De novo assembly and analysis of the Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

Liu, Miaomiao; Zhu, Jiaquan; Wu, Sheng-Bing; Wang, Chenkai; Wu, Jiawen; Zhou, Meiqi

doi:10.1038/s41598-018-24201-9

Cited by 33 publications

(22 citation statements)

References 44 publications

(46 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In particular, RNA sequencing (RNA-Seq) has been shown to be the most efficient, cost effective method for the analysis of functional genes as well as for the accurate quantification of their expression in the absence of a reference genome [20–22]. Dozens of medicinal plants have so far been subjected to RNA-Seq analysis, including Artemisia argyi [23], A. annua [24], Eugenia uniflora L. [25], P. sibiricum [26], and Dendrobium officinale [27]. The use of this approach has enabled the identification of a number of new functional genes involved in specific metabolic pathways.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis

et al. 2019

Self Cite

View full text Add to dashboard Cite

Background Polygonatum cyrtonema Hua ( P. cyrtonema ) is one of the most important herbs in traditional Chinese medicine. Polysaccharides in P. cyrtonema plants comprise a class of important secondary metabolites and exhibit a broad range of pharmacological functions. Results In order to identify genes involved in polysaccharide biosynthesis, we performed RNA sequencing analysis of leaf, root, and rhizome tissues of P. cyrtonema . A total of 164,573 unigenes were obtained by assembling transcripts from all three tissues and 86,063 of these were annotated in public databases. Differentially expressed genes (DEGs) were determined based on expression profile analysis, and DEG levels in rhizome tissues were then compared with their counterparts in leaf and root tissues. This analysis revealed numerous genes that were either up-regulated or uniquely expressed in the rhizome. Multiple genes encoding important enzymes, such as UDP glycosyltransferases (UGTs), or transcription factors involved in polysaccharide biosynthesis were identified and further analyzed, while a few genes encoding key enzymes were experimentally validated using quantitative real-time PCR. Conclusion Our results substantially expand the public transcriptome dataset of P. cyrtonema and provide valuable clues for the identification of candidate genes involved in metabolic pathways. Electronic supplementary material The online version of this article (10.1186/s13007-019-0441-9) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

“…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%

See 1 more Smart Citation

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

Shi

Zhang

Peng

et al. 2020

PeerJ

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…RNA-sequencing can provide comprehensive information for gene expression to improve our understanding of gene regulation and metabolic pathways [21]. Some medicinal plant genomes have been sequenced, including Artemisia argyi [22], Dendrobium officinale [23], Pueraria lobata [24], Gentiana rigescens [25] and Arisaema heterophyllum Blume [26], and novel genes encoding key enzymes involved in specific metabolic pathways have been identified. However, genomic information 4 for P. odoratum has not yet been reported, which hinders further research on this species.…”

Section: Introductionmentioning

confidence: 99%

De novo Assembly and Transcriptome Analysis of Polygonatum odoratum (Mill.) Druce : Detection of Potential Genes Involved in Polysaccharide Synthesis

zhang

shi

huang

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Background: Polygonatum odoratum (Mill.) Druceis a well-known traditional Chinese herb. Polysaccharide is one of the main bioactive components from Polygonatum odoratum, with broad pharmacological effects, including improving immunity, and is used in the treatment of rheumatic heart disease, cardiovascular disease, and diabetes. Results: This study identifies potential genes and transcription factors (TFs) that regulate polysaccharide synthesis in Polygonatum odoratum by using RNA sequencing data from leaf, stem and rhizome tissues. A total of 112,443 unigenes were de novo assembled, and 76,714 were annotated in public databases. Differentially expressed gene analysis showed that most upregulated and uniquely expressed unigenes were enriched in rhizome tissue compared with leaf or stem tissue. UV-spectrophotometry results showed that polysaccharide content was the greatest in the rhizome tissue. Additionally, 2,865 unigenes relevant to TF families were predicted, including 73 involved in polysaccharide synthesis. A few key enzyme genes were also verified by quantitative real-time PCR (qRT-PCR). Seven β-fructofuranosidases with different amino acid sequences showed similar spatial structures and all had well-conserved catalytic triads. Conclusion: This study substantially enlarges the public transcriptome datasets of this species, and provides insight into the detection of novel genes involed polysaccharide and other secondary metabolite synthesis. Keywords: Polygonatum odoratum, transcriptome , polysaccharide synthesis, Differentially expressed gene, key enzyme genes

show abstract

De novo assembly and analysis of the Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

Cited by 33 publications

References 44 publications

Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis

Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis

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

De novo Assembly and Transcriptome Analysis of Polygonatum odoratum (Mill.) Druce : Detection of Potential Genes Involved in Polysaccharide Synthesis

Contact Info

Product

Resources

About