Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers

Guo, Xu; Liu, Ying; Li, Chunfang; Luo, Hongmei; Wang, Lizhi; Qian, Jun; Luo, Xiang; Li, Xiang; Song, Jingyuan; Sun, Chao; Xu, Haibin; Yao, Hui; Chen, Shilin

doi:10.1016/j.gene.2013.05.073

Cited by 102 publications

(99 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Out of the 79,256 unigenes, 29,013 generated significant BLAXTX hit to genes encoding proteins or putative function in at least one of public databases (Supplementary Table S2 in Supplementary Material). In comparison with previous publication for DOKM (Guo et al, 2013), the low rate of annotated genes indicated that assembled unigenes, particularly sequences without a significant homologous hit, may potentially represent special sequences expressed during CA.…”

Section: Resultscontrasting

confidence: 53%

“…Gene specific qRT-PCR primers were designed using Primer-BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi), and the sequences are listed in Supplementary Table S4 in Supplementary Material. The qPCR reactions were performed as described in Guo et al (2013). All quantifications were normalized to the EF-1a gene (Accession: JF825419) and calculated using the 2 –ΔΔ Ct method (Livak and Schmittgen, 2001).…”

Section: Methodsmentioning

confidence: 99%

“…Such research on plant CA using multiple omic tools can discover useful genes for molecular breeding and facilitate the improvement of corp yields under cold ambient environment. Previous studies on DOKM were focused on exploring molecular markers and investigating alkaloid or polysaccharide biosynthetic genes (Lu et al, 2012; Guo et al, 2013; Zhang et al, 2016). According to our knowledge, no efforts have been made to investigate the molecular basis of CA for DOKM using whole-genome expression technologies.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Insights from the Cold Transcriptome and Metabolome of Dendrobium officinale: Global Reprogramming of Metabolic and Gene Regulation Networks during Cold Acclimation

Chen

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

Plant cold acclimation (CA) is a genetically complex phenomenon involving gene regulation and expression. Little is known about the cascading pattern of gene regulatroy network and the link between genes and metabolites during CA. Dendrobium officinale (DOKM) is an important medicinal and ornamental plant and hypersensitive to low temperature. Here, we used the large scale metabolomic and transcriptomic technologies to reveal the response to CA in DOKM seedlings based on the physiological profile analyses. Lowering temperature from 4 to –2°C resulted in significant increase (P < 0.01) in antioxidant activities and electrolyte leakage (EL) during 24 h. The fitness CA piont of 0°C and control (20°C) during 20 h were firstly obtained according to physiological analyses. Subsequently, massive transcriptome and metabolome reprogramming occurred during CA. The gene to metabolite network demonstrated that the CA associated processes are highly energy demanding through activating hydrolysis of sugars, amino acids catabolism and citrate cycle. The expression levels of 2,767 genes were significantly affected by CA, including 153-fold upregulation of CBF transcription factor, 56-fold upregulation of MAPKKK16 protein kinase. Moreover, the gene interaction and regulation network analysis revealed that the CA as an active process, was regulated at the transcriptional, post-transcriptional, translational and post-translational levels. Our findings highligted a comprehensive regulatory mechanism including cold signal transduction, transcriptional regulation, and gene expression, which contributes a deeper understanding of the highly complex regulatory program during CA in DOKM. Some marker genes identified in DOKM seedlings will allow us to understand the role of each individual during CA by further functional analyses.

show abstract

Section: Resultscontrasting

confidence: 53%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Insights from the Cold Transcriptome and Metabolome of Dendrobium officinale: Global Reprogramming of Metabolic and Gene Regulation Networks during Cold Acclimation

Chen

et al. 2016

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…It was later proved to be the special content of D. nobile [48]. As reported, the alkaloid in Dendrobium officinale belongs to the terpenoid indole alkaloid (TIA) class, with its total content measured at approximately 0.02% [49]. However, the isolation and identification of one single kind of alkaloid have been rarely reported.…”

Section: Phytochemistrymentioning

confidence: 99%

Dendrobium officinale Kimura et Migo: A Review on Its Ethnopharmacology, Phytochemistry, Pharmacology, and Industrialization

Tang

Zhao

Sheng

et al. 2017

Evidence-Based Complementary and Alternative Medicine

162

124

View full text Add to dashboard Cite

Ethnopharmacological Relevance. Dendrobii Officinalis Caulis, the stems of Dendrobium officinale Kimura et Migo, as a tonic herb in Chinese materia medica and health food in folk, has been utilized for the treatment of yin-deficiency diseases for decades. Methods. Information for analysis of Dendrobium officinale Kimura et Migo was obtained from libraries and Internet scientific databases such as PubMed, Web of Science, Google Scholar, ScienceDirect, Wiley InterScience, Ingenta, Embase, CNKI, and PubChem. Results. Over the past decades, about 190 compounds have been isolated from Dendrobium officinale Kimura et Migo. Its wide modern pharmacological actions in hepatoprotective effect, anticancer effect, hypoglycemic effect, antifatigue effect, gastric ulcer protective effect, and so on were reported. This may mainly attribute to the major and bioactive components: polysaccharides. However, other small molecule components require further study. Conclusions. Due to the lack of systematic data of Dendrobium officinale, it is important to explore its ingredient-function relationships with modern pharmacology. Recently, studies on the chemical constituents of Dendrobium officinale concentrated in crude polysaccharides and its structure-activity relationships remain scant. Further research is required to determine the Dendrobium officinale toxicological action and pharmacological mechanisms of other pure ingredients and crude extracts. In addition, investigation is needed for better quality control and novel drug or product development.

show abstract

“…Employing transcriptomic approaches to collect and analyze bioinformation for understanding its genetic makeup and biosynthetic pathways of important secondary metabolites is a practical way to better protect and utilize this medicinal resource by using biotechnologies to produce products of interest in the future. By far, studies on genomic and transcriptomic level of Dendrobium plants have been confined to a few species such as D. officinal and D. nobile [13,15,16]. To our best knowledge, no transcriptomic report on D. huoshanense was retrieved up to date.…”

Section: Digital Signaturementioning

confidence: 99%

Transcriptomic landscape of Dendrobium huoshanense and its genes related to polysaccharide biosynthesis

et al. 2018

View full text Add to dashboard Cite

Dendrobium huoshanense has long been used to treat various diseases in oriental medicine. In order to study its gene expression profile, transcripts involved in the biosynthesis of precursors of polysaccharides, as well as mechanisms underlining morphological differences between wild and cultivated plants, three organs of both wild type and cultivated D. huoshanense were collected and sequenced by Illumina HiSeq4000 platform, yielding 919,409,540 raw reads in FASTQ format. After Trinity de novo assembly and quality control, 241,242 nonredundant contigs with the average length of 967.5 bp were generated. qRT-PCR experiment on the selected transcripts showed the transcriptomic data were reliable. BLASTx was conducted against NR, SwissProt, String, Pfam, and KEGG. Gene ontology annotation revealed more than 40,000 contigs assigned to catalytic activity and metabolic process, suggesting its dynamic physiological activities. By searching KEGG pathway, six genes potentially involved in mannose biosynthetic pathway were retrieved. Gene expression analysis for stems between wild and cultivated D. huoshanense resulted in 956 genes differentially expressed. Simple sequence repeats (SSRs) analysis revealed 143 SSRs with the unit size of 4 and 3,437 SSRs the size of 3. The obtained SSRs are the potential molecular markers for discriminating distinct cultivars of D. huoshanense.

show abstract

Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers

Cited by 102 publications

References 39 publications

Insights from the Cold Transcriptome and Metabolome of Dendrobium officinale: Global Reprogramming of Metabolic and Gene Regulation Networks during Cold Acclimation

Insights from the Cold Transcriptome and Metabolome of Dendrobium officinale: Global Reprogramming of Metabolic and Gene Regulation Networks during Cold Acclimation

Dendrobium officinale Kimura et Migo: A Review on Its Ethnopharmacology, Phytochemistry, Pharmacology, and Industrialization

Transcriptomic landscape of Dendrobium huoshanense and its genes related to polysaccharide biosynthesis

Contact Info

Product

Resources

About