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SRX1299433: GSM1899803: SGE; Gastrodia elata; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 18.4M spots, 2.7G bases, 1.5Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes
show Abstracthide Abstract
Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of G. elata, the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi Mycena spp. and Armillaria mellea during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in G. elata, and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in G. elata, a comparative analysis of de novo transcriptome sequencing among the vegetative propagation corms and tubers of G. elata and A. mellea was conducted using deep sequencing. Transcriptome comparison between the vegetative propagation corms and juvenile tubers of G. elata revealed 582 differentially expressed unigenes, of which 415 and 167 genes were, respectively up-regulated (fold-change = 2, p-value < 0.05) and down-regulated (fold-change = 0.5, p-value <0.05) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, forty-seven up-regulated unigenes with enzyme commission (EC) were assigned to 269 isogroups involved in 100 different pathways, and twenty-four down-regulated unigenes with enzyme commission (EC) were assigned to 586 isogroups, involved in 167 different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes at locus 25,051 (one of monooxygenases) and locus 22,288 (one of glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway. The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of G. elata is proposed. Overall design: Transcriptome comparative between vegetative propagation corms and tubers of G. elata, and between tubers of G. elata (symbiosis A. mellea) and A. mellea
Sample: SGE
SAMN04125670 • SRS1096846 • All experiments • All runs
Organism: Gastrodia elata
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA purified was quantified at OD260 by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA). RNA libraries were prepared for sequencing using TruSeq RNA Library Preparation Kit v2 with standard Illumina protocols
Experiment attributes:
GEO Accession: GSM1899803
Links:
Runs: 1 run, 18.4M spots, 2.7G bases, 1.5Gb
Run# of Spots# of BasesSizePublished
SRR254591518,436,7942.7G1.5Gb2016-08-24

ID:
1856306

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