title: Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of fivePanax ginsengcultivars.
abstract: BACKGROUND
  VariousPanax ginsengcultivars exhibit a range of diversity for morphological and physiological traits. However, there are few studies on diversity of metabolic profiles and genetic background to understand the complex metabolic pathway in ginseng.
  
  
  METHODS
  To understand the complex metabolic pathway and related genes in ginseng, we tried to conduct integrated analysis of primary metabolite profiles and related gene expression using five ginseng cultivars showing different morphology. We investigated primary metabolite profiles via gas chromatography-mass spectrometry (GC-MS) and analyzed transcriptomes by Illumina sequencing using adventitious roots grown under the same conditions to elucidate the differences in metabolism underlying such genetic diversity.
  
  
  RESULTS
  GC-MS analysis revealed that primary metabolite profiling allowed us to classify the five cultivars into three independent groups and the grouping was also explained by eight major primary metabolites as biomarkers. We selected three cultivars (Chunpoong, Cheongsun, and Sunhyang) to represent each group and analyzed their transcriptomes. We inspected 100 unigenes involved in seven primary metabolite biosynthesis pathways and found that 21 unigenes encoding 15 enzymes were differentially expressed among the three cultivars. Integrated analysis of transcriptomes and metabolomes revealed that the ginseng cultivars differ in primary metabolites as well as in the putative genes involved in the complex process of primary metabolic pathways.
  
  
  CONCLUSIONS
  Our data derived from this integrated analysis provide insights into the underlying complexity of genes and metabolites that co-regulate flux through these pathways in ginseng.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Yun Sun
authors.initials: YS
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Hyun-Seung
authors.initials: HS
authors.lastname: Park
authors.affiliation: College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea.
authors.forename: Dong-Kyu
authors.initials: DK
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Murukarthick
authors.initials: M
authors.lastname: Jayakodi
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Nam-Hoon
authors.initials: NH
authors.lastname: Kim
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.
authors.forename: Sang-Choon
authors.initials: SC
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea; Department of Biological Sciences, Presidency University, Kolkata, West Bengal, India.
authors.forename: Atreyee
authors.initials: A
authors.lastname: Kundu
authors.affiliation: Bioprocessing Technology Institute, ASTAR (Agency for Science, Technology and Research), Centros, Singapore; Department of Chemical and Biomolecular Engineering, Synthetic Biology Research Consortium, National University of Singapore, Singapore.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
authors.affiliation: Ginseng Research Division, National Institute of Horitcultural and Herbal Science, Rural Development Administration, Eumseong, Korea.
authors.forename: Young Chang
authors.initials: YC
authors.lastname: Kim
authors.affiliation: Ginseng Resources Research Laboratory, R&D Headquarters, Korea Ginseng Corporation, Daejeon, Korea.
authors.forename: Jun Gyo
authors.initials: JG
authors.lastname: In
authors.affiliation: College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Korea.
authors.forename: Sung Won
authors.initials: SW
authors.lastname: Kwon
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea; Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, Korea.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
keywords: Panax ginseng; adventitious root; metabolome; primary metabolic pathways; transcriptome