Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species
Native to Southern China, Ilex pubescens and Ilex asprella are frequently used in traditional Chinese medicine. Both of them produce a large variety of ursane-type triterpenoid saponins, which have been demonstrated to have different pharmacological effects. However, little is known about their bios...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2017.00634/full |
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| author | Hui Xu Lingling Wen Xiaoyun Yun Xiasheng Zheng Ruoting Zhan Weiwen Chen Yaping Xu Ye Chen Jie Zhang |
| author_facet | Hui Xu Lingling Wen Xiaoyun Yun Xiasheng Zheng Ruoting Zhan Weiwen Chen Yaping Xu Ye Chen Jie Zhang |
| author_sort | Hui Xu |
| collection | DOAJ |
| description | Native to Southern China, Ilex pubescens and Ilex asprella are frequently used in traditional Chinese medicine. Both of them produce a large variety of ursane-type triterpenoid saponins, which have been demonstrated to have different pharmacological effects. However, little is known about their biosynthesis. In this study, transcriptomic analysis of I. pubescens and comparison with its closely related specie I. asprella were carried out to identify potential genes involved in triterpenoid saponin biosynthesis. Through RNA sequencing (RNA-seq) and de novo transcriptome assembly of I. pubescens, a total of 68,688 UniGene clusters are obtained, of which 32,184 (46.86%) are successfully annotated by comparison with the sequences in major public databases (NCBI, Swiss-Prot, and KEGG). It includes 128 UniGenes related to triterpenoid backbone biosynthesis, 11 OSCs (oxidosqualene cyclases), 233 CYPs (cytochrome P450), and 269 UGTs (UDP-glycosyltransferases). By homology-based blast and phylogenetic analysis with well-characterized genes involved in triterpenoid saponin biosynthesis, 5 OSCs, 14 CYPs, and 1 UGT are further proposed as the most promising candidate genes. Transcriptomic comparison between two Ilex species using blastp and OrthoMCL method reveals high sequence similarity. All OSCs and UGTs as well as most CYPs are classified as orthologous genes, while only 5 CYPs in I. pubescens and 3 CYPs in I. asprella are species-specific. One of OSC candidates, named as IpAS1, was successfully cloned and expressed in Saccharomyces cerevisiae INVSc1. Analysis of the yeast extract by gas chromatography (GC) and gas chromatography–mass spectrometry (GC-MS) shows IpAS1 is a mixed amyrin synthase, producing α-amyrin and β-amyrin at ratio of 5:1, which is similar to its ortholog IaAS1 from I. asprella. This study is the first exploration to profile the transcriptome of I. pubescens, the generated data and gene models will facilitate further molecular studies on the physiology and metabolism in this plant. By comparative transcriptomic analysis, a series of candidate genes involved in the biosynthetic pathway of triterpenoid saponins are identified, providing new insight into their biosynthesis at transcriptome level. |
| first_indexed | 2024-12-16T11:23:02Z |
| format | Article |
| id | doaj.art-c96ee5131d41433f9268768d888f6c5f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
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| last_indexed | 2024-12-16T11:23:02Z |
| publishDate | 2017-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c96ee5131d41433f9268768d888f6c5f2022-12-21T22:33:26ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2017-04-01810.3389/fpls.2017.00634252156Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex SpeciesHui Xu0Lingling Wen1Xiaoyun Yun2Xiasheng Zheng3Ruoting Zhan4Weiwen Chen5Yaping Xu6Ye Chen7Jie Zhang8Key Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaZhongshan Zhongzhi Pharmaceutical Group, Key Laboratory for Technologies and Applications of Ultrafine Granular Powder of Herbal Medicine, State Administration of Traditional Chinese MedicineZhongshan, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaKey Laboratory of Chinese Medicinal Resource from Lingnan, Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese MedicineGuangzhou, ChinaNative to Southern China, Ilex pubescens and Ilex asprella are frequently used in traditional Chinese medicine. Both of them produce a large variety of ursane-type triterpenoid saponins, which have been demonstrated to have different pharmacological effects. However, little is known about their biosynthesis. In this study, transcriptomic analysis of I. pubescens and comparison with its closely related specie I. asprella were carried out to identify potential genes involved in triterpenoid saponin biosynthesis. Through RNA sequencing (RNA-seq) and de novo transcriptome assembly of I. pubescens, a total of 68,688 UniGene clusters are obtained, of which 32,184 (46.86%) are successfully annotated by comparison with the sequences in major public databases (NCBI, Swiss-Prot, and KEGG). It includes 128 UniGenes related to triterpenoid backbone biosynthesis, 11 OSCs (oxidosqualene cyclases), 233 CYPs (cytochrome P450), and 269 UGTs (UDP-glycosyltransferases). By homology-based blast and phylogenetic analysis with well-characterized genes involved in triterpenoid saponin biosynthesis, 5 OSCs, 14 CYPs, and 1 UGT are further proposed as the most promising candidate genes. Transcriptomic comparison between two Ilex species using blastp and OrthoMCL method reveals high sequence similarity. All OSCs and UGTs as well as most CYPs are classified as orthologous genes, while only 5 CYPs in I. pubescens and 3 CYPs in I. asprella are species-specific. One of OSC candidates, named as IpAS1, was successfully cloned and expressed in Saccharomyces cerevisiae INVSc1. Analysis of the yeast extract by gas chromatography (GC) and gas chromatography–mass spectrometry (GC-MS) shows IpAS1 is a mixed amyrin synthase, producing α-amyrin and β-amyrin at ratio of 5:1, which is similar to its ortholog IaAS1 from I. asprella. This study is the first exploration to profile the transcriptome of I. pubescens, the generated data and gene models will facilitate further molecular studies on the physiology and metabolism in this plant. By comparative transcriptomic analysis, a series of candidate genes involved in the biosynthetic pathway of triterpenoid saponins are identified, providing new insight into their biosynthesis at transcriptome level.http://journal.frontiersin.org/article/10.3389/fpls.2017.00634/fullIlex pubescenstranscriptometriterpenoid saponinsbiosynthesistranscriptomic comparisongene identification |
| spellingShingle | Hui Xu Lingling Wen Xiaoyun Yun Xiasheng Zheng Ruoting Zhan Weiwen Chen Yaping Xu Ye Chen Jie Zhang Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species Frontiers in Plant Science Ilex pubescens transcriptome triterpenoid saponins biosynthesis transcriptomic comparison gene identification |
| title | Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species |
| title_full | Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species |
| title_fullStr | Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species |
| title_full_unstemmed | Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species |
| title_short | Transcriptomic Comparison Reveals Candidate Genes for Triterpenoid Biosynthesis in Two Closely Related Ilex Species |
| title_sort | transcriptomic comparison reveals candidate genes for triterpenoid biosynthesis in two closely related ilex species |
| topic | Ilex pubescens transcriptome triterpenoid saponins biosynthesis transcriptomic comparison gene identification |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2017.00634/full |
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