Transcriptome Analysis of Clinopodium chinense (Benth.) O. Kuntze and Identification of Genes Involved in Triterpenoid Saponin Biosynthesis

Shi, Yuanyuan; Zhang, Shengxiang; Peng, Daiyin; Wang, Chenkai; Zhao, Derui; Ma, Kelong; Wu, Jiawen; Huang, Luqi

doi:10.3390/ijms20112643

Cited by 11 publications

(11 citation statements)

References 42 publications

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“…In addition, 119,177 (68.52%) genes were mapped in at least one public database, while 54,761 (31.48%) genes remained unannotated because of the lack of available genomic information. The KEGG database is a useful tool for determining candidate genes in biological processes (Liu et al, 2017;Shi et al, 2019;Wang et al, 2018). We identified numerous unigenes participating in coumarin biosynthesis through KEGG annotations.…”

Section: Discussionmentioning

confidence: 99%

“…The KEGG database is a useful tool for determining candidate genes in biological processes ( Liu et al, 2017 ; Shi et al, 2019 ; Wang et al, 2018 ). We identified numerous unigenes participating in coumarin biosynthesis through KEGG annotations.…”

Section: Discussionmentioning

confidence: 99%

“…RNA-sequencing (RNA-Seq) has been widely applied as a powerful method for discovering and predicting functional genes, and revealing gene expression patterns, especially in non-model species for which reference genome sequences are insufficient ( Chu & Corey, 2012 ). To date, dozens of medicinal plants have been subjected to RNA-Seq analysis, including recent transcriptome analyses of Melilotus albus ( Luo et al, 2017 ), Artemisia argyi ( Liu et al, 2017 ), Arisaema heterophyllum ( Wang et al, 2018 ), Clinopodium chinense ( Shi et al, 2019 ) and Polygonatum cyrtonema ( Wang et al, 2019 ). However, such analytical approaches have not been used to obtain comprehensive transcriptomic resources for C. monnieri .…”

Section: Introductionmentioning

confidence: 99%

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De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis

Shi

Zhang

Peng

et al. 2020

PeerJ

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Cnidium monnieri (L.) Cuss (C. monnieri) is one of the most widely used traditional herbal medicines, exhibiting a wide range of pharmacological functions for treating asynodia, trichomonas vaginitis, and osphyalgia. Its important medicinal value comes from its abundance of coumarins. To identify genes involved in coumarin biosynthesis and accumulation, we analyzed transcriptome data from flower, leaf, root and stem tissues of C. monnieri. A total of 173,938 unigenes with a mean length of 1,272 bp, GC content of 38.79%, and N50 length of 2,121 bp were assembled using the Trinity program. Of these, 119,177 unigenes were annotated in public databases. We identified differentially expressed genes (DEGs) based on expression profile analysis. These DEGs exhibited higher expression levels in flower tissue than in leaf, stem or root tissues. We identified and analyzed numerous genes encoding enzymes involved in coumarin biosynthesis, and verified genes encoding key enzymes using quantitative real-time PCR. Our transcriptome data will make great contributions to research on C. monnieri and provide clues for identifying candidate genes involved in coumarin metabolic pathways.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis

Shi

Zhang

Peng

et al. 2020

PeerJ

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“…Therefore, comprehensive and systematic studies are needed for analyzing the total triterpenoids and triterpenoid variation pattern in leave coloring stages. Transcriptomic and metabolomic methods have helped progress the analysis of plant tissue metabolites dynamics [11][12][13]. Screening and selection of plant evaluation are directly dependent on differences in chemical composition, metabonomics method (which has unique advantages in the evaluation of medicinal plants for testing multiple ingredients at the same time) [14], comprehensive testing data [13], directly fitting the metabolic pathway, and conducting association analysis with transcriptomic results [12].…”

Section: Introductionmentioning

confidence: 99%

Triterpenoids Biosynthesis Regulation for Leaf Coloring of Wheel Wingnut (Cyclocaryapaliurus)

Sun

Fang

Shang

2021

Forests

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Cyclocaryapaliurus leaves are rich in triterpenoids with positive results in the treatment of diabetes, antioxidation, and scavenging free radicals. C. paliurus red leaves have been found to contain higher flavonoids including anthocyanin, however, the triterpenoids accumulation pattern is still unclear. For the purpose of researching the triterpenoid accumulating mechanism during red new leaf development, transcriptome and metabolome analysis was conducted during C. paliurus the red leaf development process. The results uncovered that most triterpenoid ingredients were found to accumulate during leaves turning green, while the unique ingredients content including cyclocaric acid A, cyclocarioside I, cyclocarioside Ⅱand cyclocarioside Ⅲ decreased or remained unchanged. Functional structure genes (hydroxymethylglutaryl-CoA synthase, hydroxymethylglutaryl-CoA reductase, and farnesyl-diphosphate synthase) were identified for promoting triterpenoids accumulation mainly in the mevalonic acid pathway (MVA). Moreover, glycosyltransferase (UGT73C, UGT85A, and UGT85K) was also found attributed to triterpenoids accumulation. These findings provide information for a better understanding of the triterpenoid biosynthesis mechanism during leaf development and will be useful for targeted breeding.

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“…Thus, RNA-Seq is a powerful tool for acquiring gene expression information and is of great significance in the mining of functional genes, analysis of gene expression profiles, and discovery of genetic metabolic networks [20]. At present, transcriptome sequencing has been applied to medicinal plants of the Labiatae family, including Scutellaria baicalensis Georgi [21], Ocimum sanctum and Ocimum basilicum [22], Mentha piperita and Mentha arvensis [23], and Clinopodium chinense [24]; however, the use of RNA-Seq analysis has not been reported in C. gracile to date.…”

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confidence: 99%

Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis

et al. 2020

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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.

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Transcriptome Analysis of Clinopodium chinense (Benth.) O. Kuntze and Identification of Genes Involved in Triterpenoid Saponin Biosynthesis

Cited by 11 publications

References 42 publications

De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis

De novo transcriptome analysis of Cnidium monnieri (L.) Cuss and detection of genes related to coumarin biosynthesis

Triterpenoids Biosynthesis Regulation for Leaf Coloring of Wheel Wingnut (Cyclocaryapaliurus)

Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis

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