De novo transcriptome sequencing-based discovery and expression analyses of verbascoside biosynthesis-associated genes in Rehmannia glutinosa tuberous roots

Zhou, Yanqing; Wang, Xiangnan; Wang, Wanshen; Duan, Hongying

doi:10.1007/s11032-016-0548-x

Cited by 18 publications

(24 citation statements)

References 23 publications

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“…Sun et al generated a total of 81,003 unique sequences from the cDNA library constructed from the ARs, TARs, and DTRs of R. glutinosa by using the Illumina sequencing platform [41]. In this study, we obtained 38,678~54,378 unigenes from the 24 cDNA libraries of radial striations and non-radial striations of R. glutinosa tuberous roots and eventually assembled a final set of 150,405 entries with an average length of 1244 bp higher than mixed roots unigenes (383 bp and 678 bp) [17,41] and mixed leaf and root unigenes (868 bp) [43]. This novel unigene database provides a high-quality reference transcriptome on gene expression detection and molecular mechanisms for R. glutinosa .…”

Section: Discussionmentioning

confidence: 99%

“…Catalpol and acteoside are usually selected as the two quality-control components in the R. glutinosa herb and have been included in the Chinese Pharmacopoeia since the 2015 edition. Considering limited genomic information coupled with genome complexity (polyploidy), several reports about the catalpol and acteoside biosynthesis pathway have been seen in some studies [16,17,18], but the molecular regulation mechanism needs to be deeply studied.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root

Zhi

Zhang

Yang

et al. 2018

IJMS

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Rehmannia glutinosa L., a perennial plant of Scrophulariaceae, is one of the most commonly used herbs in traditional Chinese medicine (TCM) that have been widely cultivated in China. However, to date, the biosynthetic pathway of its two quality-control components, catalpol and acteoside, are only partially elucidated and the mechanism for their tissue-specific accumulation remains unknown. To facilitate the basic understanding of the key genes and transcriptional regulators involved in the biosynthesis of catalpol and acteoside, transcriptome sequencing of radial striation (RS) and non-radial striation (nRS) from four R. glutinosa cultivars was performed. A total of 715,158,202 (~107.27 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 150,405 transcripts. Functional annotation with multiple public databases identified 155 and 223 unigenes involved in catalpol and acteoside biosynthesis, together with 325 UGTs, and important transcription factor (TF) families. Comparative analysis of the transcriptomes identified 362 unigenes, found to be differentially expressed in all RS vs. nRS comparisons, with 143 upregulated unigenes, including those encoding enzymes of the catalpol and acteoside biosynthetic pathway, such as geranyl diphosphate synthase (RgGPPS), geraniol 8-hydroxylase (RgG10H), and phenylalanine ammonia-lyase (RgPAL). Other differentially expressed unigenes predicted to be related to catalpol and acteoside biosynthesis fall into UDP-dependent glycosyltransferases (UGTs), as well as transcription factors. In addition, 16 differentially expressed genes were selectively confirmed by real-time PCR. In conclusion, a large unigene dataset of R. glutinosa generated in the current study will serve as a resource for the identification of potential candidate genes for investigation of the tuberous root development and biosynthesis of active components.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root

Zhi

Zhang

Yang

et al. 2018

IJMS

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“…Among these compounds, catalpol and verbascoside are used as index components of R. glutinosa in the Pharmacopoeia of the People’s Republic of China. Verbascoside possesses pharmacological bioactivities for human health, such as antioxidant, anti-inflammatory, antineoplastic, wound-healing and neuroprotective properties 10 . Catalpol has important roles to play in the treatment of many diseases, including kidney diseases, neurodegenerative diseases and diabetes 11 .…”

Section: Introductionmentioning

confidence: 99%

Metabolite accumulation and metabolic network in developing roots of Rehmannia glutinosa reveals its root developmental mechanism and quality

Zhou

Yang

Zhang

et al. 2018

Sci Rep

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Rehmannia glutinosa root contains many compounds with important medicinal properties and nutritional benefits, but only more than 140 compounds have been reported so far. Many other compounds and their accumulation and metabolic networks during its development remain unclear. In order to clarify them, its metabolic profiles at three different developmental stages were analyzed using untargeted LC-MS analysis. Multivariate analysis revealed that 434 metabolites differently accumulated in its different stages, suggesting different change trends. The metabolites having the same trend share common metabolic pathways, the metabolites showing increasing contents during its development have medical and nutritional values, and some mature root-specific metabolites may be better candidates for its quality control; 434 metabolites were mapped onto 111 KEGG pathways including 62 enzymes, whose increasing and decreasing patterns were shown during its development. Some metabolites complicatedly interacted with some enzymes and the top-10 pathways enriched from 111 KEGG pathways in network analysis. These findings extended the dataset of its identified compounds, and revealed that its development and quality were associated with the accumulation of different metabolites. Our work will lay the foundation for the better understanding of its chemical constituents, quality and developmental mechanism.

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“…The full-length transcripts can be used to investigate alternative splicing, alternative polyadenylation, novel genes, non-coding RNAs and fusion transcripts [31], Based on these advantages of full-length transcriptome sequencing, we conducted the full-length transcriptome sequencing of R. glutinosa, a non-model plant, and constructed its full-length transcriptome database for the rst time, which would be used as a reference database for other studies. Its database capacity of 26.61Gb clean data with cDNA size of 1-6kb is bigger than its NGS transcriptome databases such as 42.91Gb clean data in this study and one of its previous studies [20]. 46,412 coding sequences with complete ORF, obtained based on this full-length transcriptome database, made its gene cloning faster and more e cient and easier than homology cloning and electronic cloning [32,33].…”

Section: Discussionmentioning

confidence: 99%

Multi-omics Analysis Reveals Whether and how Naphthylacetic Acid Affects the Quality of Rehmannia Glutinosa

Li¹,

Shao²,

Zhu³

et al. 2020

Preprint

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Background: Rehmannia glutinosa (R.glutinosa) is an important medicinal plant. The tuberous root of R.glutinosa is often used as herbal medicine. Naphthylacetic acid (NAA) as expansin can improve its yield, but knowledge about gene regulation and metabolome in its root is limited.Results: Full-length transcriptome, next generation transcriptome(NGS), small RNA and degradome sequencing and metabolomics were used to elucidate whether and how NAA affected its quality.30 differential expression metabolites (DEMs) (11 upregulated, 19downregulated) were identified, but catalpol and Rehmannioside D as quality standards were unchanged in its tuberous roots under control and NAA conditions (CKs and NTs); Their NGS identified 1,113 differentially expressed transcripts (DETs) (596 upregulated, 517downregulated) verified by RT-qPCR; Small RNA sequencing identified 78miRNAs (11known, 67 novel), of which 3 were differentially expressed miRNAs (1upregulated, 2downregulated). Among them, 274 differentially expressed miRNAs target transcripts (DEMTs) were predicted found and then validated by degradome sequencing; DETs and DEMTs were mainly related to metabolism. 4 miRNA-mRNA interaction pairs that regulates 4 metabolites (2 negatively correlated, 2 positively correlated) were identified; DETs, DEMs, differentially expressed miRNAs and DEMTs involved in phenylpropanoid biosynthesis regulated metabolites.Conclusions: The identification of DETs, DEMs, differentially expressed miRNAs and DEMTs could help to elucidate the regulatory networks and molecular mechanisms important for NAA-improving root quality of R.glutinosa.

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De novo transcriptome sequencing-based discovery and expression analyses of verbascoside biosynthesis-associated genes in Rehmannia glutinosa tuberous roots

Cited by 18 publications

References 23 publications

Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root

Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root

Metabolite accumulation and metabolic network in developing roots of Rehmannia glutinosa reveals its root developmental mechanism and quality

Multi-omics Analysis Reveals Whether and how Naphthylacetic Acid Affects the Quality of Rehmannia Glutinosa

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