De novo characterization of Panax japonicus C. A. Mey transcriptome and genes related to triterpenoid saponin biosynthesis

Zhang, Shaopeng; Wu, Yayun; Jin, Jian; Hu, Bin; Zeng, Wanyong; Zhu, Wenjun; Zheng, Yanyan; Chen, Ping

doi:10.1016/j.bbrc.2015.09.048

Cited by 26 publications

(15 citation statements)

References 22 publications

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“…Recent advances in transcriptome deep-sequencing technology and bioinformatics have opened a new avenue for such investigations (Hwang et al, 2015; Zhang et al, 2015; Rai et al, 2016). The transcriptomes of various plants have previously been investigated, e.g., Polygonum quinquefolium (Sun et al, 2010), Lolium multiflorum (Pan et al, 2016), Ipomoea batatas (Ma et al, 2016), Chrysanthemum morifolium (Xu et al, 2013), and Juglans mandshurica (Hu et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis to Identify the Putative Biosynthesis and Transport Genes Associated with the Medicinal Components of Achyranthes bidentata Bl.

Wang

Han

et al. 2016

Front. Plant Sci.

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Achyranthes bidentata is a popular perennial medicine herb used for 1000s of years in China to treat various diseases. Although this herb has multiple pharmaceutical purposes in China, no transcriptomic information has been reported for this species. In addition, the understanding of several key pathways and enzymes involved in the biosynthesis of oleanolic acid and ecdysterone, two pharmacologically active classes of metabolites and major chemical constituents of A. bidentata root extracts, is limited. The aim of the present study was to characterize the transcriptome profile of the roots and leaves of A. bidentata to uncover the biosynthetic and transport mechanisms of the active components. In this study, we identified 100,987 transcripts, with an average length of 1146.8 base pairs. A total of 31,634 (31.33%) unigenes were annotated, and 12,762 unigenes were mapped to 303 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. Moreover, we identified a total of 260 oleanolic acid and ecdysterone genes encoding biosynthetic enzymes. Furthermore, the key enzymes involved in the oleanolic acid and ecdysterone synthesis pathways were analyzed using quantitative real-time polymerase chain reaction, revealing that the roots expressed these enzymes to a greater extent than the leaves. In addition, we identified 85 ATP-binding cassette transporters, some of which might be involved in the translocation of secondary metabolites.

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Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis to Identify the Putative Biosynthesis and Transport Genes Associated with the Medicinal Components of Achyranthes bidentata Bl.

Wang

Han

et al. 2016

Front. Plant Sci.

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“…The longest transcript of each gene was selected as the unigene, and 96,738 unigenes were generated with an average length of 605.3 bp and an N50 length of 859 bp (Table 1). The average lengths of the unigenes and N50 were close to those of Panax japonicus 18 and Lily 28 and slightly longer than those of safflower 14 , Polygonum cuspidate 16 , and Ornithogalum caudatum 29 . A detailed size distribution of ZMD transcripts and unigenes is shown in Fig.…”

Section: Resultsmentioning

confidence: 68%

“…The downstream pathway includes two primary branches for triterpene saponin and steroidal saponin biosynthesis. The branch of triterpene saponin biosynthesis is distributed primarily in plants from Araliaceae , Leguminosae , Cucurbitaceae and Polygalaceae ; this biosynthesis is catalysed by beta-amyrin synthase (bAs) or dammarenediol synthase (DS) to synthesize β-amyrin or dammarenediol, which is further modified by glycosyltransferases (GTs) 18 . O .…”

Section: Resultsmentioning

confidence: 99%

“…japonicus tubers produce steroidal saponins, and the downstream branch metabolizes 2,3-oxidosqualene catalysed by cycloartenol synthase (CAS) to biosynthesize cycloartenol. Further modifications occur through the actions of many enzymes, including oxidase, reductase, desaturase, isomerase, methyltransferase and glucosyltransferase 18, 38 . In the downstream pathway, 67 unigenes were identified (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…As a result of the rapid development of next generation sequencing, RNA sequencing (RNA-seq) is a useful method for studying the metabolic pathways of medicinal components and related gene expression in different samples or tissues, such as flavonoid biosynthesis in Carthamus tinctorius 14 , Pueraria lobata 15 and Polygonum cuspidatum 16 ; saponin biosynthesis in Asparagus racemosus 17 , Panax japonicus 18 , Panax notoginseng 19 and Panax quinquefolius 20 ; glycyrrhizin biosynthesis in Glycyrrhiza uralensis 21 ; and fatty acid biosynthesis in Eucommia ulmoides 22 . With this method, related gene expression across samples or tissues can also be analyzed.…”

Section: Introductionmentioning

confidence: 99%

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De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) transcriptome in different growth stages

Liu

Wang

et al. 2017

Sci Rep

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Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) is a traditional medicinal herb in the family Liliaceae that has significant pharmacological effects on immunity and cardiovascular disease. In this study, three different growth stages of Zhe-Maidong were investigated using RNA-seq, and a total of 16.4 Gb of raw data was obtained. After filtering and assembling, 96,738 unigenes with an average length of 605.3 bp were ultimately generated. A total of 77,300 unigenes were annotated using information from five databases, including the NT, NR, SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Additionally, the mechanisms of flavonoid, saponin and polysaccharide biosynthesis and of accumulation at different stages of tuber development were also characterized. From the first to third years, the contents of flavonoids, saponins and polysaccharides all increased, whereas the expression levels of related genes decreased in the flavonoid and saponin pathways and first increased and then decreased in the polysaccharide pathway. The results of this study provide the most comprehensive expressed sequence resource for Zhe-Maidong and will expand the available O. japonicus gene library and facilitate further genome-wide research and analyses of this species.

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An Update to the Transcriptome Sequencing for the Genus Panax

Yang

2021

The Ginseng Genome

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De novo characterization of Panax japonicus C. A. Mey transcriptome and genes related to triterpenoid saponin biosynthesis

Cited by 26 publications

References 22 publications

Transcriptome Analysis to Identify the Putative Biosynthesis and Transport Genes Associated with the Medicinal Components of Achyranthes bidentata Bl.

Transcriptome Analysis to Identify the Putative Biosynthesis and Transport Genes Associated with the Medicinal Components of Achyranthes bidentata Bl.

De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) transcriptome in different growth stages

An Update to the Transcriptome Sequencing for the Genus Panax

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