454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng

S. Chen, H. Luo, Y. Li, Y. Sun, Q. Wu, Y. Niu, J. Song, A. Lv, Yingjie Zhu, C. Sun, A. Steinmetz, Z. Qian

Research output: Contribution to journalArticle

111 Citations (Scopus)

Abstract

Panax ginseng C. A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.

Original languageEnglish (US)
Pages (from-to)1593-1601
Number of pages9
JournalPlant Cell Reports
Volume30
Issue number9
DOIs
StatePublished - Sep 1 2011
Externally publishedYes

Fingerprint

Panax ginseng
expressed sequence tags
biosynthesis
glycosyltransferases
genes
skeleton
cytochromes
transcriptome
medicinal plants
biochemical pathways
herbs
ginsenosides
RNA
taxonomy
genomics
drugs
genome

Keywords

  • 454 GS FLX
  • Expressed sequence tag (EST)
  • Ginsenoside biosynthesis
  • Panax ginseng
  • Transcriptome

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science

Cite this

454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. / Chen, S.; Luo, H.; Li, Y.; Sun, Y.; Wu, Q.; Niu, Y.; Song, J.; Lv, A.; Zhu, Yingjie; Sun, C.; Steinmetz, A.; Qian, Z.

In: Plant Cell Reports, Vol. 30, No. 9, 01.09.2011, p. 1593-1601.

Research output: Contribution to journalArticle

Chen, S, Luo, H, Li, Y, Sun, Y, Wu, Q, Niu, Y, Song, J, Lv, A, Zhu, Y, Sun, C, Steinmetz, A & Qian, Z 2011, '454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng', Plant Cell Reports, vol. 30, no. 9, pp. 1593-1601. https://doi.org/10.1007/s00299-011-1070-6
Chen, S. ; Luo, H. ; Li, Y. ; Sun, Y. ; Wu, Q. ; Niu, Y. ; Song, J. ; Lv, A. ; Zhu, Yingjie ; Sun, C. ; Steinmetz, A. ; Qian, Z. / 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. In: Plant Cell Reports. 2011 ; Vol. 30, No. 9. pp. 1593-1601.
@article{a9cc016021a4409e9868ba05afab09dc,
title = "454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng",
abstract = "Panax ginseng C. A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6{\%}) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.",
keywords = "454 GS FLX, Expressed sequence tag (EST), Ginsenoside biosynthesis, Panax ginseng, Transcriptome",
author = "S. Chen and H. Luo and Y. Li and Y. Sun and Q. Wu and Y. Niu and J. Song and A. Lv and Yingjie Zhu and C. Sun and A. Steinmetz and Z. Qian",
year = "2011",
month = "9",
day = "1",
doi = "10.1007/s00299-011-1070-6",
language = "English (US)",
volume = "30",
pages = "1593--1601",
journal = "Plant Cell Reports",
issn = "0721-7714",
publisher = "Springer Verlag",
number = "9",

}

TY - JOUR

T1 - 454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng

AU - Chen, S.

AU - Luo, H.

AU - Li, Y.

AU - Sun, Y.

AU - Wu, Q.

AU - Niu, Y.

AU - Song, J.

AU - Lv, A.

AU - Zhu, Yingjie

AU - Sun, C.

AU - Steinmetz, A.

AU - Qian, Z.

PY - 2011/9/1

Y1 - 2011/9/1

N2 - Panax ginseng C. A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.

AB - Panax ginseng C. A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.

KW - 454 GS FLX

KW - Expressed sequence tag (EST)

KW - Ginsenoside biosynthesis

KW - Panax ginseng

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=80051546221&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80051546221&partnerID=8YFLogxK

U2 - 10.1007/s00299-011-1070-6

DO - 10.1007/s00299-011-1070-6

M3 - Article

VL - 30

SP - 1593

EP - 1601

JO - Plant Cell Reports

JF - Plant Cell Reports

SN - 0721-7714

IS - 9

ER -