Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics
Abstract Background Sophora tonkinensis Gagnep is a significant Chinese herbal medicine, primarily composed of alkaloids and flavonoids, which are its key pharmacological components. Despite its importance, the metabolic pathways of these substances in S. tonkinensis remain inadequately explored. Re...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06865-4 |
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| author | Ying Liang Guili Wei Ximei Liang Meiqiong Tang Hong He Danfeng Tang Yang Lin Linxuan Li Shuangshuang Qin Fan Wei |
| author_facet | Ying Liang Guili Wei Ximei Liang Meiqiong Tang Hong He Danfeng Tang Yang Lin Linxuan Li Shuangshuang Qin Fan Wei |
| author_sort | Ying Liang |
| collection | DOAJ |
| description | Abstract Background Sophora tonkinensis Gagnep is a significant Chinese herbal medicine, primarily composed of alkaloids and flavonoids, which are its key pharmacological components. Despite its importance, the metabolic pathways of these substances in S. tonkinensis remain inadequately explored. Results This study investigates the molecular regulation of alkaloid and flavonoid accumulation in S. tonkinensis. Through high-throughput transcriptome sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS) of seeds, leaves, stems, and roots, the research identifies differential metabolites and genes involved in alkaloid and flavonoid biosynthesis. The transcriptome analysis reveals 2,727 differentially expressed genes (DEGs), with 35 related to alkaloids and 48 to flavonoids. Metabolome analysis uncovers 296 differentially accumulated metabolites (DAMs), including 23 alkaloid-related DAMs and 23 flavonoid-related DAMs. Additionally, weighted gene co-expression network analysis suggests StCAO (evm.model.3.924) as a key regulator of alkaloid biosynthesis and StCHIs (evm.model.3.2047, evm.model.1.2104, and evm.model.1.2101) as crucial genes for flavonoid biosynthesis. To validate these findings, qPCR validation confirmed the consistency of expression trends for 12 selected DEGs across the roots, stems, leaves, and seeds of S. tonkinensis. Conclusion This study offers a comprehensive analysis of the regulatory mechanisms governing alkaloid and flavonoid accumulation, as well as the associated key genes, across various S. tonkinensis tissues. These findings pave the way for future research into the regulatory processes of alkaloids and flavonoids in S. tonkinensis. |
| format | Article |
| id | doaj-art-4424d2a2d0f44b67a5e77ca2e7c29e6a |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
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| series | BMC Plant Biology |
| spelling | doaj-art-4424d2a2d0f44b67a5e77ca2e7c29e6a2025-08-20T04:01:26ZengBMCBMC Plant Biology1471-22292025-07-0125111410.1186/s12870-025-06865-4Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomicsYing Liang0Guili Wei1Ximei Liang2Meiqiong Tang3Hong He4Danfeng Tang5Yang Lin6Linxuan Li7Shuangshuang Qin8Fan Wei9Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsGuangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal PlantsAbstract Background Sophora tonkinensis Gagnep is a significant Chinese herbal medicine, primarily composed of alkaloids and flavonoids, which are its key pharmacological components. Despite its importance, the metabolic pathways of these substances in S. tonkinensis remain inadequately explored. Results This study investigates the molecular regulation of alkaloid and flavonoid accumulation in S. tonkinensis. Through high-throughput transcriptome sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS) of seeds, leaves, stems, and roots, the research identifies differential metabolites and genes involved in alkaloid and flavonoid biosynthesis. The transcriptome analysis reveals 2,727 differentially expressed genes (DEGs), with 35 related to alkaloids and 48 to flavonoids. Metabolome analysis uncovers 296 differentially accumulated metabolites (DAMs), including 23 alkaloid-related DAMs and 23 flavonoid-related DAMs. Additionally, weighted gene co-expression network analysis suggests StCAO (evm.model.3.924) as a key regulator of alkaloid biosynthesis and StCHIs (evm.model.3.2047, evm.model.1.2104, and evm.model.1.2101) as crucial genes for flavonoid biosynthesis. To validate these findings, qPCR validation confirmed the consistency of expression trends for 12 selected DEGs across the roots, stems, leaves, and seeds of S. tonkinensis. Conclusion This study offers a comprehensive analysis of the regulatory mechanisms governing alkaloid and flavonoid accumulation, as well as the associated key genes, across various S. tonkinensis tissues. These findings pave the way for future research into the regulatory processes of alkaloids and flavonoids in S. tonkinensis.https://doi.org/10.1186/s12870-025-06865-4Sophora tonkinensisTranscriptomicsMetabolomicsAlkaloidsFlavonoids |
| spellingShingle | Ying Liang Guili Wei Ximei Liang Meiqiong Tang Hong He Danfeng Tang Yang Lin Linxuan Li Shuangshuang Qin Fan Wei Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics BMC Plant Biology Sophora tonkinensis Transcriptomics Metabolomics Alkaloids Flavonoids |
| title | Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics |
| title_full | Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics |
| title_fullStr | Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics |
| title_full_unstemmed | Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics |
| title_short | Genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of Sophora tonkinensis via transcriptomics and metabolomics |
| title_sort | genes involved in the regulation of alkaloid and flavonoid biosynthesis in different tissues of sophora tonkinensis via transcriptomics and metabolomics |
| topic | Sophora tonkinensis Transcriptomics Metabolomics Alkaloids Flavonoids |
| url | https://doi.org/10.1186/s12870-025-06865-4 |
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