Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars
Background: Various Panax ginseng cultivars 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 met...
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| Format: | Article |
| Language: | English |
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Elsevier
2017-01-01
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| Series: | Journal of Ginseng Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1226845316000026 |
| _version_ | 1818152020987609088 |
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| author | Yun Sun Lee Hyun-Seung Park Dong-Kyu Lee Murukarthick Jayakodi Nam-Hoon Kim Sang-Choon Lee Atreyee Kundu Dong-Yup Lee Young Chang Kim Jun Gyo In Sung Won Kwon Tae-Jin Yang |
| author_facet | Yun Sun Lee Hyun-Seung Park Dong-Kyu Lee Murukarthick Jayakodi Nam-Hoon Kim Sang-Choon Lee Atreyee Kundu Dong-Yup Lee Young Chang Kim Jun Gyo In Sung Won Kwon Tae-Jin Yang |
| author_sort | Yun Sun Lee |
| collection | DOAJ |
| description | Background: Various Panax ginseng cultivars 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.
Conclusion: 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. |
| first_indexed | 2024-12-11T13:48:05Z |
| format | Article |
| id | doaj.art-209e6b2f2bd740aa959e9127d427d184 |
| institution | Directory Open Access Journal |
| issn | 1226-8453 |
| language | English |
| last_indexed | 2024-12-11T13:48:05Z |
| publishDate | 2017-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Ginseng Research |
| spelling | doaj.art-209e6b2f2bd740aa959e9127d427d1842022-12-22T01:04:24ZengElsevierJournal of Ginseng Research1226-84532017-01-01411606810.1016/j.jgr.2015.12.012Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivarsYun Sun Lee0Hyun-Seung Park1Dong-Kyu Lee2Murukarthick Jayakodi3Nam-Hoon Kim4Sang-Choon Lee5Atreyee Kundu6Dong-Yup Lee7Young Chang Kim8Jun Gyo In9Sung Won Kwon10Tae-Jin Yang11Department 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, KoreaDepartment 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, KoreaCollege of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, KoreaDepartment 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, KoreaDepartment 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, KoreaDepartment 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, KoreaDepartment 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, KoreaBioprocessing Technology Institute, A*STAR (Agency for Science, Technology and Research), Centros, SingaporeGinseng Research Division, National Institute of Horitcultural and Herbal Science, Rural Development Administration, Eumseong, KoreaGinseng Resources Research Laboratory, R&D Headquarters, Korea Ginseng Corporation, Daejeon, KoreaCollege of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, KoreaDepartment 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, KoreaBackground: Various Panax ginseng cultivars 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. Conclusion: 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.http://www.sciencedirect.com/science/article/pii/S1226845316000026adventitious rootmetabolomePanax ginsengprimary metabolic pathwaystranscriptome |
| spellingShingle | Yun Sun Lee Hyun-Seung Park Dong-Kyu Lee Murukarthick Jayakodi Nam-Hoon Kim Sang-Choon Lee Atreyee Kundu Dong-Yup Lee Young Chang Kim Jun Gyo In Sung Won Kwon Tae-Jin Yang Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars Journal of Ginseng Research adventitious root metabolome Panax ginseng primary metabolic pathways transcriptome |
| title | Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars |
| title_full | Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars |
| title_fullStr | Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars |
| title_full_unstemmed | Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars |
| title_short | Comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five Panax ginseng cultivars |
| title_sort | comparative analysis of the transcriptomes and primary metabolite profiles of adventitious roots of five panax ginseng cultivars |
| topic | adventitious root metabolome Panax ginseng primary metabolic pathways transcriptome |
| url | http://www.sciencedirect.com/science/article/pii/S1226845316000026 |
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