Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots
Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essentia...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2014-10-01
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| Series: | Journal of Ginseng Research |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1226845314000633 |
| _version_ | 1818970629857083392 |
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| author | Murukarthick Jayakodi Sang-Choon Lee Hyun-Seung Park Woojong Jang Yun Sun Lee Beom-Soon Choi Gyoung Ju Nah Do-Soon Kim Senthil Natesan Chao Sun Tae-Jin Yang |
| author_facet | Murukarthick Jayakodi Sang-Choon Lee Hyun-Seung Park Woojong Jang Yun Sun Lee Beom-Soon Choi Gyoung Ju Nah Do-Soon Kim Senthil Natesan Chao Sun Tae-Jin Yang |
| author_sort | Murukarthick Jayakodi |
| collection | DOAJ |
| description | Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential.
Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed.
Results: Assemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots.
Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use. |
| first_indexed | 2024-12-20T14:39:31Z |
| format | Article |
| id | doaj.art-2ee55d0fa0244c85a850da028a9cd355 |
| institution | Directory Open Access Journal |
| issn | 1226-8453 |
| language | English |
| last_indexed | 2024-12-20T14:39:31Z |
| publishDate | 2014-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Ginseng Research |
| spelling | doaj.art-2ee55d0fa0244c85a850da028a9cd3552022-12-21T19:37:20ZengElsevierJournal of Ginseng Research1226-84532014-10-0138427828810.1016/j.jgr.2014.05.008Transcriptome profiling and comparative analysis of Panax ginseng adventitious rootsMurukarthick Jayakodi0Sang-Choon Lee1Hyun-Seung Park2Woojong Jang3Yun Sun Lee4Beom-Soon Choi5Gyoung Ju Nah6Do-Soon Kim7Senthil Natesan8Chao Sun9Tae-Jin Yang10Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaPhyzen Genomics Institute, Seoul, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaGenomics and Proteomics Laboratory, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, IndiaInstitute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, ChinaDepartment of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, KoreaBackground: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.http://www.sciencedirect.com/science/article/pii/S1226845314000633adventitious rootde novo assemblynext-generation sequencingPanax ginsengtranscriptome |
| spellingShingle | Murukarthick Jayakodi Sang-Choon Lee Hyun-Seung Park Woojong Jang Yun Sun Lee Beom-Soon Choi Gyoung Ju Nah Do-Soon Kim Senthil Natesan Chao Sun Tae-Jin Yang Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots Journal of Ginseng Research adventitious root de novo assembly next-generation sequencing Panax ginseng transcriptome |
| title | Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots |
| title_full | Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots |
| title_fullStr | Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots |
| title_full_unstemmed | Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots |
| title_short | Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots |
| title_sort | transcriptome profiling and comparative analysis of panax ginseng adventitious roots |
| topic | adventitious root de novo assembly next-generation sequencing Panax ginseng transcriptome |
| url | http://www.sciencedirect.com/science/article/pii/S1226845314000633 |
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