Integrated transcriptome and metabolome analyses uncover stage-specific dynamic regulatory networks during sesame floral development

Integrated Metabolome and Transcriptome Analysis Reveals Dynamic Changes in Flavonoid Accumulation and Pericarp at Different Sowing Dates in Sorghum

Findings reveal the molecular mechanism underlying sowing date-mediated seed quality formation and provide a theoretical basis for high-quality sorghum production.

Antagonistic Transcriptional and Metabolic Networks Are Associated with Anthocyanin Accumulation in Maize Seedlings

Background: Anthocyanin accumulation is a developmentally regulated trait shaped by complex interactions between metabolic and transcriptional networks. However, dissecting the regulatory mechanisms underlying anthocyanin biosynthesis is often complicated by confounding variation in plant growth and environmental conditions. Methods: Here, we used a time-resolved multi-omics approach to investigate anthocyanin accumulation in maize seedlings by comparing an anthocyanin-rich inbred line PH19401 with an anthocyanin-deficient line YPX across five developmental stages. Results: Untargeted metabolomic and transcriptomic profiling revealed progressive divergence between the two lines beginning at early development stages. Using a dual-line, intersection-based filtering strategy, we identified a refined set of metabolites and genes closely associated with anthocyanin accumulation. These candidates were enriched in pathways related to phenylpropanoid metabolism, energy metabolism, and redox regulation. Weighted gene co-expression network analysis (WGCNA) identified two transcriptional modules that showed opposing associations with anthocyanin content. The positively associated module was centered on MYB transcription factors, consistent with canonical regulation of flavonoid biosynthesis, whereas the negatively associated module was enriched in genes involved in primary metabolism and signaling. Integration of transcriptomic and metabolomic datasets further revealed coordinated relationships between MYB hub genes and flavonoid intermediates, linking transcriptional regulation with metabolic output. Together, these results support a model in which anthocyanin accumulation is associated with activation of MYB-centered transcriptional programs and broader metabolic reprogramming that enhances precursor supply and redox balance, while competing transcriptional programs favor primary metabolism. Conclusions: This study provides a systems-level perspective on anthocyanin biosynthesis in maize seedlings and establishes an analytical framework for dissecting developmentally regulated metabolic traits.

Transcriptomic and co-expression network analysis reveals coordinated multi-pathway regulation of blueberry fruit ripening

A systems-level view of blueberry fruit development is provided, highlighting coordinated transcriptional changes across multiple biological pathways during ripening and the identification of conserved gene expression patterns and key regulatory candidates offers valuable targets for improving fruit quality and health-promoting traits in blueberry.

Integrated transcriptome and metabolome analysis reveals the regulatory mechanism of postharvest sweetness changes in kiwiberry.

This study elucidates the metabolic processes and molecular mechanisms governing postharvest sweetness development in kiwiberry and provides a theoretical foundation for breeding high-quality cultivars with enhanced sweetness.

Integrated Proteomics and Metabolomics Analysis Reveals Regulatory Mechanisms Underlying Flower Bud Development in Camellia drupifera.

Integrated transcriptome and metabolome analysis reveals key genes and metabolic pathways regulating growth and development in Polygonatum cyrtonema Hua

Polygonatum cyrtonema Hua is a traditional Chinese medicine with the same origin as both medicine and food, and its medicinal components have considerable clinical value. Due to its substantial market demand, it is now primarily produced through artificial cultivation. To produce high-quality P. cyrtonema, we performed transcriptome and metabolome sequencing of one-year-old and three-year-old P. cyrtonema to explore the growth regulation mechanisms and key genes involved in improving its quality. A total of 1,957 differentially expressed genes (DEGs) and 163 differentially expressed metabolites (DEMs) were identified in this study. Integrated transcriptomic and metabolomic analyses suggested that the growth regulation of P. cyrtonema may be primarily associated with sphingolipid metabolism, phenylpropanoid biosynthesis, and starch and sucrose metabolism. Our data suggest that sucrose transport to sink organs may be facilitated by increased expression of the bidirectional sugar transporter SWEET14, and sucrose may be hydrolyzed by β-fructofuranosidase, potentially providing energy for plant growth on one hand and contributing to fructose accumulation on the other. Furthermore, the elevated abundance of L-phenylalanine may be associated with an increase in secondary metabolites, which could provide a metabolic basis for age-dependent growth and metabolite partitioning in rhizomes. The observed downregulation of sphingolipid metabolism-related genes may reflect the perennial growth habit of P. cyrtonema, whereby slower growth in the first year may promote sphingolipid-mediated root development. However, we emphasize that these inferences are based on correlative transcriptomic and metabolomic data, and functional validation is required to establish causal relationships.