Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis
Abstract Background Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bioactive compounds in C. gracile. However, the molecular understandin...
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-6454-y |
| _version_ | 1818960646087114752 |
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| author | Chunmiao Shan Chenkai Wang Shengxiang Zhang Yuanyuan Shi Kelong Ma Qingshan Yang Jiawen Wu |
| author_facet | Chunmiao Shan Chenkai Wang Shengxiang Zhang Yuanyuan Shi Kelong Ma Qingshan Yang Jiawen Wu |
| author_sort | Chunmiao Shan |
| collection | DOAJ |
| description | Abstract Background Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bioactive compounds in C. gracile. However, the molecular understanding of the triterpenoid saponin biosynthesis pathway remains unclear. Results In this study, we performed RNA sequencing (RNA-Seq) analysis of the flowers, leaves, roots, and stems of C. gracile plants using the BGISEQ-500 platform. The assembly of transcripts from all four types of tissues generated 128,856 unigenes, of which 99,020 were mapped to several public databases for functional annotation. Differentially expressed genes (DEGs) were identified via the comparison of gene expression levels between leaves and other tissues (flowers, roots, and stems). Multiple genes encoding pivotal enzymes, such as squalene synthase (SS), or transcription factors (TFs) related to triterpenoid saponin biosynthesis were identified and further analyzed. The expression levels of unigenes encoding important enzymes were verified by quantitative real-time PCR (qRT-PCR). Different chemical constituents of triterpenoid saponins were identified by Ultra-Performance Liquid Chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Conclusions Our results greatly extend the public transcriptome dataset of C. gracile and provide valuable information for the identification of candidate genes involved in the biosynthesis of triterpenoid saponins and other important secondary metabolites. |
| first_indexed | 2024-12-20T12:00:50Z |
| format | Article |
| id | doaj.art-eff13eebe8d0490c9c7e9797fcdc9a23 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T12:00:50Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-eff13eebe8d0490c9c7e9797fcdc9a232022-12-21T19:41:32ZengBMCBMC Genomics1471-21642020-01-0121111610.1186/s12864-020-6454-yTranscriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesisChunmiao Shan0Chenkai Wang1Shengxiang Zhang2Yuanyuan Shi3Kelong Ma4Qingshan Yang5Jiawen Wu6Anhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAnhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAnhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAnhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAnhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAnhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAnhui University of Chinese Medicine and Anhui Academy of Chinese MedicineAbstract Background Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bioactive compounds in C. gracile. However, the molecular understanding of the triterpenoid saponin biosynthesis pathway remains unclear. Results In this study, we performed RNA sequencing (RNA-Seq) analysis of the flowers, leaves, roots, and stems of C. gracile plants using the BGISEQ-500 platform. The assembly of transcripts from all four types of tissues generated 128,856 unigenes, of which 99,020 were mapped to several public databases for functional annotation. Differentially expressed genes (DEGs) were identified via the comparison of gene expression levels between leaves and other tissues (flowers, roots, and stems). Multiple genes encoding pivotal enzymes, such as squalene synthase (SS), or transcription factors (TFs) related to triterpenoid saponin biosynthesis were identified and further analyzed. The expression levels of unigenes encoding important enzymes were verified by quantitative real-time PCR (qRT-PCR). Different chemical constituents of triterpenoid saponins were identified by Ultra-Performance Liquid Chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Conclusions Our results greatly extend the public transcriptome dataset of C. gracile and provide valuable information for the identification of candidate genes involved in the biosynthesis of triterpenoid saponins and other important secondary metabolites.https://doi.org/10.1186/s12864-020-6454-yClinopodium gracile (Benth.) MatsumTranscriptomeRNA-SeqTriterpenoid saponin biosynthesisDifferentially expressed genes |
| spellingShingle | Chunmiao Shan Chenkai Wang Shengxiang Zhang Yuanyuan Shi Kelong Ma Qingshan Yang Jiawen Wu Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis BMC Genomics Clinopodium gracile (Benth.) Matsum Transcriptome RNA-Seq Triterpenoid saponin biosynthesis Differentially expressed genes |
| title | Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis |
| title_full | Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis |
| title_fullStr | Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis |
| title_full_unstemmed | Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis |
| title_short | Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis |
| title_sort | transcriptome analysis of clinopodium gracile benth matsum and identification of genes related to triterpenoid saponin biosynthesis |
| topic | Clinopodium gracile (Benth.) Matsum Transcriptome RNA-Seq Triterpenoid saponin biosynthesis Differentially expressed genes |
| url | https://doi.org/10.1186/s12864-020-6454-y |
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