A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways
Dendrobium moniliforme (D. moniliforme) is a traditional medicinal herb widely cultivated in Asia. Flavonoids, one of the largest groups of secondary metabolites in plants, are significant medicinal components in Dendrobium species. Several subgroups of R2R3-MYB proteins have been validated to direc...
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Elsevier
2025-04-01
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| Series: | Acta Pharmaceutica Sinica B |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211383525001236 |
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| author | Jiapeng Yang Qiqian Xue Chao Li Yingying Jin Qingyun Xue Wei Liu Zhitao Niu Xiaoyu Ding |
| author_facet | Jiapeng Yang Qiqian Xue Chao Li Yingying Jin Qingyun Xue Wei Liu Zhitao Niu Xiaoyu Ding |
| author_sort | Jiapeng Yang |
| collection | DOAJ |
| description | Dendrobium moniliforme (D. moniliforme) is a traditional medicinal herb widely cultivated in Asia. Flavonoids, one of the largest groups of secondary metabolites in plants, are significant medicinal components in Dendrobium species. Several subgroups of R2R3-MYB proteins have been validated to directly regulate flavonoid biosynthesis. Using PacBio sequencing technology, we assembled a high-quality chromosome-level D. moniliforme genome with a total length of 1.20 Gb and a contig N50 of 3.97 Mb. The BUSCO assessment of genome annotation was 91.4%. By integrating the genome and transcriptome, we identified biosynthesis pathway enzyme genes related to flavonoids, polysaccharides, carotenoids, and alkaloids. A total of 90 R2R3-MYBs were identified in D. moniliforme and classified into 21 subgroups. Studies on the functions of R2R3-MYB transcription factors revealed that R2R3-MYB in SG6 can up-regulate flavonoid biosynthesis. Various validation experiments, including subcellular localization, transient overexpression, UPLC–MS/MS, HPLC, yeast one-hybrid, and dual-luciferase assays, demonstrated that DMYB69 directly up-regulates the expression of enzyme genes involved in flavonoid biosynthesis, increasing the content of flavonoids such as anthocyanin, flavone, and flavonol. Additionally, DMYB44 was shown to directly up-regulate the expression of carotenoid biosynthesis enzyme genes, thereby increasing carotenoid content. This study provides an essential genome resource and theoretical basis for molecular breeding research in D. moniliforme. |
| format | Article |
| id | doaj-art-ea707faa2b6940cf9a9aa584b2d0afd9 |
| institution | DOAJ |
| issn | 2211-3835 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Acta Pharmaceutica Sinica B |
| spelling | doaj-art-ea707faa2b6940cf9a9aa584b2d0afd92025-08-20T03:09:12ZengElsevierActa Pharmaceutica Sinica B2211-38352025-04-011542253227210.1016/j.apsb.2025.03.005A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathwaysJiapeng Yang0Qiqian Xue1Chao Li2Yingying Jin3Qingyun Xue4Wei Liu5Zhitao Niu6Xiaoyu Ding7College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, ChinaCollege of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, China; Corresponding authors.College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; Jiangsu Provincial Engineering Research Center for Technical Industrialization of Dendrobiums, Nanjing 210023, China; Corresponding authors.Dendrobium moniliforme (D. moniliforme) is a traditional medicinal herb widely cultivated in Asia. Flavonoids, one of the largest groups of secondary metabolites in plants, are significant medicinal components in Dendrobium species. Several subgroups of R2R3-MYB proteins have been validated to directly regulate flavonoid biosynthesis. Using PacBio sequencing technology, we assembled a high-quality chromosome-level D. moniliforme genome with a total length of 1.20 Gb and a contig N50 of 3.97 Mb. The BUSCO assessment of genome annotation was 91.4%. By integrating the genome and transcriptome, we identified biosynthesis pathway enzyme genes related to flavonoids, polysaccharides, carotenoids, and alkaloids. A total of 90 R2R3-MYBs were identified in D. moniliforme and classified into 21 subgroups. Studies on the functions of R2R3-MYB transcription factors revealed that R2R3-MYB in SG6 can up-regulate flavonoid biosynthesis. Various validation experiments, including subcellular localization, transient overexpression, UPLC–MS/MS, HPLC, yeast one-hybrid, and dual-luciferase assays, demonstrated that DMYB69 directly up-regulates the expression of enzyme genes involved in flavonoid biosynthesis, increasing the content of flavonoids such as anthocyanin, flavone, and flavonol. Additionally, DMYB44 was shown to directly up-regulate the expression of carotenoid biosynthesis enzyme genes, thereby increasing carotenoid content. This study provides an essential genome resource and theoretical basis for molecular breeding research in D. moniliforme.http://www.sciencedirect.com/science/article/pii/S2211383525001236Dendrobium moniliformeGenomeR2R3-MYBFlavonoidCarotenoidUPLC–MS/MS |
| spellingShingle | Jiapeng Yang Qiqian Xue Chao Li Yingying Jin Qingyun Xue Wei Liu Zhitao Niu Xiaoyu Ding A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways Acta Pharmaceutica Sinica B Dendrobium moniliforme Genome R2R3-MYB Flavonoid Carotenoid UPLC–MS/MS |
| title | A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways |
| title_full | A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways |
| title_fullStr | A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways |
| title_full_unstemmed | A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways |
| title_short | A chromosome-level Dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways |
| title_sort | chromosome level dendrobium moniliforme genome assembly reveals the regulatory mechanisms of flavonoid and carotenoid biosynthesis pathways |
| topic | Dendrobium moniliforme Genome R2R3-MYB Flavonoid Carotenoid UPLC–MS/MS |
| url | http://www.sciencedirect.com/science/article/pii/S2211383525001236 |
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