 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 23, 2016 |
| Title |
Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes |
| Organisms |
Armillaria mellea; Gastrodia elata |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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
|
| |
|
| Contributor(s) |
Tsai C, Wu K, Chiang T, Huang C, Chou C, Li S, Chiang Y |
| Citation(s) |
26960548 |
| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chi-Chu Tsai |
| E-mail(s) |
tsaicc@mail.kdais.gov.tw
|
| Phone |
886-8-7746735
|
| Organization name |
Kaohsiung District Agricultural Research and Extension Station
|
| Department |
Crop Improvement Section
|
| Lab |
Floriculture Research Office
|
| Street address |
2-6 Dehe Rd., Dehe Village, Changjhih Township
|
| City |
Pingtung County |
| ZIP/Postal code |
90846 |
| Country |
Taiwan |
| |
|
| Platforms (2) |
| GPL20975 |
Illumina HiSeq 2000 (Armillaria mellea) |
| GPL20976 |
Illumina HiSeq 2000 (Gastrodia elata) |
|
| Samples (3) |
|
| Relations |
| BioProject |
PRJNA297618 |
| SRA |
SRP064423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE73633_Trinity-Unigenes.fa.gz |
26.9 Mb |
(ftp)(http) |
FA |
| GSE73633_Trinity-Unigenes_TMM-FPKM.matrix.gz |
919.1 Kb |
(ftp)(http) |
MATRIX |
| GSE73633_Trinity-Unigenes_annotations.tsv.gz |
6.3 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
