title: Transcriptome analysis of leaves, roots and flowers of Panax notoginseng identifies genes involved in ginsenoside and alkaloid biosynthesis.
abstract: BACKGROUND
  Panax notoginseng (Burk.) F.H. Chen is one of the most highly valued medicinal plants in the world. The major bioactive molecules are triterpene saponins, which are also known as ginsenosides. However, its large genome size has hindered the assembly of a draft genome by whole genome sequencing. Hence, genomic and transcriptomic details about P. notoginseng, especially its biosynthetic pathways and gene expression in different parts of the plant, have remained largely unknown until now.
  
  
  RESULTS
  In this study, RNA sequencing of three different P. notoginseng tissues was performed using next generation DNA sequencing. After assembling the high quality sequencing reads into 107,340 unigenes, biochemical pathways were predicted and 9,908 unigenes were assigned to 135 KEGG pathways. Among them, 270 unigenes were identified to be involved in triterpene saponin biosynthesis. In addition, 350 and 342 unigenes were predicted to encode cytochrome P450s and glycosyltransferases, respectively, based on the annotation results, some of which encode enzymes responsible for the conversion of the triterpene saponin backbone into different ginsenosides. In particular, one unigene predominantly expressed in the root was annotated as CYP716A53v2, which probably participates in the formation of protopanaxatriol from protopanaxadiol in P. notoginseng. The differential expression of this gene was further confirmed by real-time PCR.
  
  
  CONCLUSIONS
  We have established a global transcriptome dataset for P. notoginseng and provided additional genetic information for further genome-wide research and analyses. Candidate genes involved in ginsenoside biosynthesis, including putative cytochrome P450s and glycosyltransferases were obtained. The transcriptomes in different plant tissues also provide invaluable resources for future study of the differences in physiological processes and secondary metabolites in different parts of P. notoginseng.
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. liumhua@gmail.com.
authors.forename: Ming-Hua
authors.initials: MH
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China. yangbinrui.um@gmail.com.
authors.forename: Bin-Rui
authors.initials: BR
authors.lastname: Yang
authors.affiliation: Beijing Genomics Institute - Shenzhen, Shenzhen, 518083, China. cheungwaifung@genomics.cn.|Present correspondence: Groken Bioscience, Hong Kong, China. cheungwaifung@genomics.cn.
authors.forename: Wai-Fung
authors.initials: WF
authors.lastname: Cheung
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. styangyi@live.cn.|Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China. styangyi@live.cn.
authors.forename: Kevin Yi
authors.initials: KY
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China. hfztim@163.com.
authors.forename: He-Feng
authors.initials: HF
authors.lastname: Zhou
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. bi.my.heart@gmail.com.
authors.forename: Jamie Sui-Lam
authors.initials: JS
authors.lastname: Kwok
authors.affiliation: Beijing Genomics Institute - Shenzhen, Shenzhen, 518083, China. liuguocheng@bgitechsolutions.com.
authors.forename: Guo-Cheng
authors.initials: GC
authors.lastname: Liu
authors.affiliation: Beijing Genomics Institute - Shenzhen, Shenzhen, 518083, China. lixiaofeng@bgitechsolutions.com.
authors.forename: Xiao-Feng
authors.initials: XF
authors.lastname: Li
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China. silin.zhong@cuhk.edu.hk.
authors.forename: Silin
authors.initials: S
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China. simonlee@umac.mo.
authors.forename: Simon Ming-Yuen
authors.initials: SM
authors.lastname: Lee
authors.affiliation: School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China. kwtsui@cuhk.edu.hk.|Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China. kwtsui@cuhk.edu.hk.
authors.forename: Stephen Kwok-Wing
authors.initials: SK
authors.lastname: Tsui
mesh_terms: D000470:Alkaloids / Q000096:biosynthesis*; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D036145:Ginsenosides / Q000096:biosynthesis*; D016695:Glycosyltransferases / Q000378:metabolism; D053723:Panax notoginseng / Q000235:genetics / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D012502:Sapogenins / Q000378:metabolism
chemical_list: D000470:Alkaloids; D036145:Ginsenosides; D010940:Plant Proteins; D012502:Sapogenins; C081552:protopanaxatriol; D003577:Cytochrome P-450 Enzyme System; D016695:Glycosyltransferases