Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

ABSTRACT: Phylogenomics and barcoding of Panax: toward the identification of ginseng species

PROVIDER: PRJNA391291 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5725240.fastq.gz	Fastqsanger.gz
	SRR5725242.fastq.gz	Fastqsanger.gz
	SRR5725492.fastq.gz	Fastqsanger.gz
	SRR5725505.fastq.gz	Fastqsanger.gz
	SRR5738920.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Panax ginseng

Project description:Panax ginseng

| PRJNA42929 | ENA

Transcriptional profiling by high throughput sequencing of Panax ginseng C.A. Meyer leaf and stem transcriptomes during the leaf-expansion period.

Project description:In order to research the ginseng leaf-stem gene expression profiles of and dig out its function genes in the leaf-expansion period, the transcriptomic sequencing technology was set up the first time for five years the transcription of the Panax ginseng leaf-stem in the leaf-expansion period.

2012-07-31 | E-MTAB-937 | biostudies-arrayexpress

Phylogenomics and barcoding of Panax: toward the identification of ginseng species.

Project description:BACKGROUND:The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS:We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. CONCLUSIONS:MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.

| S-EPMC5883351 | biostudies-literature

Panax ginseng

Project description:Panax ginseng transcriptome

| PRJNA302554 | ENA

Panax ginseng

Project description:Panax ginseng Genome sequencing

| PRJNA189837 | ENA

Panax ginseng

Project description:resequencing of Panax ginseng

| PRJNA251960 | ENA

Panax ginseng

Project description:Panax ginseng transcriptome project

| PRJNA62877 | ENA

Panax ginseng transcriptome

Project description:Panax ginseng transcriptome

| PRJNA1111682 | ENA

Analysis of Panax ginseng secreted proteins under salt stress

Project description:Salt stress is one of the major abiotic stresses affecting the yield of ginseng (Panax ginseng C. A. Meyer). The objective of this study was to identify proteins of ginseng, which is responsive in salt stress. In this direction, ginseng plants of different growth stages (3, 4 and 5 years), were grown in the hydroponic conditions and exposed to 5 ds/m salt concentration. The secreted proteins, collected from the water, at 0, 24, 72 and 120 hours after exposure were used for the proteome analysis using shotgun approaches. Through the shotgun proteomics, a total of 155 and 88 secreted proteins were identified by searching in two RNA-sequencing (RNA-seq) database, respectively.

2022-11-17 | PXD010322 | Pride

Transcript profiles of the flowering period Panax ginseng C.A. Meyer root and analysis the gene function

Project description:Panax ginseng C.A. Meyer is one of the most popular medicinal herbs. In order to research the genes that related to the flowering period of ginseng, and find out the antifungal proteins and transcription factors that combat various biotic and abiotic stress, a cDNA sample was prepared from the flowering period ginseng root of a five-year-old plant and sequenced using the Illumina sequencing platform. In this study, we produced nearly 40 million sequencing reads. These reads were assembled into 134,045 contigs using Trinity software (mean size: 282 bp). Based on a similarity search with known proteins, we identified 79,307 sequences with a cut-off E-value of 10-5. Assembled sequences were then annotated using gene ontology (GO) terms, clusters of orthologous group (COG) classifications and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways respectively.

2014-07-25 | E-MTAB-1239 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data