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Shen G, Luo Y, Yao Y, Meng G, Zhang Y, Wang Y, Xu C, Liu X, Zhang C, Ding G, Pang Y, Zhang H, Guo B. The discovery of a key prenyltransferase gene assisted by a chromosome-level Epimedium pubescens genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1034943. [PMID: 36452098 PMCID: PMC9702526 DOI: 10.3389/fpls.2022.1034943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Epimedium pubescens is a species of the family Berberidaceae in the basal eudicot lineage, and a main plant source for the traditional Chinese medicine "Herba Epimedii". The current study achieved a chromosome-level genome assembly of E. pubescens with the genome size of 3.34 Gb, and the genome guided discovery of a key prenyltransferase (PT) in E. pubescens. Our comparative genomic analyses confirmed the absence of Whole Genome Triplication (WGT-γ) event shared in core eudicots and further revealed the occurrence of an ancient Whole Genome Duplication (WGD) event approximately between 66 and 81 Million Years Ago (MYA). In addition, whole genome search approach was successfully applied to identify 19 potential flavonoid PT genes and an important flavonoid PT (EpPT8) was proven to be an enzyme for the biosynthesis of medicinal compounds, icaritin and its derivatives in E. pubescens. Therefore, our results not only provide a good reference genome to conduct further molecular biological studies in Epimedium genus, but also give important clues for synthetic biology and industrial production of related prenylated flavonoids in future.
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Affiliation(s)
- Guoan Shen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yanjiao Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Institute of Animal Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Guoqing Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yixin Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yuanyue Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Chaoqun Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiang Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Chongqing Key Laboratory of Traditional Chinese Medicine Resource, Chongqing Academy of Chinese Materia Medica, Chongqing, China
| | - Cheng Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- Key Laboratory of Biodiversity Science and Ecological Engineering, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Yongzhen Pang
- Institute of Animal Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Baolin Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
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Lee JH, Kim K, Kim NR, Lee SC, Yang TJ, Kim YD. The complete chloroplast genome of a medicinal plantEpimedium koreanumNakai (Berberidaceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4342-4343. [DOI: 10.3109/19401736.2015.1089492] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jung-Hoon Lee
- Department of Life Science, Hallym University, Chuncheon, Gangwon-Do, Republic of Korea,
| | - Kyunghee Kim
- 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, Republic of Korea, and
- Phyzen Genomics Institute, Seoul, Gwanak-Gu, Republic of Korea
| | - Na-Rae Kim
- Department of Life Science, Hallym University, Chuncheon, Gangwon-Do, Republic of Korea,
| | - Sang-Choon Lee
- 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, Republic of Korea, and
| | - Tae-Jin Yang
- 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, Republic of Korea, and
| | - Young-Dong Kim
- Department of Life Science, Hallym University, Chuncheon, Gangwon-Do, Republic of Korea,
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