Introduction: Fenugreek (Trigonella foenum-graecum L.) is a medicinal and edible plant containing bioactive compounds with therapeutic potential. However, the tissue-specific distribution and biosynthetic pathways of these compounds remain poorly characterized.Methods: This study employed metabolomics and transcriptomics to analyze metabolite profiles and gene expression in fenugreek roots, stems, and leaves. Using UPLC-MS/MS, we identified 2,124 metabolites, and full-length transcriptome sequencing alongside RNA-seq analysis revealed tissue-specific differentially expressed genes (DEGs).Results: Our analysis revealed distinct tissue-specific accumulation patterns of alkaloids, flavonoids, and terpenoids. The roots were identified as the primary site for the biosynthesis of these secondary metabolites. Multi-omics integration pinpointed key biosynthetic genes, such as cytochrome P450s (CYP450s) and chalcone synthase (CHS). Furthermore, integrated co-expression networks and molecular docking simulations indicated functional associations between ABC transporters and bioactive compounds. Transcriptional regulation analysis suggested MYB and bHLH transcription factors as potential modulators of metabolic biosynthesis.Discussion: This study enhances understanding of metabolic regulations in fenugreek and offers molecular resources for medicinal plant breeding.

Maize, one of the world’s major food crops, is facing the challenge of rising temperature. Leaf senescence is the most significant phenotypic change of maize under heat stress at the seedling stage, but the underlying molecular mechanism is still unknown. Here, we screened for three inbred lines (PH4CV, B73, and SH19B) that showed differentially senescing phenotypes under heat stress. Among them, PH4CV showed no obviously senescing phenotype under heat stress, while SH19B demonstrated a severely senescing phenotype, with B73 being between the two extremes. Subsequently, transcriptome sequencing showed that differentially expressed genes (DEGs) were generally enriched in response to heat stress, reactive oxygen species (ROS), and photosynthesis in the three inbred lines under heat treatment. Notably, ATP synthesis and oxidative phosphorylation pathway genes were only significantly enriched in SH19B. Then, the expression differences of oxidative phosphorylation pathways, antioxidant enzymes, and senescence-related genes in response to heat stress were analyzed in the three inbred lines. In addition, we demonstrated that silencing ZmbHLH51 by virus-induced gene silencing (VIGS) inhibits the heat-stress-induced senescence of maize leaves. This study helps to further elucidate the molecular mechanisms of heat-stress-induced leaf senescence at the seedling stage of maize.

Background: Methyl jasmonate (MeJA) is a potent elicitor of secondary metabolism in plants, but its regulatory role in flavonoid biosynthesis in Scutellaria barbata remains unclear. Methods: Here, we performed an integrated transcriptomic and metabolomic analysis of S. barbata seedlings following exogenous MeJA treatment, combining differential expression and correlation network approaches to identify candidate genes, metabolites, and transcription factors (TFs) associated with flavonoid accumulation. Results: MeJA treatment significantly promoted the accumulation of multiple flavonoids and upregulated key biosynthetic genes, including Sbar2C282T9_CHS2, Sbar5A47T51_CHI , and Sbar9A209T130_C4H . A total of 2,453 differentially expressed genes (DEGs) were identified, which were significantly enriched in flavonoid biosynthesis and plant hormone signal transduction pathways. Among these, 180 differentially expressed TFs were detected, with the ERF, MYB, bHLH, NAC, and bZIP families being markedly enriched. Integrative correlation analysis revealed 40 TFs whose expression patterns were strongly correlated with 19 flavonoids. TF binding site prediction further identified seven candidate TFs predicted to target flavonoid structural genes, including Sbar2C282T9_CHS2 and Sbar9A209T130_C4H . Protein‑protein interaction prediction suggested that several of these TFs, particularly bHLH members, may interact with JAZ repressors and form intra‑family interaction clusters. Discussion: Collectively, these findings suggest a potential JA-responsive transcriptional regulatory network and point to a conserved JAZ-TF module that may modulate flavonoid biosynthesis in S. barbata . This study provides valuable insights into the regulatory mechanisms of secondary metabolism in medicinal plants and offers candidate gene resources for metabolic engineering and molecular breeding of high‑flavonoid varieties.