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Guo M, Pang X, Xu Y, Jiang W, Liao B, Yu J, Xu J, Song J, Chen S. Plastid genome data provide new insights into the phylogeny and evolution of the genus Epimedium. J Adv Res 2022; 36:175-185. [PMID: 35127172 PMCID: PMC8799909 DOI: 10.1016/j.jare.2021.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/14/2021] [Accepted: 06/26/2021] [Indexed: 10/25/2022] Open
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Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias. SCIENCE CHINA. LIFE SCIENCES 2022; 65:809-817. [PMID: 34378141 PMCID: PMC8354779 DOI: 10.1007/s11427-021-1968-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However, the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database (GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias (Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People's Republic of China, and U.S. Pharmacopoeia's Herbal Medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://www.gpgenome.com and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.
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Taxonomy of Epimedium (Berberidaceae) with special reference to Chinese species. CHINESE HERBAL MEDICINES 2021; 14:20-35. [PMID: 36120133 PMCID: PMC9476710 DOI: 10.1016/j.chmed.2021.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/17/2021] [Accepted: 05/09/2021] [Indexed: 11/20/2022] Open
Abstract
Epimedii Herba is a commonly used traditional Chinese herbal medicine. Five Epimedium species are included in Chinese Pharmacopoeia and most species of Epimedium are used as Epimedii Herba in practical application. However, as the largest herbaceous genus of the Berberidaceae, Epimedium has many taxonomic controversies which hinder the effective use of Epimedii Herba. This paper reviewed the taxonomic research related to Epimedium, including taxonomic history, taxonomic values of morphological characters, species and distribution, infra-genera taxonomic system and the taxonomic research of Chinese Epimedium. For instance, we recognized Epimedium wushanense and clarified that the species, as described in Flora Reipublicae Popularis Sinicae and Flora of China, actually includes four Epimedium species similar in leaflet shape. In general, it was recognized here that Epimedium comprises 62 species, of which 52 species are distributed in China. For Chinese Epimedium species with the most taxonomic problems, the taxonomic research on the taxa was reviewed and the newest species key was proposed along with proposals for those taxonomic problems needing further resolution. This review is of great implication for the identification, exploration and utilization of Epimedii Herba.
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Ren F, Wang L, Li Y, Zhuo W, Xu Z, Guo H, Liu Y, Gao R, Song J. Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola. Ecol Evol 2021; 11:4158-4171. [PMID: 33976800 PMCID: PMC8093665 DOI: 10.1002/ece3.7312] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 01/27/2023] Open
Abstract
The increasingly wide application of chloroplast (cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029-190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955-42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase-like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL-UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU, and trnL-CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.
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Affiliation(s)
- Fengming Ren
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | | | - Ying Li
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
| | - Wei Zhuo
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | - Zhichao Xu
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
| | | | - Yan Liu
- Medicinal Biological Technology Research CenterChongqing Institute of Medicinal Plant CultivationBio‐Resource Research and Utilization Joint Key Laboratory Sichuan and ChongqingChongqingChina
| | - Ranran Gao
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
| | - Jingyuan Song
- Institute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences & Peking Union Medical CollegeKey Lab of Chinese Medicine Resources ConservationState Administration of Traditional Chinese Medicine of the People's Republic of ChinaBeijingChina
- Engineering Research Center of Chinese Medicine ResourceMinistry of EducationBeijingChina
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Wang LJ, Gao MD, Sheng MY, Yin J. Cluster analysis of karyotype similarity coefficients in Epimedium (Berberidaceae): insights in the systematics and evolution. PHYTOKEYS 2020; 161:11-26. [PMID: 33005087 PMCID: PMC7508920 DOI: 10.3897/phytokeys.161.51046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
In order to evaluate the genome evolution and systematics, karyotype analysis of mitotic metaphase chromosomes in 51 taxa of Epimedium and two species of Vancouveria was conducted. The 53 taxa were clustered, based on their karyotype similarity coefficients. Results showed that the 53 taxa studied were all diploid with 12 chromosomes (2n = 2x = 12). Each taxon had one pair of satellites located on pair I of homologous chromosomes. Moreover, the karyotype types of the 53 taxa studied were all type 1A or 2A of Stebbins. It can be concluded that the karyotypes between species are indeed very similar and the genome of Epimedium was conservative in evolution. The cluster analysis of karyotype similarity coefficients could provide valuable clues for the systematics and taxonomy of Epimedium. Results of the cluster analysis strongly supported the previous taxonomic division of E. subg. Rhizophyllum and E. subg. Epimedium. The results also showed that the interspecific relationship was closely correlated with geographical distribution in E. subg. Epimedium and the taxa native to east Asia had the highest genetic diversity in Epimedium. Finally, the origin of the modern geographical distribution of Epimedium was inferred. Results of the present study have significant scientific values in further studies on resource utilisation, taxonomy and phylogeny in Epimedium.
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Affiliation(s)
- Lin-Jiao Wang
- Institute of Karst Research, Guizhou Normal University, Guiyang 550001, ChinaGuizhou Normal UniversityGuiyangChina
- National Engineering Research Center for Karst Rocky Desertification Control, Guiyang 550001, ChinaNational Engineering Research Center for Karst Rocky Desertification ControlGuiyangChina
| | - Meng-Di Gao
- Institute of Karst Research, Guizhou Normal University, Guiyang 550001, ChinaGuizhou Normal UniversityGuiyangChina
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry, Guiyang, Guizhou 550001, ChinaGuizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative IndustryGuiyangChina
| | - Mao-Yin Sheng
- Institute of Karst Research, Guizhou Normal University, Guiyang 550001, ChinaGuizhou Normal UniversityGuiyangChina
- National Engineering Research Center for Karst Rocky Desertification Control, Guiyang 550001, ChinaNational Engineering Research Center for Karst Rocky Desertification ControlGuiyangChina
| | - Jie Yin
- Institute of Karst Research, Guizhou Normal University, Guiyang 550001, ChinaGuizhou Normal UniversityGuiyangChina
- Guizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative Industry, Guiyang, Guizhou 550001, ChinaGuizhou Engineering Laboratory for Karst Rocky Desertification Control and Derivative IndustryGuiyangChina
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Huang R, Liang Q, Wang Y, Yang TJ, Zhang Y. The complete chloroplast genome of Epimedium pubescens Maxim. (Berberidaceae), a traditional Chinese medicine herb. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2042-2044. [PMID: 33457735 PMCID: PMC7781925 DOI: 10.1080/23802359.2020.1756490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Epimedium pubescens Maxim. is a well-known traditional Chinese medicine herb. In this study, the complete chloroplast genome of E. pubescens was sequenced. The genome was 158 956 bp in length, with a large single-copy region of 86,345 bp, a small single-copy region of 17,075 bp, and 2 inverted repeat regions of 27,768 bp. The genome consisted of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC contents were 38.82%. Phylogenetic analysis showed that E. pubescens of series Brachyrcerae was firstly clustered with E. acumiantum Franch. of ser. Dolichocerae, but not with E. brevicornu Maxim. from the same series.
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Affiliation(s)
- Ruoqi Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China.,Academy of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Ying Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - 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
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
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Zhang Y, Huang R, Wu L, Wang Y, Jin T, Liang Q. The complete chloroplast genome of Epimedium brevicornu Maxim (Berberidaceae), a traditional Chinese medicine herb. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:588-590. [PMID: 33366659 PMCID: PMC7748679 DOI: 10.1080/23802359.2019.1710593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Epimedium brevicornu Maxim. is a traditional Chinese medicine herb with good effects on many diseases. In the present paper, the complete chloroplast genome of E. brevicornu was sequenced. The complete chloroplast genome of E. brevicornu was 159572 bp in length with 38.83% GC content, including four distinct regions: large single-copy region (86535 bp), small single-copy region (17641 bp), and a pair of inverted repeat regions (27698 bp). The chloroplast genome encoded 112 unique genes, which included 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the previously reported chloroplast genomes of Epimedium showed that E. brevicornu with small flowers at first clustered with large-flowered E. acuminatum into a strongly supported branch, but not with Epimedium species having similar floral characters.
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Affiliation(s)
- Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Ruoqi Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Wu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Ying Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Tae Jin
- 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
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
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