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

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

BACKGROUND Kiwiberry is a climacteric fruit known for its unique flavor and rich nutritional profile. Fruit sweetness increases gradually during postharvest storage; however, the molecular mechanisms underlying this process remain unclear. RESULTS In this study, targeted metabolomic analysis identified 24 carbohydrate metabolites in kiwiberry. Notably, glucose, sucrose, fructose, and inositol exhibited relatively high abundance and displayed a progressive upward trend during storage. Transcriptomic profiling screened 94 genes encoding 14 key enzymes within the 'Starch and sucrose metabolism' pathway. Weighted gene co-expression network analysis identified 9 transcription factors associated with increased postharvest sweetness. Among them, AaDof was identified as a key transcription factor, showing regulatory interactions with 16 downstream genes involved in carbohydrate metabolism. CONCLUSION By integrating transcriptomic and metabolomic data, this study elucidates the metabolic processes and molecular mechanisms governing postharvest sweetness development in kiwiberry. These findings provide a theoretical foundation for breeding high-quality cultivars with enhanced sweetness. © 2026 Society of Chemical Industry.

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

Sesame is an important oilseed crop, and floral development is a key biological process that lays the foundation for pollination, fertilization, and seed formation, which are closely associated with final yield potential. However, the dynamic transcriptional and metabolic regulatory mechanisms during floral development remain unclear. Here, we performed an integrated transcriptomic and metabolomic analysis across five key developmental stages (T1–T5) of sesame flowers to systematically dissect the multi‑omics regulatory network. KEGG enrichment analysis revealed distinct stage‑specific metabolic characteristics: early stages (T1–T2) were enriched in primary energy metabolism (glycolysis and starch/sucrose metabolism); the middle stage (T3) showed enrichment in DNA replication and phenylpropanoid biosynthesis; and late stages (T4–T5) were associated with plant hormone signaling and α‑linolenic acid metabolism. WGCNA identified two modules correlated with development: a positive module involved in phenylpropanoid biosynthesis, and a negative module related to DNA replication and repair. Genes in the phenylpropanoid/flavonoid pathway displayed a clear sequential expression pattern, promoting flavonoid and anthocyanin accumulation. Collectively, this study provides a comprehensive multi‑omics resource and a descriptive framework for understanding transcriptional and metabolic dynamics during sesame floral development, and identifies candidate pathways and genes that may serve as targets for future functional validation and molecular breeding.

Multi-omics dissection of metabolic pathways for differential flavonoid accumulation in Solanum pennellii and S. lycopersicum

Integrated Analysis of Metabolome and Transcriptome Provides New Insights into the Genetic Basis Underlying the Regulation of α-Linolenic Acid Biosynthesis in Perilla frutescens Seeds

Perilla (Perilla frutescens) is an important oil-bearing crop rich in α-linolenic acid (ALA), and seed oil quality varies greatly among different germplasms. However, the molecular and metabolic mechanisms underlying genotypic differences in ALA accumulation remain unclear. In this study, four Perilla varieties with distinct seed phenotypic traits were used to investigate the variations in seed quality, metabolome, and transcriptome. Significant genotypic differences were observed in seed color, thousand-grain weight, and oil content. QO8 showed the highest seed oil content, while QS5 and QO10 exhibited relatively lower oil accumulation levels. Metabolome analysis revealed that lipid metabolism was the dominant metabolic category in Perilla seeds. Multiple differentially accumulated metabolites (DAMs), including ALA, stearic acid, traumatic acid, and 10-OPDA, displayed genotype-specific accumulation patterns. KEGG enrichment demonstrated that α-linolenic acid metabolism and unsaturated fatty acid biosynthesis were the most significantly divergent pathways among different Perilla germplasms. Transcriptome analysis identified numerous differentially expressed genes (DEGs) involved in fatty acid and ALA biosynthesis, such as FAD2, LOX, AOS, AOC, OPR, KAT, ECH, and ACOX. Integrated transcriptome and metabolome analysis further confirmed that the differential expression of structural genes altered the metabolic flux of the ALA and downstream jasmonic acid pathway, resulting in varied accumulation of core lipid intermediates. In addition, WRKY and MYB transcription factors were identified as key upstream regulators that positively or negatively modulated ALA metabolic homeostasis. This study systematically clarified the phenotypic, metabolic, and transcriptional differences in seeds of different Perilla varieties and revealed the core regulatory network of ALA biosynthesis. These findings provide valuable candidate genes and a theoretical foundation for elucidating the molecular mechanism of high ALA accumulation and quality improvement in Perilla seeds.

Metabolo-Transcriptomic Analysis Reveals the Mechanisms Underlying Seed Dormancy Release in Polygonatum sibiricum

Findings demonstrate that dormancy release in P. sibiricum is governed by coordinated hormonal reprogramming, metabolic mobilization, and transcription factor-mediated regulation, providing a theoretical foundation for improving seed germination in this medicinal plant.

Integrated Transcriptomic and Metabolomic Analyses Uncover the Molecular Mechanisms Underlying Drought Tolerance in Isodon suzhouensis

Mild drought stress modulates the expression of genes involved in phenylpropanoid, flavonoid and diterpenoid biosynthetic pathways, alters antioxidant enzyme activities, and coordinately regulates the formation of drought tolerance and the accumulation of bioactive compounds in I. suzhouensis.