Panax ginseng genome examination for ginsenoside biosynthesis

Jiang Xu, Yang Chu, Baosheng Liao, Shuiming Xiao, Qinggang Yin, Rui Bai, He Su, Linlin Dong, Xiwen Li, Jun Qian, Jingjing Zhang, Yujun Zhang, Xiaoyan Zhang, Mingli Wu, Jie Zhang, Guozheng Li, Lei Zhang, Zhenzhan Chang, Yuebin Zhang, Zhengwei Jia & 13 others Zhixiang Liu, Daniel Afreh, Ruth Nahurira, Lianjuan Zhang, Ruiyang Cheng, Yingjie Zhu, Guangwei Zhu, Wei Rao, Chao Zhou, Lirui Qiao, Zhihai Huang, Yung Chi Cheng, Shilin Chen

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Ginseng, which contains ginsenosides as bioactive compounds, has been regarded as an important traditional medicine for several millennia. However, 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 contains more than 60% repeats and encodes 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-glycosyltransferases (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 71st, 74th, and 94th families revealed a regiospecific conserved motif located at the N-terminus. Molecular docking predicted that this motif captures ginsenoside precursors. The ginseng genome represents a valuable resource for understanding and improving the breeding, cultivation, and synthesis biology of this key herb.

Original languageEnglish (US)
Article numbergix093
JournalGigaScience
Volume6
Issue number11
DOIs
StatePublished - Nov 1 2017
Externally publishedYes

Fingerprint

Ginsenosides
Panax
Biosynthesis
Glycosyltransferases
Uridine Diphosphate
Genes
Genome
Hydroxymethylglutaryl CoA Reductases
Mevalonic Acid
Tandem Repeat Sequences
Traditional Medicine
Transcriptome
Molecular modeling
Breeding
Mass Spectrometry
Nucleotides
Medicine
Mass spectrometry
Acids

Keywords

  • Genome
  • Ginsenosides
  • Mass spectrometry imaging
  • Panax ginseng

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

Cite this

Xu, J., Chu, Y., Liao, B., Xiao, S., Yin, Q., Bai, R., ... Chen, S. (2017). Panax ginseng genome examination for ginsenoside biosynthesis. GigaScience, 6(11), [gix093]. https://doi.org/10.1093/gigascience/gix093

Panax ginseng genome examination for ginsenoside biosynthesis. / Xu, Jiang; Chu, Yang; Liao, Baosheng; Xiao, Shuiming; Yin, Qinggang; Bai, Rui; Su, He; Dong, Linlin; Li, Xiwen; Qian, Jun; Zhang, Jingjing; Zhang, Yujun; Zhang, Xiaoyan; Wu, Mingli; Zhang, Jie; Li, Guozheng; Zhang, Lei; Chang, Zhenzhan; Zhang, Yuebin; Jia, Zhengwei; Liu, Zhixiang; Afreh, Daniel; Nahurira, Ruth; Zhang, Lianjuan; Cheng, Ruiyang; Zhu, Yingjie; Zhu, Guangwei; Rao, Wei; Zhou, Chao; Qiao, Lirui; Huang, Zhihai; Cheng, Yung Chi; Chen, Shilin.

In: GigaScience, Vol. 6, No. 11, gix093, 01.11.2017.

Research output: Contribution to journalArticle

Xu, J, Chu, Y, Liao, B, Xiao, S, 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, YC & Chen, S 2017, 'Panax ginseng genome examination for ginsenoside biosynthesis', GigaScience, vol. 6, no. 11, gix093. https://doi.org/10.1093/gigascience/gix093
Xu J, Chu Y, Liao B, Xiao S, Yin Q, Bai R et al. Panax ginseng genome examination for ginsenoside biosynthesis. GigaScience. 2017 Nov 1;6(11). gix093. https://doi.org/10.1093/gigascience/gix093
Xu, Jiang ; Chu, Yang ; Liao, Baosheng ; Xiao, Shuiming ; Yin, Qinggang ; Bai, Rui ; Su, He ; Dong, Linlin ; Li, Xiwen ; Qian, Jun ; Zhang, Jingjing ; Zhang, Yujun ; Zhang, Xiaoyan ; Wu, Mingli ; Zhang, Jie ; Li, Guozheng ; Zhang, Lei ; Chang, Zhenzhan ; Zhang, Yuebin ; Jia, Zhengwei ; Liu, Zhixiang ; Afreh, Daniel ; Nahurira, Ruth ; Zhang, Lianjuan ; Cheng, Ruiyang ; Zhu, Yingjie ; Zhu, Guangwei ; Rao, Wei ; Zhou, Chao ; Qiao, Lirui ; Huang, Zhihai ; Cheng, Yung Chi ; Chen, Shilin. / Panax ginseng genome examination for ginsenoside biosynthesis. In: GigaScience. 2017 ; Vol. 6, No. 11.
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