 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 01, 2016 |
| Title |
De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways |
| Organism |
Lonicera japonica |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on homology search using blastx against NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcripts expression data from all nine tissues of L. japonica showed relationships between tissues explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid were enriched in stem and leaf-2, unigenes from luteolin were enriched in stem and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with a specific pharmaceutically important metabolic pathways, and therefore, possess unique medicinal properties. Present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes.
|
| |
|
| Overall design |
De novo transcriptome assembly and characterization, and transcriptome profiling for nine tissues of Lonicera japonica
|
| |
|
| Contributor(s) |
Yamazaki M, Saito K, Rai A, Suzuki H, Nakamura M, Takahashi H |
| Citation(s) |
27629269 |
| |
| Submission date |
May 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mami Yamazaki |
| E-mail(s) |
mamiy@faculty.chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Graduate School of Pharmaceutical Sciences
|
| Lab |
Department of Molecular Biology and Biotechnology
|
| Street address |
Inohana 1-8-1, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
2608675 |
| Country |
Japan |
| |
|
| Platforms (1) |
| GPL21949 |
Illumina HiSeq 2000 (Lonicera japonica) |
|
| Samples (9)
|
|
| Relations |
| BioProject |
PRJNA323504 |
| SRA |
SRP075780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81949_Lonicera_japonica_FPKM_annotation_description.xlsx |
50.5 Mb |
(ftp)(http) |
XLSX |
| GSE81949_Lonicera_japonica_de_novo_transcriptome_assembly.fasta.gz |
55.5 Mb |
(ftp)(http) |
FASTA |
| GSE81949_RAW.tar |
30.0 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...