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Data released on September 22, 2017

Ginseng genome examination for ginsenoside biosynthesis

Xu, J; Chu, Y; Xiao, S; Liao, B; Yin, Q; Bai, R; Su, H; Dong, L; Li, X; Qian, J; Zhang, J; Zhang, Y; Zhang, X; Wu, M; Zhang, J; Li, G; Zhang, L; Chang, Z; Zhang, Y; Jia, Z; Liu, Z; Afreh, D; Nahurira, R; Zhang, L; Cheng, R; Zhu, Y; Zhu, G; Rao, W; Zhou, C; Qiao, L; Huang, Z; Cheng, Y; Chen, S (2017): Ginseng genome examination for ginsenoside biosynthesis GigaScience Database. http://dx.doi.org/10.5524/100348 RIS BibTeX Text

Ginseng, which contains ginsenosides characterized as bioactive compounds, has been regarded as an important traditional medicine for several millennia. Howerver, the genetic background of ginseng remains poorly understood partly because of the plant's large and complex genome composition.
We report the entire genome sequence of Panax ginseng using next-generation sequencing. The 3.5 Gb nucleotide sequence contained more than 60% repeats and encoded 42,006 predicted genes. Twenty-two transcriptome datasets and mass spectrometry images of ginseng roots were adopted to precisely quantify the functional genes. Thirty-one genes were identified to be involved in the mevalonic acid pathway. Eight of these genes were annotated as 3-hydroxy-3-methylglutaryl-CoA reductases, which displayed diverse structures and expression characteristics. A total of 225 UDP-glycosyltransferase (UGTs) were identified, and these UGTs accounted for one of the largest gene families of ginseng. Tandem repeats contributed to the duplication and divergence of UGTs. Molecular modeling of UGTs in the 71, 74, and 94 families revealed a regiospecific conserved motif located at the N-terminus. Molecular docking predicted that this motif captured ginsenoside precursors.
The panorama of ginseng genome represents a valuable resource for understaning and improving the breeding, cultivation, and synthesis biology of this key herb.

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Related manuscripts:

doi:10.1093/gigascience/gix093

Genome browser:

http://ginseng.vicp.io:23488/

Keywords:

panax ginseng ginsenosides genome mass spectrometry imaging 

Genomic

http://gigadb.org/images/data/cropped/100348.jpg

Funding:

  • Funding body - National Natural Science Foundation of China
  • Award ID - 81403053
  • Awardee - J Xu
  • Funding body - National Natural Science Foundation of China
  • Award ID - 81503469
  • Awardee - S Xiao
  • Funding body - Institue of Chinese Materia Medica, China Academy of Chinese Medical Sciences & Peking Union Medical College
  • Award ID - ZZ0808021
  • Awardee - S Chen
  • Funding body - Guangdong Provincial Hospital of Chinese Medicine
  • Location - China
  • Award ID - 2015KT1817
  • Awardee - Z Huang
  • Funding body - Institue of Chinese Materia Medica, China Academy of Chinese Medical Sciences & Peking Union Medical College
  • Award ID - ZZ0908067
  • Awardee - S Chen
  • Funding body - National Cancer Institute
  • Award ID - CA154295
  • Awardee - Y Cheng

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Ginseng-DESI-MS4054Chinese ginseng Panax ginseng Description:The frozen transverse sections of the ...
Analyte type:N/A
Sample source:sampled from Jingyu County in Jilin ...
...
+
Ginseng-IR8264054Chinese ginseng Panax ginseng Description:DNA extracted from leaf of 4-year old ...
Analyte type:DNA
Sample source:cultivated by the Institute of Chine...
...
+
WGC093423-2M4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the stele...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093423-2R4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the corte...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093423-2Z4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the perid...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093424-6M4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the stele...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093424-6R4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the corte...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093424-6Z4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the perid...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093424-7M4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the stele...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
WGC093424-7R4054Chinese ginseng Panax ginseng Description:Total RNA was extracted from the corte...
Analyte type:RNA
Sample source:sampled from Jingyu County in Jilin ...
...
+
Displaying 1-10 of 11 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
transcriptome sequenceFASTA-0 KB2017-09-11
Expression dataTEXT-0 KB2017-09-11
Phylogenetic treeUNKNOWN-0 KB2017-09-11
annotationGFF1.15 GB2017-09-11
ReadmeTEXT-0 KB2017-09-11
otherTAR-0 KB2017-09-11
Sequence assemblyFASTA-0 KB2017-09-11
AlignmentsFASTA-0 KB2017-09-11
protein sequenceFASTA-0 KB2017-09-11
imagePDF-0 KB2017-09-11
Displaying 1-10 of 35 File(s).

History:

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