propagation and mechanistic insight into light-mediated regulation of adventitious rooting in apple. Full article

Seed development in Brassica napus is tightly regulated at many stages. Microproteins (miPs), small regulatory peptides derived from larger ancestral proteins, have emerged as key post-translational modulators in plants; however, their role in seed development remains poorly understood. Here, a genome-wide screen for putative miPs in B. napus was performed, identifying 32 candidates. Among these, MIF1 (BnaC06g35530D), with domain similarity to ZF-HD transcription factors (TFs), showed robust expression dynamics. The integration of RNA-seq profiling, qRT-PCR, co-expression network modeling, and protein–protein interaction revealed a strong regulatory association between MIF1 and its predicted TF partner, i.e., ZHD (BnaC01g16510D), particularly at the zygote and bending cotyledon stages. Promoter analysis identified shared cis-elements among co-expressed genes, while structural modeling supported a stable MIF1–ZHD interaction interface. Evolutionary analysis demonstrated the conservation of zinc finger motifs, syntenic neighborhoods, and purifying selection on MIF1 across Brassicaceae species. Collectively, our findings suggest that MIF1 potentially functions as a conserved post-translational repressor of ZHD during seed development, contributing to fine-tuned transcriptional regulation in polyploid oilseed crops. This study provides a testable hypothesis about the interaction between MIF1 and ZHD and also paves the way for the future functional characterization of miP-TF modules in plant development. Full article

(1) Background: Seasonal breeding constraints represent a long-standing barrier to efficient sheep production worldwide. Small Tail Han sheep, a Chinese indigenous breed that exhibits year-round estrus independent of photoperiod, offers a unique natural model for investigating the regulatory mechanisms underlying estrus cyclicity—yet the molecular basis of this remarkable trait remains largely unexplored. This study therefore aimed to compare ovarian whole-transcriptome profiles between Small Tail Han sheep (year-round estrus) and Ujumqin sheep (seasonal estrus) during estrus and diestrus. Specifically, we sought to characterize breed-specific transcriptional response strategies, identify key miRNAs associated with continuous estrus, and construct ceRNA networks that mediate ovarian estrous cycle regulation. (2) Methods: To address these objectives, we profiled ovarian transcriptomes of Small Tail Han sheep (year-round estrus) and Ujumqin sheep (seasonal estrus) during both estrus and diestrus (12 samples total) using whole-transcriptome sequencing, systematically characterizing the expression landscapes of mRNAs, miRNAs, lncRNAs and circRNAs. Through differential expression analysis, GO/KEGG functional enrichment, multi-tiered miRNA screening, and ceRNA network construction, we compared the transcriptional response strategies between the two breeds. (3) Results: Our findings revealed two unexpected and divergent patterns. Small Tail Han sheep showed 1881 differentially expressed mRNAs between estrus and diestrus, 82-fold more than the 23 in Ujumqin sheep, suggesting a broader mRNA-level transcriptional response in the year-round estrus breed. circRNAs were predominantly up-regulated (80–85%) in both breeds, while mRNAs and lncRNAs were predominantly down-regulated, uncovering a conserved “circRNA-up, mRNA-down” regulatory logic across breeds. Multi-tiered screening identified 38 “brake-releaser” miRNAs (high in diestrus, down-regulated in estrus) and 21 “accelerator” miRNAs (low in diestrus, up-regulated in estrus), which together constitute a “de-repression–activation” dual regulatory mode. ceRNA network analysis further revealed a clear functional stratification: conserved core miRNAs targeted “sensor” pathways (cAMP, PI3K-Akt, MAPK), whereas accelerator miRNAs specifically targeted “executor” pathways (estrogen signaling, progesterone-mediated oocyte maturation, Hippo signaling). Network topology analysis pinpointed miR-199a-5p, miR-204-3p and miR-199b as the core hubs bridging the two regulatory modules. (4) Conclusions: Taken together, our findings redefine the molecular basis of year-round estrus—moving beyond single-gene mutations or overexpression to an enhanced global transcriptomic responsiveness of the ovary. This work provides a fresh conceptual framework for understanding the divergence of reproductive strategies in sheep and offers actionable candidate targets for genetic improvement of continuous estrus traits. Full article

Triple-negative breast cancer (TNBC) is a heterogeneous and aggressive subtype with limited therapeutic targets. We retrospectively evaluated the expression of phosphatase and tensin homolog (PTEN) and transmembrane serine protease 4 (TMPRSS4) by immunohistochemistry in formalin-fixed, paraffin-embedded tumor tissues from 145 patients with histologically confirmed TNBC, and we analyzed associations with clinicopathological features, Fudan immunohistochemistry-based subtypes, and clinical outcomes. Clinicopathological analyses included all 145 cases. Exploratory survival analyses included 59 patients with complete, verifiable follow-up and outcome data (median follow-up, 46 months), during which three deaths and eight progression events occurred. PTEN-retained expression was associated with worse overall survival (OS; log-rank p = 0.030), whereas TMPRSS4-positive expression was associated with worse progression-free survival (PFS; log-rank p = 0.034). TMPRSS4 expression showed a nominal association with Fudan subtype in the unadjusted omnibus analysis (p = 0.025), which was considered exploratory after Benjamini–Hochberg correction (q = 0.379). The PTEN and TMPRSS4 staining categories were not significantly associated. In an exploratory four-group survival analysis, patients with concurrent PTEN-retained and TMPRSS4-positive expression (PTEN⁺/TMPRSS4⁺) showed the lowest OS and PFS estimates, patients with PTEN loss and TMPRSS4 negativity (PTEN⁻/TMPRSS4⁻) showed the highest estimates, and the two single-positive groups showed intermediate estimates. Independent transcript-level validation restricted to TNBC in The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) did not reproduce these protein-level associations. These protein-level findings should therefore be considered exploratory and hypothesis-generating and warrant confirmation in larger, adequately powered cohorts using standardized immunohistochemistry with complete treatment data. Full article

Polygonatum sibiricum Red. is a medicinal and edible homologous plant whose rhizome quality determines its clinical efficacy and commercial value. However, conventional evaluations typically treat the entire rhizome as homogeneous, overlooking the intrinsic heterogeneity along age nodes, and the regulatory mechanisms governing such age-dependent quality variation remain largely unclear. In this study, four-year-old rhizomes were precisely segmented into four age nodes (HJ1–HJ4), and the contents of polysaccharides, flavonoids, and saponins were systematically determined alongside comparative transcriptome sequencing to dissect the age-dependent bioactive variation and underlying molecular mechanisms. The three bioactive components exhibited markedly asynchronous accumulation patterns, with polysaccharides peaking at HJ3, flavonoids at HJ4, and saponins at HJ1. Transcriptomic analysis identified 19,638 differentially expressed genes (DEGs), with KEGG enrichment pointing to starch and sucrose metabolism, flavonoid biosynthesis, and steroid biosynthesis as the pivotal pathways. A coordinated transcriptional reprogramming emerged across development, characterized by early upregulation of backbone-construction genes and progressive activation of modification-and-decoration genes—yet it manifested through pathway-specific regulatory logics, with Mantel tests further confirming that key genes, including β-amylase3, CYP75B11, and squalene epoxidase (SQLE), were significantly correlated with the accumulation of polysaccharides, flavonoids, and saponins, respectively. These findings challenge the conventional assumption that older nodes are universally superior and establish that age-node differentiation reflects fundamental metabolic reprogramming, supporting a node-targeted utilization strategy encompassing HJ3 for polysaccharide-based products, HJ4 for antioxidant applications, HJ1 for saponin extraction, and HJ2 for bulk materials, while providing both mechanistic insights and practical guidance for precision harvesting and quality-oriented management of P. sibiricum. Full article

Soil salinization is a major constraint on peanut production. Here, we characterized the physiological and transcriptomic responses of peanut (Arachis hypogaea L.) seedlings exposed to 200 mM NaCl. Salt stress markedly inhibited plant growth, elevated the Na⁺/K⁺ ratio, and induced oxidative stress, as reflected by increased contents of malondialdehyde, hydrogen peroxide, and superoxide anion, along with damaged chloroplast ultrastructure and reduced chlorophyll content and F_v/F_m. Transcriptomic analysis of roots at 0, 3, 6, 12, and 24 h post-treatment identified 4332 differentially expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that phenylpropanoid and flavonoid biosynthesis, glutathione metabolism, and mitogen-activated protein kinase signaling pathways were significantly activated. Weighted gene co-expression network analysis (WGCNA) revealed that the salmon and yellow modules were strongly correlated with physiological traits and identified a key co-expressed gene pair involving AhbHLH162 and AhGST. Numerous transcription factors from the ERF, MYB, bHLH, NAC, and WRKY families were differentially expressed, underscoring their roles in salt tolerance. These findings provide insights into the molecular basis of salt tolerance in peanut and offer candidate targets for genetic improvement. Full article

Background/Objectives: We compared juvenile whole-stem transcriptomes of Quercus glauca, Quercus acutissima, Quercus fabri, and Castanopsis sclerophylla to examine carbon metabolism and transport. Methods: Three seedlings per species were sampled in one session. RNA sequencing (RNA-seq) data were analyzed using differential-expression analysis, direction-specific Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, gene set enrichment analysis (GSEA), and leading-edge analysis. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed on aliquots from the same RNA extractions. Results: Reference-based analyses identified 8596–11,823 differentially expressed genes across six contrasts. GSEA detected 25 significant pathway-by-contrast associations across 13 pathways at a false discovery rate below 0.05. Q. glauca showed photosynthesis, starch turnover, and flavonoid pathway signals. Q. acutissima showed sugar-metabolism and ATP-binding cassette (ABC) transport signals, with XTH23 providing an annotation-based wall-remodeling candidate. Q. fabri showed enrichment of sulfur amino acid metabolism, nucleotide sugar metabolism, and mitogen-activated protein kinase signaling. C. sclerophylla showed ABC transport and galactose metabolism enrichment, with candidates annotated for raffinose synthesis and extracellular sucrose cleavage. Eleven of 12 candidates were present in at least one significant GSEA leading edge; XTH23 was selected using differential expression and annotation. Both assays identified the same species as having the highest expression for every candidate; eight genes also showed the same rank order across all four species. Conclusions: The sampled stems differed in the expression of genes associated with carbon metabolism, transport, and regulation. These whole-stem patterns provide candidates for tissue-resolved and physiological studies. Full article

Population-associated molecular variation in breast tissue may contribute to differences in tissue biology and disease susceptibility. Still, the extent to which such variation is shaped by underlying tissue state remains unclear. We performed a pilot RNA-seq and lipidomic analysis of histologically normal breast tissue from African American (AA) and Caucasian White (CW) individuals. Unsupervised transcriptomic analysis identified two baseline tissue states, G1 and G2, representing the dominant axis of molecular variation and associated with epithelial-enriched and vascular-enriched tissue contexts, respectively. Across the full cohort, AA and CW samples showed minimal transcriptomic differences. However, within G1, 191 genes were differentially expressed between AA and CW samples, with coordinated enrichment of extracellular matrix organization and proliferative/cytoskeletal processes in AA samples; these patterns were consistent across enrichment methods and sensitivity analyses. No comparable population-associated transcriptional signal was detected in G2. Lipidomic profiles showed limited separation and no robust population-associated differences after correction for multiple testing. Together, these pilot findings suggest that population-associated molecular variation in histologically normal breast tissue may be state-dependent, becoming detectable within a specific baseline transcriptional context rather than uniformly across the cohort. These results further underscore baseline tissue state as a major source of variation in small, heterogeneous bulk-tissue cohorts and provide a framework for future cell-resolved studies of tissue variation and disease susceptibility. Full article

Background: Osteoarthritis (OA) is a prevalent degenerative joint disease lacking effective disease-modifying therapies, which necessitates the discovery of key genes for mechanistic exploration and therapeutic development. Methods: We integrated three large-scale cis-protein quantitative trait locus datasets and two OA genome-wide association study summary statistics to screen candidate proteins by two-stage proteome-wide Mendelian randomization (MR). Causal association reliability was validated via summary-data-based Mendelian randomization (SMR) and Bayesian colocalization analyses. A phenome-wide association study (PheWAS) was performed to evaluate potential pleiotropic effects of the candidates. Subsequently, transcriptomic and single-cell RNA sequencing datasets were employed to evaluate the candidate genes’ expression stability, classification efficacy in the in vitro models of OA, cell-specific enrichment, and pseudotime expression dynamics in cartilage. Finally, drug repurposing potential was explored by integrating drug–gene interaction database searches and molecular docking. Results: Two-stage cis-pQTL MR combined with cis-eQTL-based SMR analysis identified 14 plasma proteins with consistent effects at the protein and transcript levels. RNA-seq revealed that adrenomedullin (ADM) and complement factor H (CFH) were upregulated in two in vitro models of OA, and both genes exhibited favorable classification efficacy in these models. Bayesian colocalization analysis provided evidence of shared causal variants for ADM, and PheWAS did not detect significant pleiotropic associations for ADM or CFH across the tested phenotypes. Single-cell analysis indicated that ADM was enriched in pre-fibrocartilage chondrocytes with biphasic pseudotime expression, whereas CFH was widely expressed across chondrocyte subsets. Database screening identified 15 potential drugs for ADM and 6 for CFH. Conclusions: Combining MR, multi-omics and pharmacological evidence, we prioritized ADM and CFH as OA candidate genes. Full article

Potato spindle tuber viroid (PSTVd) infection can induce tuber cracking and knob-like protuberances at tuber eyes, but the molecular differences between these two localized symptoms remain unclear. In this study, smooth surface regions and normal eye tissues were collected from mock-inoculated tubers of the potato cultivar ‘Kexin 18’, whereas crack regions and regions of knob-like protuberances at tuber eyes were collected from PSTVd-infected tubers. RNA sequencing and targeted phytohormone quantification were combined with weighted gene co-expression network analysis, infection × region interaction analysis, and gene-hormone association analysis. PSTVd infection markedly inhibited plant growth and tuber development, and 2972 genes with significant infection × region interaction effects were identified. Crack regions were characterized primarily by enhanced defense and oxidative stress related transcriptional responses, remodeling of cell wall and surface barrier related processes, and accumulation of several cytokinin (CK) metabolites, salicylic acid/salicylic acid glucoside (SA/SAG), and 12-oxo-phytodienoic acid (OPDA); CRK2, RBOHA, and CSLG2 were among the representative candidate genes. Regions of knob-like protuberances at tuber eyes showed pronounced reprogramming of processes related to DNA replication, the cell cycle, chromosome maintenance, and chromatin organization, together with decreases in several CK metabolites, a downward trend in jasmonate-related oxylipins, and an increase in indole-3-butyric acid; ACL5-like, PILS7-like, CYCA3;1, and MCM4 were identified as candidate genes. Gene-hormone association analysis further revealed distinct molecular association patterns in the two regions. Collectively, the two symptomatic regions exhibited distinct region-dependent transcriptomic and phytohormone metabolic states after symptom development. Full article

Aspergillus flavus is a major fungal pathogen that causes postharvest spoilage and carcinogenic aflatoxin contamination in agricultural commodities, necessitating the development of novel biocontrol strategies. In this study, a bacterial strain of Bacillus sp. BAF143, isolated from a Martin medium plate used for marine fungal cultivation, exhibited potent antifungal activity against A. flavus. The crude extract of BAF143 demonstrated strong inhibition of mycelial growth (62.36 ± 1.00%) and spore germination (90.10 ± 0.21%). Transcriptomic analysis revealed a distinctive response pattern: genes involved in ribosome biogenesis, oxidative phosphorylation, ergosterol biosynthesis, cell cycle, DNA replication, and energy metabolism were significantly upregulated, whereas cell wall synthesis and MAPK signaling pathway genes were downregulated. This paradoxical transcriptional landscape indicates that A. flavus mounted a desperate compensatory response to counteract cellular damage, which was ultimately overwhelmed by excessive reactive oxygen species accumulation, lipid peroxidation, and mitochondrial dysfunction. Physiological assays confirmed membrane integrity loss, mitochondrial membrane potential collapse, and DNA fragmentation, leading to apoptosis-like cell death. On peanuts, the crude extract achieved a 96.18% reduction in A. flavus spore count after 21 days with sustained protection. These findings demonstrate that the BAF143 crude extract exerts a multi-pathway antifungal mechanism, positioning Bacillus sp. BAF143 as a promising biocontrol agent for mitigating A. flavus contamination and aflatoxin risks in postharvest agricultural products. Full article