Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis

Zhichao Xu, Reuben J. Peters, Jason Weirather, Hongmei Luo, Baosheng Liao, Xin Zhang, Yingjie Zhu, Aijia Ji, Bing Zhang, Songnian Hu, Kin Fai Au, Jingyuan Song, Shilin Chen

Research output: Contribution to journalArticle

117 Citations (Scopus)

Abstract

Danshen, Salvia miltiorrhiza Bunge, is one of the most widely used herbs in traditional Chinese medicine, wherein its rhizome/roots are particularly valued. The corresponding bioactive components include the tanshinone diterpenoids, the biosynthesis of which is a subject of considerable interest. Previous investigations of the S. miltiorrhiza transcriptome have relied on short-read next-generation sequencing (NGS) technology, and the vast majority of the resulting isotigs do not represent full-length cDNA sequences. Moreover, these efforts have been targeted at either whole plants or hairy root cultures. Here, we demonstrate that the tanshinone pigments are produced and accumulate in the root periderm, and apply a combination of NGS and single-molecule real-time (SMRT) sequencing to various root tissues, particularly including the periderm, to provide a more complete view of the S. miltiorrhiza transcriptome, with further insight into tanshinone biosynthesis as well. In addition, the use of SMRT long-read sequencing offered the ability to examine alternative splicing, which was found to occur in approximately 40% of the detected gene loci, including several involved in isoprenoid/terpenoid metabolism. Significance Statement Here, we combined NGS and SMRT sequencing to generate a more complete/full-length S. miltiorrhiza transcriptome. Our study provides a general model for studying the full-length transcriptome, alternative splicing, and the biosynthesis of active constituents in medicinal plants, as well as important information about the important Danshen constituent of traditional Chinese medicine more specifically.

Original languageEnglish (US)
Pages (from-to)951-961
Number of pages11
JournalPlant Journal
Volume82
Issue number6
DOIs
StatePublished - Jan 1 2015
Externally publishedYes

Fingerprint

Salvia miltiorrhiza
Transcriptome
transcriptome
biosynthesis
periderm
alternative splicing
Oriental traditional medicine
Terpenes
Chinese Traditional Medicine
Alternative Splicing
isoprenoids
diterpenoids
terpenoids
rhizomes
medicinal plants
medicine
Rhizome
Diterpenes
pigments
Medicinal Plants

Keywords

  • alternative splicing
  • next-generation sequencing
  • Salvia miltiorrhiza
  • single-molecule real-time sequencing
  • tanshinone biosynthesis

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology

Cite this

Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis. / Xu, Zhichao; Peters, Reuben J.; Weirather, Jason; Luo, Hongmei; Liao, Baosheng; Zhang, Xin; Zhu, Yingjie; Ji, Aijia; Zhang, Bing; Hu, Songnian; Au, Kin Fai; Song, Jingyuan; Chen, Shilin.

In: Plant Journal, Vol. 82, No. 6, 01.01.2015, p. 951-961.

Research output: Contribution to journalArticle

Xu, Zhichao ; Peters, Reuben J. ; Weirather, Jason ; Luo, Hongmei ; Liao, Baosheng ; Zhang, Xin ; Zhu, Yingjie ; Ji, Aijia ; Zhang, Bing ; Hu, Songnian ; Au, Kin Fai ; Song, Jingyuan ; Chen, Shilin. / Full-length transcriptome sequences and splice variants obtained by a combination of sequencing platforms applied to different root tissues of Salvia miltiorrhiza and tanshinone biosynthesis. In: Plant Journal. 2015 ; Vol. 82, No. 6. pp. 951-961.
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abstract = "Danshen, Salvia miltiorrhiza Bunge, is one of the most widely used herbs in traditional Chinese medicine, wherein its rhizome/roots are particularly valued. The corresponding bioactive components include the tanshinone diterpenoids, the biosynthesis of which is a subject of considerable interest. Previous investigations of the S. miltiorrhiza transcriptome have relied on short-read next-generation sequencing (NGS) technology, and the vast majority of the resulting isotigs do not represent full-length cDNA sequences. Moreover, these efforts have been targeted at either whole plants or hairy root cultures. Here, we demonstrate that the tanshinone pigments are produced and accumulate in the root periderm, and apply a combination of NGS and single-molecule real-time (SMRT) sequencing to various root tissues, particularly including the periderm, to provide a more complete view of the S. miltiorrhiza transcriptome, with further insight into tanshinone biosynthesis as well. In addition, the use of SMRT long-read sequencing offered the ability to examine alternative splicing, which was found to occur in approximately 40{\%} of the detected gene loci, including several involved in isoprenoid/terpenoid metabolism. Significance Statement Here, we combined NGS and SMRT sequencing to generate a more complete/full-length S. miltiorrhiza transcriptome. Our study provides a general model for studying the full-length transcriptome, alternative splicing, and the biosynthesis of active constituents in medicinal plants, as well as important information about the important Danshen constituent of traditional Chinese medicine more specifically.",
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AU - Xu, Zhichao

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AU - Weirather, Jason

AU - Luo, Hongmei

AU - Liao, Baosheng

AU - Zhang, Xin

AU - Zhu, Yingjie

AU - Ji, Aijia

AU - Zhang, Bing

AU - Hu, Songnian

AU - Au, Kin Fai

AU - Song, Jingyuan

AU - Chen, Shilin

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