title: Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis.
abstract: BACKGROUND
  Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant.
  
  
  RESULTS
  In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes involved in the saponin biosynthetic pathway.
  
  
  CONCLUSIONS
  The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.
authors.affiliation: Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chunchun, 200-701, South Korea. whansu3368@hanmail.net.
authors.forename: Hwan-Su
authors.initials: HS
authors.lastname: Hwang
authors.affiliation: Biotechnology Division, Korea Forest Research Institute, Suwon, 441-350, South Korea. hslee@forest.go.kr.
authors.forename: Hyoshin
authors.initials: H
authors.lastname: Lee
authors.affiliation: Department of Forest Resources, College of Forest and Environmental Sciences, Kangwon National University, Chunchun, 200-701, South Korea. yechoi@kangwon.ac.kr.
authors.forename: Yong Eui
authors.initials: YE
authors.lastname: Choi
mesh_terms: D019295:Computational Biology; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D019751:Intramolecular Transferases / Q000235:genetics; D008798:Mevalonic Acid / Q000378:metabolism; D058977:Molecular Sequence Annotation; D005894:Panax / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D012503:Saponins / Q000096:biosynthesis*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D012503:Saponins; D019751:Intramolecular Transferases; C021924:lanosterol synthase; D008798:Mevalonic Acid