Computational identification and systematic classification of novel cytochrome p450 genes in Salvia miltiorrhiza

Haimei Chen, Bin Wu, David Nelson, Kai Wu, Chang Liu

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Salvia miltiorrhiza is one of the most economically important medicinal plants. Cytochrome P450 (CYP450) genes have been implicated in the biosynthesis of its active components. However, only a dozen full-length CYP450 genes have been described, and there is no systematic classification of CYP450 genes in S. miltiorrhiza. We obtained 77,549 unigenes from three tissue types of S. miltiorrhiza using RNA-Seq technology. Combining our data with previously identified CYP450 sequences and scanning with the CYP450 model from Pfam resulted in the identification of 116 full-length and 135 partial-length CYP450 genes. The 116 genes were classified into 9 clans and 38 families using standard criteria. The RNA-Seq results showed that 35 CYP450 genes were co-expressed with CYP76AH1, a marker gene for tanshinone biosynthesis, using r≥0.9 as a cutoff. The expression profiles for 16 of 19 randomly selected CYP450 obtained from RNA-Seq were validated by qRT-PCR. Comparing against the KEGG database, 10 CYP450 genes were found to be associated with diterpenoid biosynthesis. Considering all the evidence, 3 CYP450 genes were identified to be potentially involved in terpenoid biosynthesis. Moreover, we found that 15 CYP450 genes were possibly regulated by antisense transcripts (r≥0.9 or r≤-0.9). Lastly, a web resource (SMCYP450, http://www.herbalgenomics.org/samicyp450) was set up, which allows users to browse, search, retrieve and compare CYP450 genes and can serve as a centralized resource.

Original languageEnglish (US)
Article numbere115149
JournalPLoS One
Volume9
Issue number12
DOIs
StatePublished - Dec 10 2014

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Salvia miltiorrhiza
cytochrome P-450
Cytochrome P-450 Enzyme System
Genes
taxonomy
genes
Biosynthesis
biosynthesis
RNA
unigenes
Diterpenes
Terpenes
Medicinal Plants
diterpenoids
terpenoids
medicinal plants

All Science Journal Classification (ASJC) codes

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

Cite this

Computational identification and systematic classification of novel cytochrome p450 genes in Salvia miltiorrhiza. / Chen, Haimei; Wu, Bin; Nelson, David; Wu, Kai; Liu, Chang.

In: PLoS One, Vol. 9, No. 12, e115149, 10.12.2014.

Research output: Contribution to journalArticle

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