Transcript profiles of Panax quinquefolius from flower, leaf and root bring new insights into genes related to ginsenosides biosynthesis and transcriptional regulation.

American ginseng (Panax quinquefolius L.) has been used for a wide range of therapeutic purposes in China. The major bioactive phytochemicals responsible for this plant's pharmacological features are ginsenosides. Thus far, little is known regarding the genes involved in ginsenosides biosynthesis in this species. As a non-model plant, information about its genomes is generally not available. In this study, we generated 6678 expressed sequence tags (ESTs) from the flower, leaf and root cDNA libraries of American ginseng. Assembly of ESTs resulted in 3349 unigenes including 534 contigs (with ESTs number ranging from 2 to 52) and 2815 singletons. By analyzing the predominant transcripts within specific tissues, a gene expression pattern was obtained in a tissue-specific manner. They were assigned according to the functional classification of unigenes to broad ranges of Gene Ontology categories which include biological processes, cellular components and molecular functions. Based on blastx search results, 24 unigenes representing candidates related to ginsenosides biosynthesis were identified. Cloning and characterization of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR, EC: 1.1.1.34), the rate-limiting enzyme in mevalonic acid pathway, demonstrated that it belonged to the plant HMGR family and was highly expressed in leaves. Putative transcription factors were detected in 63 unigenes, including zinc finger, WRKY, homeobox and MADS-box family proteins. Five hundred and eighty-eight simple sequence repeat motifs were identified, of which, dimer was the most abundant motif. These data will provide useful information on transcript profiles, gene discovery, transcriptional regulation, flower biogenesis and marker-assisted selections. The analysis and information from this study will greatly contribute to the improvement of this medicinal plant as well as of other species in the Araliaceae family, for the purpose of ensuring adequate drug resources.

[1]  D. Dou,et al.  Dammarane-type saponins from Panax quinquefolium and their inhibition activity on human breast cancer MCF-7 cells. , 2009, Fitoterapia.

[2]  P. Ahuja,et al.  Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.) , 2009, BMC Plant Biology.

[3]  S. Y. Lee,et al.  Proteomic Analysis of the Anti-Cancer Effect of 20S-Ginsenoside Rg3 in Human Colon Cancer Cell Lines , 2009, Bioscience, biotechnology, and biochemistry.

[4]  R. Dixon,et al.  Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula , 2008, BMC Plant Biology.

[5]  Chun-Nian He,et al.  [Variation of ginsenosides in infected roots of American ginseng (Panax quinquefolium)]. , 2008, Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica.

[6]  C. T. Hash,et al.  Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags , 2008, BMC Plant Biology.

[7]  T. Kocher,et al.  Genetic and developmental basis of cichlid trophic diversity , 2006, Heredity.

[8]  Chieh-fu Chen,et al.  Comparison of the pharmacological effects of Panax ginseng and Panax quinquefolium , 2008, Acta Pharmacologica Sinica.

[9]  Kang-Chang Kim,et al.  Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense[W] , 2008, The Plant Cell Online.

[10]  M. Hattori,et al.  Cloning and Characterization of Mevalonate Pathway Genes in a Natural Rubber Producing Plant, Hevea brasiliensis , 2008, Bioscience, biotechnology, and biochemistry.

[11]  B. Fan,et al.  Roles of Arabidopsis WRKY3 and WRKY4 Transcription Factors in Plant Responses to Pathogens , 2008, BMC Plant Biology.

[12]  Y. Li,et al.  [Analysis of expressed sequence tags (EST) from Panax quinquefolium root]. , 2008, Yao xue xue bao = Acta pharmaceutica Sinica.

[13]  E. Mutasa-Göttgens,et al.  Sugar beet contains a large CONSTANS-LIKE gene family including a CO homologue that is independent of the early-bolting (B) gene locus , 2008, Journal of experimental botany.

[14]  A. Kanellis,et al.  Isolation and functional analysis of two Cistus creticus cDNAs encoding geranylgeranyl diphosphate synthase. , 2008, Phytochemistry.

[15]  Joachim Kilian,et al.  Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots , 2008, BMC Genomics.

[16]  J. Vicente-Carbajosa,et al.  The maize Dof protein PBF activates transcription of γ-zein during maize seed development , 2008, Plant Molecular Biology.

[17]  Juan Zhang,et al.  Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants , 2008, Cell Research.

[18]  A. Tyagi,et al.  A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response , 2008, Functional & Integrative Genomics.

[19]  T. He,et al.  Red American ginseng: ginsenoside constituents and antiproliferative activities of heat-processed Panax quinquefolius roots. , 2007, Planta medica.

[20]  Felipe Rodrigues da Silva,et al.  ESTs from a wild Arachis species for gene discovery and marker development , 2007, BMC Plant Biology.

[21]  A. Tyagi,et al.  Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis , 2006, Molecular Genetics and Genomics.

[22]  Y. Ebizuka,et al.  Dammarenediol‐II synthase, the first dedicated enzyme for ginsenoside biosynthesis, in Panax ginseng , 2006, FEBS letters.

[23]  J. McGraw,et al.  Effects of harvester behavior on population growth rate affects sustainability of ginseng trade , 2006 .

[24]  Lin Fang,et al.  WEGO: a web tool for plotting GO annotations , 2006, Nucleic Acids Res..

[25]  Hongbin Xiao,et al.  Identification of Ginsenosides in Panax quinquefolium by LC-MS , 2006 .

[26]  H. Hayashi,et al.  Identification of β‐amyrin and sophoradiol 24‐hydroxylase by expressed sequence tag mining and functional expression assay , 2006, The FEBS journal.

[27]  Deok-Chun Yang,et al.  Comparative analysis of expressed sequence tags (ESTs) of ginseng leaf , 2006, Plant Cell Reports.

[28]  D. Soltis,et al.  Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. , 2005, The Plant journal : for cell and molecular biology.

[29]  I. Donnison,et al.  Identification of perennial ryegrass (Lolium perenne (L.)) and meadow fescue (Festuca pratensis (Huds.)) candidate orthologous sequences to the rice Hd1(Se1) and barley HvCO1 CONSTANS-like genes through comparative mapping and microsynteny. , 2005, The New phytologist.

[30]  M. Prigge,et al.  CORONA, a Member of the Class III Homeodomain Leucine Zipper Gene Family in Arabidopsis, Regulates Stem Cell Specification and Organogenesisw⃞ , 2005, The Plant Cell Online.

[31]  Jong Hoon Park,et al.  Induction of a homeodomain-leucine zipper gene by auxin is inhibited by cytokinin in Arabidopsis roots. , 2004, Biochemical and biophysical research communications.

[32]  C. Andersen,et al.  Photoperiodic regulation of flowering in perennial ryegrass involving a CONSTANS-like homolog , 2004, Plant Molecular Biology.

[33]  J. Kim,et al.  Characterization of RNase-like major storage protein from the ginseng root by proteomic approach. , 2004, Journal of plant physiology.

[34]  Søren Bak,et al.  Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot1[w] , 2004, Plant Physiology.

[35]  S. Yanagisawa.  Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. , 2004, Plant & cell physiology.

[36]  C. Yuan,et al.  American ginseng leaf: ginsenoside analysis and hypoglycemic activity. , 2004, Pharmacological research.

[37]  方福德.  构成性表达（constitutive expression） , 2003 .

[38]  Y. Hahn,et al.  Discovery of genes for ginsenoside biosynthesis by analysis of ginseng expressed sequence tags , 2003, Plant Cell Reports.

[39]  Jesús Vicente-Carbajosa,et al.  Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families , 2003, BMC Evolutionary Biology.

[40]  H. le Guyader,et al.  MADS-box genes in Ginkgo biloba and the evolution of the AGAMOUS family. , 2003, Molecular biology and evolution.

[41]  G. Thompson,et al.  Diversity of the Superfamily of Phloem Lectins (Phloem Protein 2) in Angiosperms1 , 2003, Plant Physiology.

[42]  Hideyuki Suzuki,et al.  A genomics approach to the early stages of triterpene saponin biosynthesis in Medicago truncatula. , 2002, The Plant journal : for cell and molecular biology.

[43]  K. Siems,et al.  Arbutin synthase, a novel member of the NRD1beta glycosyltransferase family, is a unique multifunctional enzyme converting various natural products and xenobiotics. , 2002, Bioorganic & medicinal chemistry.

[44]  M. Morgante,et al.  Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes , 2002, Nature Genetics.

[45]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[46]  L. Lipovich,et al.  Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. , 2001, Genome research.

[47]  Verpoorte,et al.  Purification and partial characterisation of geranylgeranyl diphosphate synthase, from Taxus baccata cell cultures. An enzyme that regulates taxane biosynthesis. , 2000, Plant science : an international journal of experimental plant biology.

[48]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[49]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[50]  C. Fields.  Analysis of gene expression by tissue and developmental stage. , 1994, Current opinion in biotechnology.

[51]  A. Meijer,et al.  Isolation of cytochrome P-450 cDNA clones from the higher plant Catharanthus roseus by a PCR strategy , 1993, Plant Molecular Biology.

[52]  R. C. Anderson,et al.  The Ecology and Biology of Panax quinquefolium L. (Araliaceae) in Illinois , 1993 .

[53]  C. Gasser,et al.  Structure and expression of cytosolic cyclophilin/peptidyl-prolyl cis-trans isomerase of higher plants and production of active tomato cyclophilin in Escherichia coli. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[54]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[55]  A. W. Carlson.  Ginseng: America’s botanical drug connection to the orient , 1986, Economic Botany.

[56]  J. Parkinson.  Expressed Sequence Tags (ESTs) Generation and Analysis , 2009 .

[57]  J. Parkinson,et al.  Expressed sequence tags: an overview. , 2009, Methods in molecular biology.

[58]  John Parkinson,et al.  Expressed Sequence Tags (ESTs) , 2009, Methods in Molecular Biology.

[59]  Chong-Zhi Wang,et al.  Potential role of ginseng in the treatment of colorectal cancer. , 2008, The American journal of Chinese medicine.

[60]  Daniel A. S. Anjos,et al.  Guarana (Paullinia cupana var. sorbilis), an anciently consumed stimulant from the Amazon rain forest: the seeded-fruit transcriptome , 2007, Plant Cell Reports.

[61]  Andreas Graner,et al.  Genic microsatellite markers in plants: features and applications. , 2005, Trends in biotechnology.

[62]  G. Schröder,et al.  Three differentially expressed S-adenosylmethionine synthetases from Catharanthus roseus: molecular and functional characterization , 2004, Plant Molecular Biology.

[63]  Thomas Thiel,et al.  In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. , 2002, Cellular & molecular biology letters.

[64]  A. Osbourn,et al.  Biosynthesis of triterpenoid saponins in plants. , 2002, Advances in biochemical engineering/biotechnology.

[65]  A. Ong,et al.  Lipid metabolism in oil palm (Elaeis guineensis and Elaeis oleifera) protoplasts , 1987 .