title: Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling.
abstract: BACKGROUND
  Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset of I. indigotica.
  
  
  RESULTS
  A database of 36,367 unigenes (average length = 1,115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, 104 unigenes were identified covering most of the catalytic steps in the general biosynthetic pathways of indole, terpenoid, and phenylpropanoid. Subsequently, the organ-specific expression patterns of the genes involved in these pathways, and their responses to methyl jasmonate (MeJA) induction, were investigated. Metabolites profile of effective phenylpropanoid showed accumulation pattern of secondary metabolites were mostly correlated with the transcription of their biosynthetic genes. According to the analysis of UDP-dependent glycosyltransferases (UGT) family, several flavonoids were indicated to exist in I. indigotica and further identified by metabolic profile using UPLC/Q-TOF. Moreover, applying transcriptome co-expression analysis, nine new, putative UGTs were suggested as flavonol glycosyltransferases and lignan glycosyltransferases.
  
  
  CONCLUSIONS
  This database provides a pool of candidate genes involved in biosynthesis of effective metabolites in I. indigotica. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Chen
authors.forename: Xin
authors.initials: X
authors.lastname: Dong
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.forename: Xun
authors.initials: X
authors.lastname: Zhou
authors.forename: Shouhong
authors.initials: S
authors.lastname: Gao
authors.forename: Ruibing
authors.initials: R
authors.lastname: Chen
authors.forename: Lianna
authors.initials: L
authors.lastname: Sun
authors.affiliation: Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China. zhanglei@smmu.edu.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.forename: Wansheng
authors.initials: W
authors.lastname: Chen
mesh_terms: D000085:Acetates; D000470:Alkaloids / Q000096:biosynthesis; D053898:Biosynthetic Pathways / Q000235:genetics; D003517:Cyclopentanes; D030541:Databases, Genetic; D005419:Flavonoids / Q000096:biosynthesis*; D017343:Genes, Plant; D007211:Indoles / Q000737:chemistry; D031219:Isatis / Q000737:chemistry* / Q000235:genetics; D055442:Metabolome; D058977:Molecular Sequence Annotation; D054883:Oxylipins; D064210:Secondary Metabolism; D013729:Terpenes / Q000737:chemistry; D059467:Transcriptome
chemical_list: D000085:Acetates; D000470:Alkaloids; D003517:Cyclopentanes; D005419:Flavonoids; D007211:Indoles; D054883:Oxylipins; D013729:Terpenes; C072239:methyl jasmonate