Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L.
Abstract Background Rheum palmatum L. has important medicinal value because it contains biologically active anthraquinones. However, the key genes and TFs involved in anthraquinone biosynthesis and regulation in R. palmatum remain unclear. Methods Based on full length transcriptome data, in this stu...
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BMC
2024-02-01
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| Series: | Chinese Medicine |
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| Online Access: | https://doi.org/10.1186/s13020-024-00891-4 |
| _version_ | 1797273263425978368 |
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| author | Xia Zhao Feng Yan Yi-min Li Jing Tang Xiao-chen Hu Zhao Feng Jing Gao Liang Peng Gang Zhang |
| author_facet | Xia Zhao Feng Yan Yi-min Li Jing Tang Xiao-chen Hu Zhao Feng Jing Gao Liang Peng Gang Zhang |
| author_sort | Xia Zhao |
| collection | DOAJ |
| description | Abstract Background Rheum palmatum L. has important medicinal value because it contains biologically active anthraquinones. However, the key genes and TFs involved in anthraquinone biosynthesis and regulation in R. palmatum remain unclear. Methods Based on full length transcriptome data, in this study, we screened the differentially expressed genes in the anthraquinone biosynthesis pathway. The R2R3-MYB family genes of R. palmatum were systematically identified based on full-length transcriptome sequencing followed by bioinformatics analyses. The correlation analysis was carried out by using co-expression analysis, protein interaction analysis, and real-time fluorescence quantitative analysis after MeJA treatment. The RpMYB81 and RpMYB98 genes were amplified by RT-PCR, and their subcellular localization and self-activation characteristics were analyzed. Results Comparative transcriptome analysis results revealed a total of 3525 upregulated and 6043 downregulated DEGs in the CK versus MeJA group; 28 DEGs were involved in the anthraquinone pathway. Eleven CHS genes that belonged to the PKS family were differentially expressed and involved in anthraquinone biosynthesis. Twelve differentially expressed MYBs genes were found to be co-expressed and interact with CHS genes. Furthermore, 52 MYB genes were identified as positive regulators of anthraquinone biosynthesis and were further characterized. Three MYB genes including RpMYB81, RpMYB98, and RpMYB100 responded to MeJA treatment in R. palmatum, and the levels of these genes were verified by qRT-PCR. RpMYB81 was related to anthraquinone biosynthesis. RpMYB98 had an interaction with genes in the anthraquinone biosynthesis pathway. RpMYB81 and RpMYB98 were mainly localized in the nucleus. RpMYB81 had self-activation activity, while RpMYB98 had no self-activation activity. Conclusion RpMYB81, RpMYB98, and RpMYB100 were significantly induced by MeJA treatment. RpMYB81 and RpMYB98 are located in the nucleus, and RpMYB81 has transcriptional activity, suggesting that it might be involved in the transcriptional regulation of anthraquinone biosynthesis in R. palmatum. |
| first_indexed | 2024-03-07T14:41:01Z |
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| id | doaj.art-a462ec5f930f4ef98595aedb15362e7a |
| institution | Directory Open Access Journal |
| issn | 1749-8546 |
| language | English |
| last_indexed | 2024-03-07T14:41:01Z |
| publishDate | 2024-02-01 |
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| spelling | doaj.art-a462ec5f930f4ef98595aedb15362e7a2024-03-05T20:21:24ZengBMCChinese Medicine1749-85462024-02-0119111810.1186/s13020-024-00891-4Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L.Xia Zhao0Feng Yan1Yi-min Li2Jing Tang3Xiao-chen Hu4Zhao Feng5Jing Gao6Liang Peng7Gang Zhang8Key Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineKey Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Traditional Chinese Medicine, Shaanxi University of Chinese MedicineAbstract Background Rheum palmatum L. has important medicinal value because it contains biologically active anthraquinones. However, the key genes and TFs involved in anthraquinone biosynthesis and regulation in R. palmatum remain unclear. Methods Based on full length transcriptome data, in this study, we screened the differentially expressed genes in the anthraquinone biosynthesis pathway. The R2R3-MYB family genes of R. palmatum were systematically identified based on full-length transcriptome sequencing followed by bioinformatics analyses. The correlation analysis was carried out by using co-expression analysis, protein interaction analysis, and real-time fluorescence quantitative analysis after MeJA treatment. The RpMYB81 and RpMYB98 genes were amplified by RT-PCR, and their subcellular localization and self-activation characteristics were analyzed. Results Comparative transcriptome analysis results revealed a total of 3525 upregulated and 6043 downregulated DEGs in the CK versus MeJA group; 28 DEGs were involved in the anthraquinone pathway. Eleven CHS genes that belonged to the PKS family were differentially expressed and involved in anthraquinone biosynthesis. Twelve differentially expressed MYBs genes were found to be co-expressed and interact with CHS genes. Furthermore, 52 MYB genes were identified as positive regulators of anthraquinone biosynthesis and were further characterized. Three MYB genes including RpMYB81, RpMYB98, and RpMYB100 responded to MeJA treatment in R. palmatum, and the levels of these genes were verified by qRT-PCR. RpMYB81 was related to anthraquinone biosynthesis. RpMYB98 had an interaction with genes in the anthraquinone biosynthesis pathway. RpMYB81 and RpMYB98 were mainly localized in the nucleus. RpMYB81 had self-activation activity, while RpMYB98 had no self-activation activity. Conclusion RpMYB81, RpMYB98, and RpMYB100 were significantly induced by MeJA treatment. RpMYB81 and RpMYB98 are located in the nucleus, and RpMYB81 has transcriptional activity, suggesting that it might be involved in the transcriptional regulation of anthraquinone biosynthesis in R. palmatum.https://doi.org/10.1186/s13020-024-00891-4Comparative transcriptomicsGene familyAnthraquinone biosynthesisR2R3-MYBRheum palmatum |
| spellingShingle | Xia Zhao Feng Yan Yi-min Li Jing Tang Xiao-chen Hu Zhao Feng Jing Gao Liang Peng Gang Zhang Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. Chinese Medicine Comparative transcriptomics Gene family Anthraquinone biosynthesis R2R3-MYB Rheum palmatum |
| title | Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. |
| title_full | Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. |
| title_fullStr | Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. |
| title_full_unstemmed | Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. |
| title_short | Comparative transcriptome analysis and identification of candidate R2R3-MYB genes involved in anthraquinone biosynthesis in Rheum palmatum L. |
| title_sort | comparative transcriptome analysis and identification of candidate r2r3 myb genes involved in anthraquinone biosynthesis in rheum palmatum l |
| topic | Comparative transcriptomics Gene family Anthraquinone biosynthesis R2R3-MYB Rheum palmatum |
| url | https://doi.org/10.1186/s13020-024-00891-4 |
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