Transcriptome Analysis of Buds and Leaves Using 454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of Active Ingredients in Lonicera japonica Thunb

Liu He, Xiaolan Xu, Ying Li, Chunfang Li, Yingjie Zhu, Haixia Yan, Zhiying Sun, Chao Sun, Jingyuan Song, Yu'an Bi, Juan Shen, Ruiyang Cheng, Zhenzhong Wang, Wei Xiao, Shilin Chen

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Background:Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are relatively well known, the genetic information available for this species, especially the biosynthetic pathways of its active ingredients, is limited.Methodology/Principal Findings:We obtained one million reads (average length of 400 bp) in a whole sequence run using a Roche/454 GS FLX titanium platform. Altogether, 85.69% of the unigenes covering the entire life cycle of the plant were annotated and 325 unigenes were assigned to secondary metabolic pathways. Moreover, 2039 unigenes were predicted as transcription factors. Nearly all of the possible enzymes involved in the biosynthesis of CGA and luteoloside were discovered in L. japonica. Three hydroxycinnamoyl transferase genes, including two hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase genes and one hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) gene featuring high similarity to known genes from other species, were cloned. The HCT gene was discovered for the first time in L. japonica. In addition, 188 candidate cytochrome P450 unigenes and 245 glycosyltransferase unigenes were found in the expressed sequence tag (EST) dataset.Conclusion:This study provides a high quality EST database for L. japonica by 454 pyrosequencing. Based on the EST annotation, a set of putative genes involved in CGA and luteoloside biosynthetic pathways were discovered. The database serves as an important source of public information on genetic markers, gene expression, genomics, and functional genomics in L. japonica.

Original languageEnglish (US)
Article numbere62922
JournalPLoS One
Volume8
Issue number4
DOIs
StatePublished - Apr 25 2013
Externally publishedYes

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Lonicera
Lonicera japonica
Biosynthesis
Gene Expression Profiling
unigenes
active ingredients
hydroxycinnamoyltransferase
transcriptomics
Genes
buds
biosynthesis
Chlorogenic Acid
biochemical pathways
Biosynthetic Pathways
Expressed Sequence Tags
chlorogenic acid
Transferases
expressed sequence tags
leaves
genes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Transcriptome Analysis of Buds and Leaves Using 454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of Active Ingredients in Lonicera japonica Thunb. / He, Liu; Xu, Xiaolan; Li, Ying; Li, Chunfang; Zhu, Yingjie; Yan, Haixia; Sun, Zhiying; Sun, Chao; Song, Jingyuan; Bi, Yu'an; Shen, Juan; Cheng, Ruiyang; Wang, Zhenzhong; Xiao, Wei; Chen, Shilin.

In: PLoS One, Vol. 8, No. 4, e62922, 25.04.2013.

Research output: Contribution to journalArticle

He, Liu ; Xu, Xiaolan ; Li, Ying ; Li, Chunfang ; Zhu, Yingjie ; Yan, Haixia ; Sun, Zhiying ; Sun, Chao ; Song, Jingyuan ; Bi, Yu'an ; Shen, Juan ; Cheng, Ruiyang ; Wang, Zhenzhong ; Xiao, Wei ; Chen, Shilin. / Transcriptome Analysis of Buds and Leaves Using 454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of Active Ingredients in Lonicera japonica Thunb. In: PLoS One. 2013 ; Vol. 8, No. 4.
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abstract = "Background:Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are relatively well known, the genetic information available for this species, especially the biosynthetic pathways of its active ingredients, is limited.Methodology/Principal Findings:We obtained one million reads (average length of 400 bp) in a whole sequence run using a Roche/454 GS FLX titanium platform. Altogether, 85.69{\%} of the unigenes covering the entire life cycle of the plant were annotated and 325 unigenes were assigned to secondary metabolic pathways. Moreover, 2039 unigenes were predicted as transcription factors. Nearly all of the possible enzymes involved in the biosynthesis of CGA and luteoloside were discovered in L. japonica. Three hydroxycinnamoyl transferase genes, including two hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase genes and one hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) gene featuring high similarity to known genes from other species, were cloned. The HCT gene was discovered for the first time in L. japonica. In addition, 188 candidate cytochrome P450 unigenes and 245 glycosyltransferase unigenes were found in the expressed sequence tag (EST) dataset.Conclusion:This study provides a high quality EST database for L. japonica by 454 pyrosequencing. Based on the EST annotation, a set of putative genes involved in CGA and luteoloside biosynthetic pathways were discovered. The database serves as an important source of public information on genetic markers, gene expression, genomics, and functional genomics in L. japonica.",
author = "Liu He and Xiaolan Xu and Ying Li and Chunfang Li and Yingjie Zhu and Haixia Yan and Zhiying Sun and Chao Sun and Jingyuan Song and Yu'an Bi and Juan Shen and Ruiyang Cheng and Zhenzhong Wang and Wei Xiao and Shilin Chen",
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T1 - Transcriptome Analysis of Buds and Leaves Using 454 Pyrosequencing to Discover Genes Associated with the Biosynthesis of Active Ingredients in Lonicera japonica Thunb

AU - He, Liu

AU - Xu, Xiaolan

AU - Li, Ying

AU - Li, Chunfang

AU - Zhu, Yingjie

AU - Yan, Haixia

AU - Sun, Zhiying

AU - Sun, Chao

AU - Song, Jingyuan

AU - Bi, Yu'an

AU - Shen, Juan

AU - Cheng, Ruiyang

AU - Wang, Zhenzhong

AU - Xiao, Wei

AU - Chen, Shilin

PY - 2013/4/25

Y1 - 2013/4/25

N2 - Background:Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are relatively well known, the genetic information available for this species, especially the biosynthetic pathways of its active ingredients, is limited.Methodology/Principal Findings:We obtained one million reads (average length of 400 bp) in a whole sequence run using a Roche/454 GS FLX titanium platform. Altogether, 85.69% of the unigenes covering the entire life cycle of the plant were annotated and 325 unigenes were assigned to secondary metabolic pathways. Moreover, 2039 unigenes were predicted as transcription factors. Nearly all of the possible enzymes involved in the biosynthesis of CGA and luteoloside were discovered in L. japonica. Three hydroxycinnamoyl transferase genes, including two hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase genes and one hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) gene featuring high similarity to known genes from other species, were cloned. The HCT gene was discovered for the first time in L. japonica. In addition, 188 candidate cytochrome P450 unigenes and 245 glycosyltransferase unigenes were found in the expressed sequence tag (EST) dataset.Conclusion:This study provides a high quality EST database for L. japonica by 454 pyrosequencing. Based on the EST annotation, a set of putative genes involved in CGA and luteoloside biosynthetic pathways were discovered. The database serves as an important source of public information on genetic markers, gene expression, genomics, and functional genomics in L. japonica.

AB - Background:Lonicera japonica Thunb. is a plant used in traditional Chinese medicine known for its anti-inflammatory, anti-oxidative, anti-carcinogenic, and antiviral pharmacological properties. The major active secondary metabolites of this plant are chlorogenic acid (CGA) and luteoloside. While the biosynthetic pathways of these metabolites are relatively well known, the genetic information available for this species, especially the biosynthetic pathways of its active ingredients, is limited.Methodology/Principal Findings:We obtained one million reads (average length of 400 bp) in a whole sequence run using a Roche/454 GS FLX titanium platform. Altogether, 85.69% of the unigenes covering the entire life cycle of the plant were annotated and 325 unigenes were assigned to secondary metabolic pathways. Moreover, 2039 unigenes were predicted as transcription factors. Nearly all of the possible enzymes involved in the biosynthesis of CGA and luteoloside were discovered in L. japonica. Three hydroxycinnamoyl transferase genes, including two hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase genes and one hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) gene featuring high similarity to known genes from other species, were cloned. The HCT gene was discovered for the first time in L. japonica. In addition, 188 candidate cytochrome P450 unigenes and 245 glycosyltransferase unigenes were found in the expressed sequence tag (EST) dataset.Conclusion:This study provides a high quality EST database for L. japonica by 454 pyrosequencing. Based on the EST annotation, a set of putative genes involved in CGA and luteoloside biosynthetic pathways were discovered. The database serves as an important source of public information on genetic markers, gene expression, genomics, and functional genomics in L. japonica.

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DO - 10.1371/journal.pone.0062922

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