Discovery of genes related to steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generating and mining a dataset of expressed sequence tags (ESTs)

Chao Sun, Yongqiao Sun, Jingyuan Song, Chenji Li, Xiwen Li, Xiaowei Zhang, Ying Li, Songnian Hu, Hongmei Luo, Yingjie Zhu, Shilin Chen

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Fritillaria cirrhosa D. Don is an endangered species in the Liliaceae family, the bulb of which is the primary plant source for the Chinese traditional medicine "Chuan-beimu", having activities that relieve coughs and eliminates phlegm. The major pharmacologically active constituents of F. cirrhosa are steroidal alkaloids. Two thousand one hundred and fifty-eight high-quality expressed sequence tags (ESTs) were generated from a cDNA library of F. cirrhosa bulbs and assembled to total 1343 unique transcripts. After removing ribosomal RNA sequences, 1330 putative protein coding sequences were obtained; among these, 765 (57.5%) had at least one significant match to the Swiss-Prot protein database via a BLASTX similarity search. The 1330 unique transcripts were further functionally classified for gene discovery purposes using the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. More than ten transcripts that are likely involved in the biosynthesis of F. cirrhosa alkaloids and corresponding regulatory activities were discovered in this EST dataset, including HMGR, FPSs, CYP450s and aminotransferases. This report describes the first example of EST analysis from the Fritillaria genus and lays the foundation for further cloning and identification of candidate genes related to steroidal alkaloid biosynthesis in F. cirrhosa.

Original languageEnglish (US)
Pages (from-to)5307-5314
Number of pages8
JournalJournal of Medicinal Plant Research
Volume5
Issue number21
StatePublished - Oct 9 2011
Externally publishedYes

Fingerprint

Fritillaria cirrhosa
Fritillaria
Expressed Sequence Tags
Genetic Association Studies
expressed sequence tags
Alkaloids
alkaloids
biosynthesis
Liliaceae
Encyclopedias
Endangered Species
Protein Databases
Gene Ontology
Ribosomal RNA
genes
bulbs
Chinese Traditional Medicine
Transaminases
Gene Library
Cough

Keywords

  • Expressed sequence tags
  • Fritillaria cirrhosa
  • Steroidal alkaloids

ASJC Scopus subject areas

  • Pharmacology
  • Pharmaceutical Science
  • Drug Discovery
  • Plant Science
  • Complementary and alternative medicine

Cite this

Discovery of genes related to steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generating and mining a dataset of expressed sequence tags (ESTs). / Sun, Chao; Sun, Yongqiao; Song, Jingyuan; Li, Chenji; Li, Xiwen; Zhang, Xiaowei; Li, Ying; Hu, Songnian; Luo, Hongmei; Zhu, Yingjie; Chen, Shilin.

In: Journal of Medicinal Plant Research, Vol. 5, No. 21, 09.10.2011, p. 5307-5314.

Research output: Contribution to journalArticle

Sun, Chao ; Sun, Yongqiao ; Song, Jingyuan ; Li, Chenji ; Li, Xiwen ; Zhang, Xiaowei ; Li, Ying ; Hu, Songnian ; Luo, Hongmei ; Zhu, Yingjie ; Chen, Shilin. / Discovery of genes related to steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generating and mining a dataset of expressed sequence tags (ESTs). In: Journal of Medicinal Plant Research. 2011 ; Vol. 5, No. 21. pp. 5307-5314.
@article{2fcf6c5670a548ff8045f2dcf890293b,
title = "Discovery of genes related to steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generating and mining a dataset of expressed sequence tags (ESTs)",
abstract = "Fritillaria cirrhosa D. Don is an endangered species in the Liliaceae family, the bulb of which is the primary plant source for the Chinese traditional medicine {"}Chuan-beimu{"}, having activities that relieve coughs and eliminates phlegm. The major pharmacologically active constituents of F. cirrhosa are steroidal alkaloids. Two thousand one hundred and fifty-eight high-quality expressed sequence tags (ESTs) were generated from a cDNA library of F. cirrhosa bulbs and assembled to total 1343 unique transcripts. After removing ribosomal RNA sequences, 1330 putative protein coding sequences were obtained; among these, 765 (57.5{\%}) had at least one significant match to the Swiss-Prot protein database via a BLASTX similarity search. The 1330 unique transcripts were further functionally classified for gene discovery purposes using the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. More than ten transcripts that are likely involved in the biosynthesis of F. cirrhosa alkaloids and corresponding regulatory activities were discovered in this EST dataset, including HMGR, FPSs, CYP450s and aminotransferases. This report describes the first example of EST analysis from the Fritillaria genus and lays the foundation for further cloning and identification of candidate genes related to steroidal alkaloid biosynthesis in F. cirrhosa.",
keywords = "Expressed sequence tags, Fritillaria cirrhosa, Steroidal alkaloids",
author = "Chao Sun and Yongqiao Sun and Jingyuan Song and Chenji Li and Xiwen Li and Xiaowei Zhang and Ying Li and Songnian Hu and Hongmei Luo and Yingjie Zhu and Shilin Chen",
year = "2011",
month = "10",
day = "9",
language = "English (US)",
volume = "5",
pages = "5307--5314",
journal = "Journal of Medicinal Plant Research",
issn = "1996-0875",
publisher = "Academic Journals",
number = "21",

}

TY - JOUR

T1 - Discovery of genes related to steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generating and mining a dataset of expressed sequence tags (ESTs)

AU - Sun, Chao

AU - Sun, Yongqiao

AU - Song, Jingyuan

AU - Li, Chenji

AU - Li, Xiwen

AU - Zhang, Xiaowei

AU - Li, Ying

AU - Hu, Songnian

AU - Luo, Hongmei

AU - Zhu, Yingjie

AU - Chen, Shilin

PY - 2011/10/9

Y1 - 2011/10/9

N2 - Fritillaria cirrhosa D. Don is an endangered species in the Liliaceae family, the bulb of which is the primary plant source for the Chinese traditional medicine "Chuan-beimu", having activities that relieve coughs and eliminates phlegm. The major pharmacologically active constituents of F. cirrhosa are steroidal alkaloids. Two thousand one hundred and fifty-eight high-quality expressed sequence tags (ESTs) were generated from a cDNA library of F. cirrhosa bulbs and assembled to total 1343 unique transcripts. After removing ribosomal RNA sequences, 1330 putative protein coding sequences were obtained; among these, 765 (57.5%) had at least one significant match to the Swiss-Prot protein database via a BLASTX similarity search. The 1330 unique transcripts were further functionally classified for gene discovery purposes using the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. More than ten transcripts that are likely involved in the biosynthesis of F. cirrhosa alkaloids and corresponding regulatory activities were discovered in this EST dataset, including HMGR, FPSs, CYP450s and aminotransferases. This report describes the first example of EST analysis from the Fritillaria genus and lays the foundation for further cloning and identification of candidate genes related to steroidal alkaloid biosynthesis in F. cirrhosa.

AB - Fritillaria cirrhosa D. Don is an endangered species in the Liliaceae family, the bulb of which is the primary plant source for the Chinese traditional medicine "Chuan-beimu", having activities that relieve coughs and eliminates phlegm. The major pharmacologically active constituents of F. cirrhosa are steroidal alkaloids. Two thousand one hundred and fifty-eight high-quality expressed sequence tags (ESTs) were generated from a cDNA library of F. cirrhosa bulbs and assembled to total 1343 unique transcripts. After removing ribosomal RNA sequences, 1330 putative protein coding sequences were obtained; among these, 765 (57.5%) had at least one significant match to the Swiss-Prot protein database via a BLASTX similarity search. The 1330 unique transcripts were further functionally classified for gene discovery purposes using the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. More than ten transcripts that are likely involved in the biosynthesis of F. cirrhosa alkaloids and corresponding regulatory activities were discovered in this EST dataset, including HMGR, FPSs, CYP450s and aminotransferases. This report describes the first example of EST analysis from the Fritillaria genus and lays the foundation for further cloning and identification of candidate genes related to steroidal alkaloid biosynthesis in F. cirrhosa.

KW - Expressed sequence tags

KW - Fritillaria cirrhosa

KW - Steroidal alkaloids

UR - http://www.scopus.com/inward/record.url?scp=80054820333&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80054820333&partnerID=8YFLogxK

M3 - Article

VL - 5

SP - 5307

EP - 5314

JO - Journal of Medicinal Plant Research

JF - Journal of Medicinal Plant Research

SN - 1996-0875

IS - 21

ER -