title: Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins.
abstract: BACKGROUND
  Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. The 454 pyrosequencing technology provides a promising opportunity for finding novel genes that participate in plant metabolism. Consequently, this technology may help to identify the candidate genes involved in the saikosaponin biosynthetic pathway.
  
  
  RESULTS
  One-quarter of the 454 pyrosequencing runs produced a total of 195, 088 high-quality reads, with an average read length of 356 bases (NCBI SRA accession SRA039388). A de novo assembly generated 24, 037 unique sequences (22, 748 contigs and 1, 289 singletons), 12, 649 (52.6%) of which were annotated against three public protein databases using a basic local alignment search tool (E-value ≤1e-10). All unique sequences were compared with NCBI expressed sequence tags (ESTs) (237) and encoding sequences (44) from the Bupleurum genus, and with a Sanger-sequenced EST dataset (3, 111). The 23, 173 (96.4%) unique sequences obtained in the present study represent novel Bupleurum genes. The ESTs of genes related to saikosaponin biosynthesis were found to encode known enzymes that catalyze the formation of the saikosaponin backbone; 246 cytochrome P450 (P450s) and 102 glycosyltransferases (GTs) unique sequences were also found in the 454 dataset. Full length cDNAs of 7 P450s and 7 uridine diphosphate GTs (UGTs) were verified by reverse transcriptase polymerase chain reaction or by cloning using 5' and/or 3' rapid amplification of cDNA ends. Two P450s and three UGTs were identified as the most likely candidates involved in saikosaponin biosynthesis. This finding was based on the coordinate up-regulation of their expression with β-AS in methyl jasmonate-treated adventitious roots and on their similar expression patterns with β-AS in various B. chinense tissues.
  
  
  CONCLUSIONS
  A collection of high-quality ESTs for B. chinense obtained by 454 pyrosequencing is provided here for the first time. These data should aid further research on the functional genomics of B. chinense and other Bupleurum species. The candidate genes for enzymes involved in saikosaponin biosynthesis, especially the P450s and UGTs, that were revealed provide a substantial foundation for follow-up research on the metabolism and regulation of the saikosaponins.
authors: Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, No, 151, Malianwa North Road, Haidian District, Beijing 100193, China.
authors: Chun
authors: C
authors: Sui
authors: Jie
authors: J
authors: Zhang
authors: Jianhe
authors: J
authors: Wei
authors: Shilin
authors: S
authors: Chen
authors: Ying
authors: Y
authors: Li
authors: Jiesen
authors: J
authors: Xu
authors: Yue
authors: Y
authors: Jin
authors: Caixiang
authors: C
authors: Xie
authors: Zhihui
authors: Z
authors: Gao
authors: Hongjiang
authors: H
authors: Chen
authors: Chengmin
authors: C
authors: Yang
authors: Zheng
authors: Z
authors: Zhang
authors: Yanhong
authors: Y
authors: Xu
mesh_terms: D029972:Bupleurum / Q000235:genetics* / Q000378:metabolism; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D015723:Gene Library; D017343:Genes, Plant; D014453:Glucuronosyltransferase / Q000235:genetics; D058977:Molecular Sequence Annotation; D009828:Oleanolic Acid / Q000031:analogs & derivatives* / Q000096:biosynthesis; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D010946:Plants, Medicinal / Q000235:genetics / Q000378:metabolism; D012503:Saponins / Q000096:biosynthesis*; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018744:DNA, Plant; D012503:Saponins; D009828:Oleanolic Acid; D003577:Cytochrome P-450 Enzyme System; D014453:Glucuronosyltransferase; C025759:saikosaponin D