title: Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers.
abstract: BACKGROUND
  P. vietnamensis var. fuscidiscus, called "Yesanqi" in Chinese, is a new variety of P. vietnamensis, which was first found in Jinping County, the southern part of Yunnan Province, China. Compared with other Panax plants, this species contains higher content of ocotillol-type saponin, majonoside R2. Despite the pharmacological importance of ocotillol-type saponins, little is known about their biosynthesis in plants. Hence, P. vietnamensis var. fuscidiscus is a suitable medicinal herbal plant species to study biosynthesis of ocotillol-type saponins. In addition, the available genomic information of this important herbal plant is lacking.
  
  
  RESULTS
  To investigate the P. vietnamensis var. fuscidiscus transcriptome, Illumina HiSeq™ 2000 sequencing platform was employed. We produced 114,703,210 clean reads, assembled into 126,758 unigenes, with an average length of 1,304 bp and N50 of 2,108 bp. Among these 126,758 unigenes, 85,214 unigenes (67.23%) were annotated based on the information available from the public databases. The transcripts encoding the known enzymes involved in triterpenoid saponins biosynthesis were identified in our Illumina dataset. A full-length cDNA of three Squalene epoxidase (SE) genes were obtained using reverse transcription PCR (RT-PCR) and the expression patterns of ten unigenes were analyzed by reverse transcription quantitative real-time PCR (RT-qPCR). Furthermore, 15 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely to involve in triterpenoid saponins biosynthesis pathway were discovered from transcriptome sequencing of P. vietnamensis var. fuscidiscus. We further analyzed the data and found 21,320 simple sequence repeats (SSRs), 30 primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism in 13 P. vietnamensis var. fuscidiscus accessions. Meanwhile, five major triterpene saponins in roots of P. vietnamensis var. fuscidicus were determined using high performance liquid chromatography (HPLC) and evaporative light scattering detector (ELSD).
  
  
  CONCLUSIONS
  The genomic resources generated from P. vietnamensis var. fuscidiscus provide new insights into the identification of putative genes involved in triterpenoid saponins biosynthesis pathway. This will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level. The SSR markers identified and developed in this study show genetic diversity for this important crop and will contribute to marker-assisted breeding for P. vietnamensis var. fuscidiscus.
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. zgh73107310@163.com.
authors.forename: Guang-Hui
authors.initials: GH
authors.lastname: Zhang
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. machunhua27@hotmail.com.
authors.forename: Chun-Hua
authors.initials: CH
authors.lastname: Ma
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. zjjclc@163.com.
authors.forename: Jia-Jin
authors.initials: JJ
authors.lastname: Zhang
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. cjw31412@hotmail.com.
authors.forename: Jun-Wen
authors.initials: JW
authors.lastname: Chen
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. 28289440@qq.com.
authors.forename: Qing-Yan
authors.initials: QY
authors.lastname: Tang
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. 543673791@qq.com.
authors.forename: Mu-Han
authors.initials: MH
authors.lastname: He
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. 351966214@qq.com.
authors.forename: Xiang-Zeng
authors.initials: XZ
authors.lastname: Xu
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. jnhskip@hotmail.com.
authors.forename: Ni-Hao
authors.initials: NH
authors.lastname: Jiang
authors.affiliation: Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China. shengchaoyang@163.com.
authors.forename: Sheng-Chao
authors.initials: SC
authors.lastname: Yang
mesh_terms: D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D020869:Gene Expression Profiling; D063990:Gene Ontology; D017343:Genes, Plant; D005819:Genetic Markers; D036145:Ginsenosides / Q000032:analysis / Q000096:biosynthesis*; D016695:Glycosyltransferases / Q000235:genetics; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D005894:Panax / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; D036145:Ginsenosides; D003577:Cytochrome P-450 Enzyme System; D016695:Glycosyltransferases