Transcriptome and Metabolome Analyses Reveal the Role of FaLEC2 in Regulating Lipid Metabolism in Strawberry.

Transcriptomic and metabolomic analyses revealed the action mechanism of nesfatin-1 gene on glucolipid metabolism in early development stage of largemouth bass.

Nesfatin-1 has biological roles including the suppression of food intake and the regulation of glucose and lipid metabolisms. However, th8e information available regarding nesfatin-1 in the glycolipid metabolism in the early development stage of fish is still limited. In order to investigate the role of the nesfatin-1 gene in the early development stage of the largemouth bass (Micropterus salmoides), the nesfatin-1 gene was inhibited using siRNA interference technology. Then, we evaluated their mRNA expression levels, transcriptomes and metabolomes. The mRNA expression levels of nesfatin-1 gene were appreciably decreased at 48 h,72 h and 96 h after injection of nesfatin-1 siRNA in the early development stage. The omics results revealed that the nesfatin-1 gene was interfered to induce 1833 differentially expressed genes (DEGs) and 2370 differentially expressed metabolites (DEMs). Bioinformatic analysis enriched the most affected molecular pathways (sphingolipid metabolism, fatty acid elongation, amino sugar and nucleotide sugar metabolism and biosynthesis of unsaturated fatty acids) and metabolic pathways (biosynthesis of unsaturated fatty acids, sphingolipid metabolism and amino sugar and nucleotide sugar metabolism) in early development of largemouth bass. In amino sugar and nucleotide sugar metabolism, increased expression levels of genes such as chic, chs1, and gck genes, alongside decreased expression levels of the chia.1 gene, resulted in significantly elevated concentrations of N-Acetyl-D-glucosamine, beta-d-Fructose 6-phosphate, beta-d-Fructose, D-Mannose 6-phosphate, d-Glucose, d-Glucose 1-phosphate, UDP-glucose, UDP-glucuronate, whilst the concentration of UDP-N-acetyl-alpha-D-glucosamine was markedly reduced. Therefore, the nesfatin-1 gene could influence the early development stage of largemouth bass by affecting signaling pathways associated with glycolipid metabolism. Our findings further expand the molecular mechanisms of nesfatin-1 gene, and provide further theoretical support for the initial breeding and feed adaptation of largemouth bass.

Whole transcriptome sequencing and metabolism analysis reveal new insight into Ginkgo biloba terpene trilactones biosynthesis

Integrated Transcriptomic and Metabolomic Profiling Reveals the Involvement of the miR397-5p–SbLAC14 Module in Condensed Tannin Accumulation in Developing Sorghum Seeds

Results provide a genetic entry point for metabolic engineering and breeding efforts aimed at modulating grain phenolic profiles and indicate that SbmiR397-5p negatively regulates the expression of SbLAC14 in relation to CT biosynthesis, identifying it as a potential target for manipulating CT metabolism in sorghum.

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.

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.

Co-Analysis of Metabolomics and Transcriptomics Reveals Key Pathways and Genes Associated with Pigment and Flavonoid Regulation in Mint

: Mint is notably rich in phenolic acids, flavonoids, antioxidants and other bioactive components, and is widely used as food, medicine, spices, and flavoring agents. Thus, metabolite composition serves as a critical indicator for assessing mint quality. In this study, two mint genotypes of Mentha canadensis L., were sampled, namely purple mint and green mint. The two genotypes are distinguished by stem color: the purple mint exhibits purple stems, whereas the green mint has green stems. The purple mint exhibited significantly higher anthocyanin and total flavone contents than green mint. Integrated transcriptomic and metabolomic analyses were performed to elucidate the regulatory mechanisms underlying pigment and flavonoid accumulation in mint stems. High-throughput RNA-Seq yielded 167,901 unigenes, of which 34,608 genes were differentially expressed. These differentially expressed genes (DEGs) were mainly involved in the lignin metabolic process and flavonoid biosynthetic process. A total of 143 differentially expressed metabolites (DEMs) were enriched in isoflavonoid, flavonoid biosynthesis, flavone and flavonol biosynthesis, and anthocyanin biosynthesis pathways. Co-analysis of DEGs and DEMs revealed that the flavone and flavonol biosynthesis pathway (ko00944) contained the most DEMs, followed by the flavonoid biosynthesis pathway (ko00941) and the anthocyanin biosynthesis pathway (ko00942). Furthermore, nine key genes and metabolites were identified using the O2PLS model. These findings provide a theoretical basis for understanding the key pathways and genes involved in pigment and flavonoid regulation in mint stems.