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

Li, Jinting; Wang, Can; Han, Xiaohu; Qi, Wanzhen; Chen, Yanqiong; Wang, Taixia; Zheng, Yanyan; Zhao, Xuhong

doi:10.3389/fpls.2016.01860

Cited by 15 publications

(10 citation statements)

References 67 publications

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“…Equal amounts of total RNA extracted from samples taken at different time points were pooled together. The methods for total RNA extraction and cDNA library construction were described previously [16]. Three biological replicates were used for RNA extraction and two replicates were used for leaf transcriptome sequencing.…”

Section: Library Construction and High-throughput Rna Sequencingmentioning

confidence: 99%

“…The raw RNA-seq reads were processed to remove sequencing adapters and low quality bases using Trimmomatic [33], and clean reads shorter than 80 bp were discarded. Then, the highquality reads were assembled into unigenes with previously published data [16] using Trinity [34] with "min_kmer_cov" set to 10. The unigenes were compared to the ribosome RNA database [35] and GenBank Nucleotide (nt) database using BLAST+ [36] to remove ribosome RNA, viral and bacterial DNA, and other contaminants.…”

Section: Rna Sequencing Data Analysismentioning

confidence: 99%

“…To enhance data reliability, cDNA libraries were prepared for two biological repeats of each sequencing sample. Combined with clean reads generated by our previous study [16], about 164 million clean read pairs (16.4 Gbp) were used for de novo transcriptome assembly. A total of 102,126 unigenes were assembled.…”

Section: Rna-seq Analysis Of a Bidentata Leavesmentioning

confidence: 99%

“…Transcription factors differentially expressed in response to auxin and cytokinin treatment in A. bidentata. Up-regulated TF genes Down-regulated TF genes MADS box transcription factor 34 27 7 Ethylene-responsive transcription factor 31 20 11 AP2-like ethylene-responsive transcription factor 21 19 2 bHLH transcription factor 21 16 5 bZIP transcription factor 21 7 14 Heat stress transcription factor 19 12 7 Nuclear transcription factor Y 17 16 using qRT-PCR. The expression patterns of these genes in the T and Control leaves were consistent with the expression patterns based on RNA-seq, and there was a close correlation (r = 0.94) between the expression changes determined by RNA-seq and by qRT-PCR ( Fig 6).…”

Section: Rna-seq Accuracy Determined By Real-time Pcrmentioning

confidence: 99%

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NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl

et al. 2020

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Application of plant growth regulators has become one of the most important means of improving yield and quality of medicinal plants. To understand the molecular basis of phytohormone-regulated oleanolic acid metabolism, RNA-seq was used to analyze global gene expression in Achyranthes bidentata treated with 2.0 mg/L 1-naphthaleneacetic acid (NAA) and 1.0 mg/L 6-benzyladenine (6-BA). Compared with untreated controls, the expression levels of 20,896 genes were significantly altered with phytohormone treatment. We found that 13071 (62.5%) unigenes were up-regulated, and a lot of differentially expressed genes involved in hormone or terpenoid biosynthesis, or transcription factors were significantly upregulated. These results suggest that oleanolic acid biosynthesis induced by NAA and 6-BA occurs due to the expression of key genes involved in jasmonic acid signal transduction. This study is the first to analyze the production and hormonal regulation of medicinal A. bidentata metabolites at the molecular level. The results herein contribute to a better understanding of the regulation of oleanane-type triterpenoid saponins accumulation and define strategies to improve the yield of these useful metabolites. OPEN ACCESSCitation: Liu Y, Tang L, Wang C, Li J (2020) NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl. PLoS ONE 15(2): e0229490. https://doi.org/10.triterpenoid biosynthetic pathway can be divided into three steps: synthesis of universal terpenoid precursors, formation of carbon skeletons, and modification of triterpenoid skeletons. Triterpenoid precursors are synthesized mainly through the cytoplasmic mevalonate (MVA) pathway. The plastidic 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway is believed to be a minor pathway for triterpenoid biosynthesis [17]. Triterpenoid skeleton synthesis genes include FPS (farnesyl diphosphate synthase), SS (squalene synthase), SE (squalene epoxidase), and OSCs (oxidosqualene cyclases). The cyclization of 2,3-oxidosqualene catalyzed by OSCs is a key step in the biosynthesis of triterpenoid saponins and sterols. β-amyrin synthase (β-AS) and cycloartenol synthase (CAS) catalyze the conversion of 2,3-oxidosqualene to β-amyrin and cycloartenol, which are precursors for oleanolic acid and phytosterols, respectively. A lot is known about several genes involved in modification of the triterpenoid skeleton downstream of the cyclization step are known. Some cytochrome P450 monooxygenases (CYP450s) and glycosyl transferases (GTs) were shown to catalyze modifications of triterpenoid skeletons, including hydroxylation and glycosidation. An increasing number of studies have indicated that the CYP716 family belongs to the CYP85 clan of CYP450s, and is involved in biosynthesis of various triterpenoids including oleanane backbones [18,19]. For example, CYP716A12 is involved in oxidation of the β-amyrin skeleton, which modifies the oleanane backbone [20]. CYP716A52v2 catalyzes the conversion of βamyrin to oleanolic acid in P. ginseng [21]. Howeve...

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Section: Library Construction and High-throughput Rna Sequencingmentioning

confidence: 99%

Section: Rna Sequencing Data Analysismentioning

confidence: 99%

Section: Rna-seq Analysis Of a Bidentata Leavesmentioning

confidence: 99%

Section: Rna-seq Accuracy Determined By Real-time Pcrmentioning

confidence: 99%

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NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl

et al. 2020

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“…Transcriptome deep sequencing not only provides comprehensive information of the plant genome, but also contributes to the development of numerous unigene-based simple sequences repeat (SSR) markers [13,14]. Recent progress in RNA-seq technology and bioinformatics has opened up a new pathway for genetic research [15,16]. Compared to other molecular markers such as ISSR, RAPD, AFLP and SNP, SSR markers are more suitable for use in genetic linkage analysis, molecular breeding, genetic diversity analysis, and in the determining the location of target genes [17,18].…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq for excavation of genes involved in the biosynthesis of primary active components and identification of new EST-SSR markers in medicinal chrysanthemum

Zhao

Song

et al. 2019

ARCH BIOL SCI BELGRA

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Chrysanthemum morifolium cv. 'Huaihuang' has great medicinal and commercial value. However, limited genomic and transcriptional information restricts the further research of 'Huaihuang' . In this study, using 'Huaihuang' leaf as the sample, we performed RNA-Seq and obtained numerous unigene sequences for functional characterization, and developed new EST-SSR markers. The results show that 176 unigenes were assigned to the 'antioxidant activity' in GO annotations, 998 unigenes were assigned to 'Secondary metabolite biosynthesis, transport and catabolism' in the KOG database, 381 unigenes were assigned to 'Biosynthesis of other secondary metabolites' , and 377 unigenes were assigned to 'Metabolism of terpenoids and polyketides' in the KEGG database. A number of genes involved in the biosynthesis of flavones and terpenes, such as CHS, CHI, FLS, HMGR and MVD, were found in the transcription data of 'Huaihuang' . Also, 36 new polymorphic EST-SSR markers were developed and validated. Using them, the genetic diversity was analyzed and a dendrogram of six clades was constructed among 15 medicinal chrysanthemum varieties. The excavated unigenes and identified new EST-SSR markers will provide useful resources for the study of biosynthesis of active components, genetic diversity analysis, population structure identification and in molecular breeding research of 'Huaihuang' and related species.

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The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

Yang

Yan

et al. 2018

Plant Cell Rep

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The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.

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

Cited by 15 publications

References 67 publications

NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl

NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl

RNA-Seq for excavation of genes involved in the biosynthesis of primary active components and identification of new EST-SSR markers in medicinal chrysanthemum

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

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