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Jia Z, Wang J, Meng X, Yang X, Tian Y, Wang B, Chen M, Yang J, Das D, Cao Y. Evolution and stress response potential of the plant splicing factor U1C. Sci Rep 2024; 14:17212. [PMID: 39060315 PMCID: PMC11282270 DOI: 10.1038/s41598-024-68190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/22/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing is a crucial process in multicellular eukaryote, facilitated by the assembly of spliceosomal complexes comprising numerous small ribonucleoproteins. At an early stage, U1C is thought to be required for 5' splice site recognition and base pairing. However, a systematic analysis of the U1C gene family in response to developmental cues and stress conditions has not yet been conducted in plants. This study identified 114 U1C genes in 72 plant species using basic bioinformatics analyses. Phylogenetic analysis was used to compare gene and protein structures, promoter motifs, and tissue- and stress-specific expression levels, revealing their functional commonalities or diversity in response to developmental cues, such as embryonic expression, or stress treatments, including drought and heat. Fluorescence quantitative expression analysis showed that U1C gene expression changed under salt, low temperature, drought, and Cd stress in rice seedlings. However, gene expression in shoots and roots was not consistent under different stress conditions, suggesting a complex regulatory mechanism. This research provides foundational insights into the U1C gene family's role in plant development and stress responses, highlighting potential targets for future studies.
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Affiliation(s)
- Zichang Jia
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Junjie Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiangfeng Meng
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Xue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Moxian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jingfang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65201, USA.
| | - Yunying Cao
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China.
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2
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Oberc C, Li PC. Next-generation DNA sequencing of Panax samples revealed new genotypes: Burrows-Wheeler Aligner, Python-based abundance and clustering analysis. Heliyon 2024; 10:e29104. [PMID: 38660284 PMCID: PMC11039973 DOI: 10.1016/j.heliyon.2024.e29104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024] Open
Abstract
Background There are two major species of the Panax genus, namely Panax ginseng and Panax quinquefolius. Other than the nucleic acid test and nucleic acid amplification test, DNA sequencing can be used to authenticate the species of ginseng samples, especially when their physical forms cannot be used for differentiation. Method In this work, next generation sequencing was used to obtain millions of reads from fourteen ginseng samples (root, powder, and granule). Then Gaussian Mixture clustering analysis was applied to analyze the reads from each sample. Results and Discussion A new genotype has been revealed in this study. Two samples have been authenticated with certainty, while the others may be hybrid in nature as revealed by the clustering results.
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Affiliation(s)
- Christopher Oberc
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Paul C.H. Li
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
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3
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Ito H, Ito M. Genetic diversity of Panax ginseng cultivated in Japan and its relation with some plant characteristics. J Nat Med 2024; 78:91-99. [PMID: 37707717 DOI: 10.1007/s11418-023-01747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023]
Abstract
In East Asia, Panax ginseng is one of the most important medicinal plants and has been used in traditional medicines from ancient times. Today, P. ginseng is cultivated in Korea, China, and Japan. Although the genetic diversity of P. ginseng in Korea and China has been reported previously, that of P. ginseng cultivated in Japan is largely unknown. In the present study, genetic diversity of P. ginseng cultivated in Japan was analyzed using eight simple sequence repeat markers that have been used in other studies, and the results were compared with previous results for Korea and China. The correlation between genetic diversity and plant characteristics, such as ginsenoside contents, were also examined. The genetic diversity of P. ginseng in Japan was substantially different from that in Korea and China, probably due to Japan's history of cultivation and the ginseng reproduction system of agamospermy. The genetic analysis indicated that P. ginseng cultivated in Japan could be classified into two clusters. The classification was related to the contents of ginsenosides Re and Ro in the main root but not to the cultivation region of the samples. These results may be useful for the cultivation and quality control of P. ginseng in Japan.
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Affiliation(s)
- Honoka Ito
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-Cho, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Michiho Ito
- National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-Ku, Kawasaki City, Kanagawa, 210-9501, Japan.
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4
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Kang JS, Giang VNL, Park HS, Park YS, Cho W, Nguyen VB, Shim H, Waminal NE, Park JY, Kim HH, Yang TJ. Evolution of the Araliaceae family involved rapid diversification of the Asian Palmate group and Hydrocotyle specific mutational pressure. Sci Rep 2023; 13:22325. [PMID: 38102332 PMCID: PMC10724125 DOI: 10.1038/s41598-023-49830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
The Araliaceae contain many valuable species in medicinal and industrial aspects. We performed intensive phylogenomics using the plastid genome (plastome) and 45S nuclear ribosomal DNA sequences. A total of 66 plastome sequences were used, 13 of which were newly assembled in this study, 12 from new sequences, and one from existing data. While Araliaceae plastomes showed conserved genome structure, phylogenetic reconstructions based on four different plastome datasets revealed phylogenetic discordance within the Asian Palmate group. The divergence time estimation revealed that splits in two Araliaceae subfamilies and the clades exhibiting phylogenetic discordances in the Asian Palmate group occurred at two climatic optima, suggesting that global warming events triggered species divergence, particularly the rapid diversification of the Asian Palmate group during the Middle Miocene. Nucleotide substitution analyses indicated that the Hydrocotyloideae plastomes have undergone accelerated AT-biased mutations (C-to-T transitions) compared with the Aralioideae plastomes, and the acceleration may occur in their mitochondrial and nuclear genomes as well. This implies that members of the genus Hydrocotyle, the only aquatic plants in the Araliaceae, have experienced a distinct evolutionary history from the other species. We also discussed the intercontinental disjunction in the genus Panax and proposed a hypothesis to complement the previously proposed hypothesis. Our results provide the evolutionary trajectory of Araliaceae and advance our current understanding of the evolution of Araliaceae species.
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Affiliation(s)
- Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Vo Ngoc Linh Giang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea
| | - Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Woohyeon Cho
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Van Binh Nguyen
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Faculty of Biology, Dalat University, Dalat, 670000, Vietnam
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Nomar Espinosa Waminal
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland, Gatersleben, Germany
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, 01795, South Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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5
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Wang R, Wu B, Jian J, Tang Y, Zhang T, Song Z, Zhang W, Qiong L. How to survive in the world's third poplar: Insights from the genome of the highest altitude woody plant, Hippophae tibetana (Elaeagnaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:1051587. [PMID: 36589082 PMCID: PMC9797102 DOI: 10.3389/fpls.2022.1051587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Hippophae tibetana (Tibetan sea-buckthorn) is one of the highest distributed woody plants in the world (3,000-5,200 meters a.s.l.). It is characterized by adaptation to extreme environment and important economic values. Here, we combined PacBio Hifi platform and Hi-C technology to assemble a 1,452.75 Mb genome encoding 33,367 genes with a Contig N50 of 74.31 Mb, and inferred its sexual chromosome. Two Hippophae-specific whole-genome duplication events (18.7-21.2 million years ago, Ma; 28.6-32.4 Ma) and long terminal repeats retroelements (LTR-RTs) amplifications were detected. Comparing with related species at lower altitude, Ziziphus jujuba (<1, 700 meters a.s.l.), H. tibetana had some significantly rapid evolving genes involved in adaptation to high altitude habitats. However, comparing with Hippophae rhamnoides (<3, 700 meters a.s.l.), no rapid evolving genes were found except microtubule and microtubule-based process genes, H. tibetana has a larger genome, with extra 2, 503 genes (7.5%) and extra 680.46 Mb transposable elements (TEs) (46.84%). These results suggest that the changes in the copy number and regulatory pattern of genes play a more important role for H. tibetana adapting to more extreme and variable environments at higher altitude by more TEs and more genes increasing genome variability and expression plasticity. This suggestion was supported by two findings: nitrogen-fixing genes of H. tibetana having more copies, and intact TEs being significantly closer genes than fragmentary TEs. This study provided new insights into the evolution of alpine plants.
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Affiliation(s)
- Ruoqiu Wang
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen, China
| | | | - Yiwei Tang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ticao Zhang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiping Song
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenju Zhang
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - La Qiong
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, China
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6
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Zhang YX, Niu YQ, Wang XF, Wang ZH, Wang ML, Yang J, Wang YG, Zhang WJ, Song ZP, Li LF. Phenotypic and transcriptomic responses of the shade-grown species Panax ginseng to variable light conditions. ANNALS OF BOTANY 2022; 130:749-762. [PMID: 35961674 PMCID: PMC9670753 DOI: 10.1093/aob/mcac105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear. METHODS We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species. KEY RESULTS Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions. CONCLUSIONS Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.
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Affiliation(s)
- Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen-Hui Wang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Meng-Li Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu-Guo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Wen-Ju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhi-Ping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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7
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Wang ZH, Wang XF, Lu T, Li MR, Jiang P, Zhao J, Liu ST, Fu XQ, Wendel JF, Van de Peer Y, Liu B, Li LF. Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax. Nat Commun 2022; 13:1902. [PMID: 35393424 PMCID: PMC8989883 DOI: 10.1038/s41467-022-29561-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
All extant core-eudicot plants share a common ancestral genome that has experienced cyclic polyploidizations and (re)diploidizations. Reshuffling of the ancestral core-eudicot genome generates abundant genomic diversity, but the role of this diversity in shaping the hierarchical genome architecture, such as chromatin topology and gene expression, remains poorly understood. Here, we assemble chromosome-level genomes of one diploid and three tetraploid Panax species and conduct in-depth comparative genomic and epigenomic analyses. We show that chromosomal interactions within each duplicated ancestral chromosome largely maintain in extant Panax species, albeit experiencing ca. 100–150 million years of evolution from a shared ancestor. Biased genetic fractionation and epigenetic regulation divergence during polyploidization/(re)diploidization processes generate remarkable biochemical diversity of secondary metabolites in the Panax genus. Our study provides a paleo-polyploidization perspective of how reshuffling of the ancestral core-eudicot genome leads to a highly dynamic genome and to the metabolic diversification of extant eudicot plants. The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
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Affiliation(s)
- Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, 130118, Changchun, China.,Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China.,Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Tianyuan Lu
- McGill University and Genome Quebec Innovation Center, Montreal, QC, H3A 0G1, Canada
| | - Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China
| | - Si-Tong Liu
- School of Life Sciences, Jilin University, 130061, Changchun, China
| | - Xue-Qi Fu
- School of Life Sciences, Jilin University, 130061, Changchun, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Gent, Belgium. .,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. .,College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, 210095, Nanjing, China.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, 130024, Changchun, China.
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China.
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8
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Linh NN, Hang PLB, Hue HTT, Ha NH, Hanh HH, Ton ND, Hien LTT. Species discrimination of novel chloroplast DNA barcodes and their application for identification of Panax (Aralioideae, Araliaceae). PHYTOKEYS 2022; 188:1-18. [PMID: 35095289 PMCID: PMC8758638 DOI: 10.3897/phytokeys.188.75937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Certain species within the genus Panax L. (Araliaceae) contain pharmacological precious ginsenosides, also known as ginseng saponins. Species containing these compounds are of high commercial value and are thus of particular urgency for conservation. However, within this genus, identifying the particular species that contain these compounds by morphological means is challenging. DNA barcoding is one method that is considered promising for species level identification. However, in an evolutionarily complex genus such as Panax, commonly used DNA barcodes such as nrITS, matK, psbA-trnH, rbcL do not provide species-level resolution. A recent in silico study proposed a set of novel chloroplast markers, trnQ-rps16, trnS-trnG, petB, and trnE-trnT for species level identification within Panax. In the current study, the discriminatory efficiency of these molecular markers is assessed and validated using 91 reference barcoding sequences and 38 complete chloroplast genomes for seven species, one unidentified species and one sub-species of Panax, and two outgroup species of Aralia L. along with empirical data of Panax taxa present in Vietnam via both distance-based and tree-based methods. The obtained results show that trnQ-rps16 can classify with species level resolution every clade tested here, including the highly valuable Panaxvietnamensis Ha et Grushv. We thus propose that this molecular marker to be used for identification of the species within Panax to support both its conservation and commercial trade.
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Affiliation(s)
- Nguyen Nhat Linh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Pham Le Bich Hang
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Huynh Thi Thu Hue
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Ha Hong Hanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
| | - Le Thi Thu Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Genome Research, Vietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamGraduate University of Science and TechnologyHanoiVietnam
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9
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Liu S, Wang X, Ding N, Liu Y, Li N, Ma Y, Zhao J, Wang Z, Li X, Fu X, Li L. Nucleotide Sequence Variation in Long-Term Tissue Cultures of Chinese Ginseng ( Panax ginseng C. A. Mey.). PLANTS (BASEL, SWITZERLAND) 2021; 11:79. [PMID: 35009083 PMCID: PMC8747682 DOI: 10.3390/plants11010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022]
Abstract
Plants have the salient biological property of totipotency, i.e., the capacity to regenerate a whole plant from virtually any kind of fully differentiated somatic cells after a process of dedifferentiation. This property has been well-documented by successful plant regeneration from tissue cultures of diverse plant species. However, the accumulation of somaclonal variation, especially karyotype alteration, during the tissue culture process compromises cell totipotency. In this respect, Chinese ginseng (Panax ginseng C. A. Mey.) is an exception in that it shows little decline in cell totipotency accompanied by remarkable chromosomal stability even after prolonged tissue cultures. However, it remains unclear whether chromosomal level stability necessarily couples with molecular genetic stability at the nucleotide sequence level, given that the two types of stabilities are generated by largely distinct mechanisms. Here, we addressed this issue by genome-wide comparisons at the single-base resolution of long-term tissue culture-regenerated P. ginseng plants. We identified abundant single nucleotide polymorphisms (SNPs) that have accumulated in cultured ginseng callus and are retained in the process of plant regeneration. These SNPs did not occur at random but showed differences among chromosomes and biased regional aggregation along a given chromosome. In addition, our results demonstrate that, compared with the overall genes, genes related to processes of cell totipotency and chromosomal stability possess lower mutation rates at both coding and flanking regions. In addition, collectively, the mutated genes exhibited higher expression levels than non-mutated genes and are significantly enriched in fundamental biological processes, including cellular component organization, development, and reproduction. These attributes suggest that the precipitated molecular level genetic variations during the process of regeneration in P. ginseng are likely under selection to fortify normal development. As such, they likely did not undermine chromosomal stability and totipotency of the long-term ginseng cultures.
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Affiliation(s)
- Sitong Liu
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Xinfeng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.W.); (N.D.)
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.W.); (N.D.)
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Sciences, Changchun 130033, China;
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Zhenhui Wang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China;
| | - Xiaomeng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (Y.L.); (N.L.); (J.Z.); (X.L.)
| | - Xueqi Fu
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.W.); (N.D.)
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10
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Hou M, Wang R, Zhao S, Wang Z. Ginsenosides in Panax genus and their biosynthesis. Acta Pharm Sin B 2021; 11:1813-1834. [PMID: 34386322 PMCID: PMC8343117 DOI: 10.1016/j.apsb.2020.12.017] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Ginsenosides are a series of glycosylated triterpenoids which belong to protopanaxadiol (PPD)-, protopanaxatriol (PPT)-, ocotillol (OCT)- and oleanane (OA)-type saponins known as active compounds of Panax genus. They are accumulated in plant roots, stems, leaves, and flowers. The content and composition of ginsenosides are varied in different ginseng species, and in different parts of a certain plant. In this review, we summarized the representative saponins structures, their distributions and the contents in nearly 20 Panax species, and updated the biosynthetic pathways of ginsenosides focusing on enzymes responsible for structural diversified ginsenoside biosynthesis. We also emphasized the transcription factors in ginsenoside biosynthesis and non-coding RNAs in the growth of Panax genus plants, and highlighted the current three major biotechnological applications for ginsenosides production. This review covered advances in the past four decades, providing more clues for chemical discrimination and assessment on certain ginseng plants, new perspectives for rational evaluation and utilization of ginseng resource, and potential strategies for production of specific ginsenosides.
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Key Words
- ABA, abscisic acid
- ADP, adenosine diphosphate
- AtCPR (ATR), Arabidopsis thaliana cytochrome P450 reductase
- BARS, baruol synthase
- Biosynthetic pathway
- Biotechnological approach
- CAS, cycloartenol synthase
- CDP, cytidine diphosphate
- CPQ, cucurbitadienol synthase
- CYP, cytochrome P450
- DDS, dammarenediol synthase
- DM, dammarenediol-II
- DMAPP, dimethylallyl diphosphate
- FPP, farnesyl pyrophosphate
- FPPS (FPS), farnesyl diphosphate synthase
- GDP, guanosine diphosphate
- Ginsenoside
- HEJA, 2-hydroxyethyl jasmonate
- HMGR, HMG-CoA reductase
- IPP, isopentenyl diphosphate
- ITS, internal transcribed spacer
- JA, jasmonic acid
- JA-Ile, (+)-7-iso-jasmonoyl-l-isoleucine
- JAR, JA-amino acid synthetase
- JAZ, jasmonate ZIM-domain
- KcMS, Kandelia candel multifunctional triterpene synthases
- LAS, lanosterol synthase
- LUP, lupeol synthase
- MEP, methylerythritol phosphate
- MVA, mevalonate
- MVD, mevalonate diphosphate decarboxylase
- MeJA, methyl jasmonate
- NDP, nucleotide diphosphate
- Non-coding RNAs
- OA, oleanane or oleanic acid
- OAS, oleanolic acid synthase
- OCT, ocotillol
- OSC, oxidosqualene cyclase
- PPD, protopanaxadiol
- PPDS, PPD synthase
- PPT, protopanaxatriol
- PPTS, PPT synthase
- Panax species
- RNAi, RNA interference
- SA, salicylic acid
- SE (SQE), squalene epoxidase
- SPL, squamosa promoter-binding protein-like
- SS (SQS), squalene synthase
- SUS, sucrose synthase
- TDP, thymine diphosphate
- Transcription factors
- UDP, uridine diphosphate
- UGPase, UDP-glucose pyrophosphosphprylase
- UGT, UDP-dependent glycosyltransferase
- WGD, whole genome duplication
- α-AS, α-amyrin synthase
- β-AS, β-amyrin synthase
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Affiliation(s)
- Maoqi Hou
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Rufeng Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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11
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Yang Z, Chen S, Wang S, Hu Y, Zhang G, Dong Y, Yang S, Miao J, Chen W, Sheng J. Chromosomal-scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae. Mol Ecol Resour 2021; 21:2204-2220. [PMID: 33891787 DOI: 10.1111/1755-0998.13403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 03/29/2021] [Accepted: 04/15/2021] [Indexed: 01/09/2023]
Abstract
Siberian ginseng (Eleutherococcus senticosus, also known as ciwujia) belongs to the Araliaceae family, which contains more than 1,500 species in 41 genera with diverse chromosome numbers and genome sizes. General consensus posits that ancient whole-genome duplication events and rapid evolutionary radiation are the driving forces for this variation in genome properties. In an attempt to generate more genomic information for the Araliaceae family, we report a 1.30 Gb high-quality draft genome assembly (contig N50 = 309.43 kb) of E. senticosus via PacBio long reads and Hi-C chromatin interaction maps. We found that transposable elements accounted for 72.82% of the genome and a total of 36,372 protein-coding genes were predicted. Comparative analyses of the E. senticosus, Panax notoginseng and Daucus carota genomes revealed a burst expansion of Tekay chromoviral elements in Araliaceae after its divergence with Apiaceae. We also found that E. senticosus underwent a lineage-specific whole-genome duplication event Es-α and a whole-genome duplication event Araliaceae-β that was probably shared by all Araliaceae species. Even though the rediploidization of the E. senticosus genome is evident, pathway analyses show that these two whole-genome duplication events may have contributed to the adaptation of E. senticosus to a cold environment. Taken together, the high-quality genome assembly of E. senticosus provides a valuable genomic resource for future research on the evolution of Araliaceae.
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Affiliation(s)
- Zijiang Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Shanshan Chen
- BGI College, Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Shufen Wang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Ying Hu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guanghui Zhang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
| | - Shengchao Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China.,College of Agronomy and Biotechnology, Yunnan Agriculture University, Kunming, China
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
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12
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Liu S, Zhao J, Liu Y, Li N, Wang Z, Wang X, Liu X, Jiang L, Liu B, Fu X, Li X, Li L. High Chromosomal Stability and Immortalized Totipotency Characterize Long-Term Tissue Cultures of Chinese Ginseng ( Panax Ginseng). Genes (Basel) 2021; 12:genes12040514. [PMID: 33807422 PMCID: PMC8067114 DOI: 10.3390/genes12040514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 01/21/2023] Open
Abstract
Chinese ginseng (Panax ginseng C. A. Meyer) is a highly cherished traditional Chinese medicine, with several confirmed medical effects and many more asserted health-boosting functions. Somatic chromosomal instability (CIN) is a hallmark of many types of human cancers and also related to other pathogenic conditions such as miscarriages and intellectual disabilities, hence, the study of this phenomenon is of wide scientific and translational medical significance. CIN also ubiquitously occurs in cultured plant cells, and is implicated as a major cause of the rapid decline/loss of totipotency with culture duration, which represents a major hindrance to the application of transgenic technologies in crop improvement. Here, we report two salient features of long-term cultured callus cells of ginseng, i.e., high chromosomal stability and virtually immortalized totipotency. Specifically, we document that our callus of ginseng, which has been subcultured for 12 consecutive years, remained highly stable at the chromosomal level and showed little decline in totipotency. We show that these remarkable features of cultured ginseng cells are likely relevant to the robust homeostasis of the transcriptional expression of specific genes (i.e., genes related to tissue totipotency and chromosomal stability) implicated in the manifestation of these two complex phenotypes. To our knowledge, these two properties of ginseng have not been observed in any animals (with respect to somatic chromosomal stability) and other plants. We posit that further exploration of the molecular mechanisms underlying these unique properties of ginseng, especially somatic chromosomal stability in protracted culture duration, may provide novel clues to the mechanistic understanding of the occurrence of CIN in human disease.
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Affiliation(s)
- Sitong Liu
- School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
| | - Zhenhui Wang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China;
| | - Xinfeng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China;
| | - Xiaodong Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
- Jilin Academy of Agricultural Science, Changchun 130118, China
| | - Lili Jiang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
| | - Xueqi Fu
- School of Life Sciences, Jilin University, Changchun 130012, China;
- Correspondence: (X.F.); (X.L.); (L.L.)
| | - Xiaomeng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; (J.Z.); (Y.L.); (N.L.); (X.L.); (L.J.); (B.L.)
- Correspondence: (X.F.); (X.L.); (L.L.)
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China;
- Correspondence: (X.F.); (X.L.); (L.L.)
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13
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Li MR, Ding N, Lu T, Zhao J, Wang ZH, Jiang P, Liu ST, Wang XF, Liu B, Li LF. Evolutionary Contribution of Duplicated Genes to Genome Evolution in the Ginseng Species Complex. Genome Biol Evol 2021; 13:6169528. [PMID: 33713106 PMCID: PMC8103499 DOI: 10.1093/gbe/evab051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2021] [Indexed: 11/22/2022] Open
Abstract
Genes duplicated by whole genome duplication (WGD) and small-scale duplication (SSD) have played important roles in adaptive evolution of all flowering plants. However, it still remains underinvestigated how the distinct models of duplication events and their contending evolutionary patterns have shaped the genome and epigenomes of extant plant species. In this study, we investigated the contribution of the WGD- and SSD-derived duplicate genes to the genome evolution of one diploid and three closely related allotetraploid Panax species based on genome, methylome, and proteome data sets. Our genome-wide comparative analyses revealed that although the ginseng species complex was recently diverged, they have evolved distinct overall patterns of nucleotide variation, cytosine methylation, and protein-level expression. In particular, genetic and epigenetic asymmetries observed in the recent WGD-derived genes are largely consistent across the ginseng species complex. In addition, our results revealed that gene duplicates generated by ancient WGD and SSD mechanisms exhibited distinct evolutionary patterns. We found the ancient WGD-derived genes (i.e., ancient collinear gene) are genetically more conserved and hypomethylated at the cytosine sites. In contrast, some of the SSD-derived genes (i.e., dispersal duplicated gene) showed hypermethylation and high variance in nucleotide variation pattern. Functional enrichment analyses of the duplicated genes indicated that adaptation-related traits (i.e., photosynthesis) created during the distant ancient WGDs are further strengthened by both the more recent WGD and SSD. Together, our findings suggest that different types of duplicated genes may have played distinct but relaying evolutionary roles in the polyploidization and speciation processes in the ginseng species complex.
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Affiliation(s)
- Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Tianyuan Lu
- McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Si-Tong Liu
- School of Life Sciences, Jilin University, Changchun, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
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14
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Li L, Hu Y, He M, Zhang B, Wu W, Cai P, Huo D, Hong Y. Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia. BMC Genomics 2021; 22:138. [PMID: 33637038 PMCID: PMC7912895 DOI: 10.1186/s12864-021-07427-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 02/05/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea ('Wuyi narcissus' cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed. RESULTS Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4-8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4-1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia. CONCLUSIONS The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.
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Affiliation(s)
- Li Li
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China.
| | - Yunfei Hu
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Min He
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Bo Zhang
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Wei Wu
- College of Mathematics and Computer Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Pumo Cai
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Da Huo
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China
| | - Yongcong Hong
- College of Tea and Food Science, Wuyi University, 358# Baihua Road, Wuyishan, 354300, China.
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15
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Yu N, Han J, Deng T, Chen L, Zhang J, Xing R, Wang P, Zhao G, Chen Y. A Novel Analytical Droplet Digital PCR Method for Identification and Quantification of Raw Health Food Material Powder from Panax notoginseng. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01887-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Zhou M, Yang G, Sun G, Guo Z, Gong X, Pan Y. Resolving complicated relationships of the Panax bipinnatifidus complex in southwestern China by RAD-seq data. Mol Phylogenet Evol 2020; 149:106851. [PMID: 32438045 DOI: 10.1016/j.ympev.2020.106851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 11/26/2022]
Abstract
The P. binpinnatifidus complex included most of the Panax species distributed in Sino-Himalaya regions except for P. pseudoginseng, P. stipuleanatus and P. notoginseng. However, the delimitation and identification of these taxa within the species complex are very difficult due to the existence of morphological intermediates, and their evolutionary relationships remain unresolved despite several studies have been carried out based on traditional DNA markers. The taxonomic uncertainty hinders the identification, conservation and exploration of these wild populations of Panax. To study this species complex, we employed ddRAD-seq data of these taxa from 18 different localities of southwestern China, using two RAD analysis pipelines, STACKS and pyRAD. Based on the results of phylogenetic analysis, the species complex was divided into four clades with high supports, which largely agreed with morphologically described species. Two clades, corresponding to P. vietnamensis and P. zingiberensis, respectively, were sister groups, indicating that these two species had a closer genetic relationship; the third clade was consisted of samples with bamboo-like rhizomes named as P. wangianus clade, and the fourth one with moniliform rhizomes was named as P. bipinnatifidus clade. The population genetic structure analysis and D-statistics test showed the localized admixture among these species, which indicated that introgression had occurred among the related lineages continuously distributed in southeastern Yunnan and adjacent regions.
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Affiliation(s)
- Mingmei Zhou
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqian Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guiling Sun
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Henan 475001, China
| | - Zhenhua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xun Gong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yuezhi Pan
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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17
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Till 2018: a survey of biomolecular sequences in genus Panax. J Ginseng Res 2020; 44:33-43. [PMID: 32095095 PMCID: PMC7033366 DOI: 10.1016/j.jgr.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.
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18
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Nguyen VB, Linh Giang VN, Waminal NE, Park HS, Kim NH, Jang W, Lee J, Yang TJ. Comprehensive comparative analysis of chloroplast genomes from seven Panax species and development of an authentication system based on species-unique single nucleotide polymorphism markers. J Ginseng Res 2020; 44:135-144. [PMID: 32148396 PMCID: PMC7033337 DOI: 10.1016/j.jgr.2018.06.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P . quinqu e folius and P . trifolius) from North America and five (P . ginseng, P . notoginseng, P . japonicus, P . vietnamensis, and P . stipuleanatus) from Asia. METHODS We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. RESULTS We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. CONCLUSION The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.
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Affiliation(s)
- Van Binh Nguyen
- 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
| | - Vo Ngoc Linh Giang
- 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
| | - Nomar Espinosa Waminal
- 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
| | - Hyun-Seung Park
- 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
| | - Nam-Hoon 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
| | - Woojong Jang
- 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
| | - Junki 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
| | - 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
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, Republic of Korea
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19
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Review: Molecular techniques to assess genetic variation within and between Panax ginseng and Panax quinquefolius. Fitoterapia 2019; 138:104343. [PMID: 31472181 DOI: 10.1016/j.fitote.2019.104343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/19/2019] [Accepted: 08/25/2019] [Indexed: 11/23/2022]
Abstract
A variety of methods have been used to examine genetic differences in P. ginseng and P. quinquefolius. They have shown genetic differences within populations of P. ginseng (within and between elite cultivars, landraces and wild accessions), within populations of P. quinquefolius (within and between wild and cultivated accessions) and between P. ginseng and P. quinquefolius as well as other Panax species. Some examples of their applications have been to show that some elite cultivars are not uniform, there are possible founder effects in certain populations, there has been the spread of cultivated types into wild populations, relative diversity differs between different populations and identification of the source and purity of commercial samples. More work in the use of molecular markers for ginseng are needed, however, particularly the use of Next Generation Sequencing. Potential applications are the use of sequence analysis for genetic selection, breeding to develop new cultivars and providing traceability from field to consumer. Research on molecular markers in ginseng has lagged compared to other crops probably because of less of an emphasis on breeding for cultivar development and relatively small areas of production. The many potential benefits for ginseng production have yet to be realized.
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20
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Ji Y, Liu C, Yang Z, Yang L, He Z, Wang H, Yang J, Yi T. Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in
Panax
(Araliaceae). Mol Ecol Resour 2019; 19:1333-1345. [DOI: 10.1111/1755-0998.13050] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Lifang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- School of Life Science Yunnan University Kunming China
| | - Zhengshan He
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
| | - Junbo Yang
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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21
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Liu C, Yang Z, Yang L, Yang J, Ji Y. The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae). PLANT DIVERSITY 2018; 40:265-276. [PMID: 30740573 PMCID: PMC6317490 DOI: 10.1016/j.pld.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/03/2023]
Abstract
Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.
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Affiliation(s)
- Changkun Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhenyan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lifang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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22
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Jiang P, Shi FX, Li MR, Liu B, Wen J, Xiao HX, Li LF. Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax. FRONTIERS IN PLANT SCIENCE 2018; 9:359. [PMID: 29670636 PMCID: PMC5893753 DOI: 10.3389/fpls.2018.00359] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 03/05/2018] [Indexed: 05/30/2023]
Abstract
Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.
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Affiliation(s)
- Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Feng-Xue Shi
- Northeast Normal University Natural History Museum, Changchun, China
| | - Ming-Rui Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Hong-Xing Xiao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China
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23
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Manzanilla V, Kool A, Nguyen Nhat L, Nong Van H, Le Thi Thu H, de Boer HJ. Phylogenomics and barcoding of Panax: toward the identification of ginseng species. BMC Evol Biol 2018; 18:44. [PMID: 29614961 PMCID: PMC5883351 DOI: 10.1186/s12862-018-1160-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The economic value of ginseng in the global medicinal plant trade is estimated to be in excess of US$2.1 billion. At the same time, the evolutionary placement of ginseng (Panax ginseng) and the complex evolutionary history of the genus is poorly understood despite several molecular phylogenetic studies. In this study, we use a full plastome phylogenomic framework to resolve relationships in Panax and to identify molecular markers for species discrimination. RESULTS We used high-throughput sequencing of MBD2-Fc fractionated Panax DNA to supplement publicly available plastid genomes to create a phylogeny based on fully assembled and annotated plastid genomes from 60 accessions of 8 species. The plastome phylogeny based on a 163 kbp matrix resolves the sister relationship of Panax ginseng with P. quinquefolius. The closely related species P. vietnamensis is supported as sister of P. japonicus. The plastome matrix also shows that the markers trnC-rps16, trnS-trnG, and trnE-trnM could be used for unambiguous molecular identification of all the represented species in the genus. CONCLUSIONS MBD2 depletion reduces the cost of plastome sequencing, which makes it a cost-effective alternative to Sanger sequencing based DNA barcoding for molecular identification. The plastome phylogeny provides a robust framework that can be used to study the evolution of morphological characters and biosynthesis pathways of ginsengosides for phylogenetic bioprospecting. Molecular identification of ginseng species is essential for authenticating ginseng in international trade and it provides an incentive for manufacturers to create authentic products with verified ingredients.
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Affiliation(s)
- V Manzanilla
- The Natural History Museum, University of Oslo, Oslo, Norway.
| | - A Kool
- The Natural History Museum, University of Oslo, Oslo, Norway
| | - L Nguyen Nhat
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Nong Van
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H Le Thi Thu
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - H J de Boer
- The Natural History Museum, University of Oslo, Oslo, Norway
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24
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Li MR, Shi FX, Li YL, Jiang P, Jiao L, Liu B, Li LF. Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer). Genome Biol Evol 2018; 9:2159-2169. [PMID: 28922794 PMCID: PMC5737880 DOI: 10.1093/gbe/evx160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 11/15/2022] Open
Abstract
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions. In complement, the 45s rDNA, chloroplast and mitochondrial genomes were included to perform phylogenetic and population genetic analyses. The observed spatial genetic structure between northern cultivated ginseng (NCG) and southern cultivated ginseng (SCG) accessions suggested multiple independent origins of cultivated ginseng. Genome-wide scanning further demonstrated that NCG and SCG have undergone distinct selection pressures during the domestication process, with more genes identified in the NCG (97 genes) than in the SCG group (5 genes). Functional analyses revealed that these genes are involved in diverse pathways, including DNA methylation, lignin biosynthesis, and cell differentiation. These findings suggested that the SCG and NCG groups have distinct demographic histories. Candidate genes identified are useful for future molecular breeding of cultivated ginseng.
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Affiliation(s)
- Ming-Rui Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Feng-Xue Shi
- Northeast Normal University Natural History Museum, Changchun, China
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lili Jiao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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25
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Du Z, Wu J, Meng X, Li J, Huang L. Predicting the Global Potential Distribution of Four Endangered Panax Species in Middle-and Low-Latitude Regions of China by the Geographic Information System for Global Medicinal Plants (GMPGIS). Molecules 2017; 22:molecules22101630. [PMID: 28956837 PMCID: PMC6151741 DOI: 10.3390/molecules22101630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/18/2017] [Accepted: 09/25/2017] [Indexed: 12/02/2022] Open
Abstract
Global biodiversity is strongly influenced by the decrease in endangered biological species. Predicting the distribution of endangered medicinal plants is necessary for resource conservation. A spatial distribution model—geographic information system for global medicinal plants (GMPGIS)—is used to predict the global potential suitable distribution of four endangered Panax species, including Panax japonicas (T. Nees) C. A. Meyer and Panax japonicas var. major (Burkill) C. Y. Wu & K. M. Feng distributed in low- and middle-latitude, Panax zingiberensis C. Y. Wu & K. M. Feng and Panax stipuleanatus C. T. Tsai & K. M. Feng in low-latitude regions of China based on seven bioclimatic variables and 600 occurrence points. Results indicate that areas of P. japonicus and P. japonicusvar. major are 266.29 × 105 and 77.5 × 105 km2, respectively, which are mainly distributed in China and America. By contrast, the areas of P. zingiberensis and P. stipuleanatus are 5.09 × 105 and 2.05 × 105 km2, respectively, which are mainly distributed in Brazil and China. P. japonicus has the widest distribution among the four species. The data also indicate that the mean temperature of coldest quarter is the most critical factor. This scientific prediction can be used as reference for resource conservation of endangered plants and as a guide to search for endangered species in previously unknown areas.
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Affiliation(s)
- Zhixia Du
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing 100193, China.
| | - Jie Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Xiangxiao Meng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Jinhua Li
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing 100193, China.
| | - Linfang Huang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences (CAMS), Peking Union Medical College (PUMC), Beijing 100193, China.
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26
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Zuo YJ, Wen J, Zhou SL. Intercontinental and intracontinental biogeography of the eastern Asian - Eastern North American disjunct Panax (the ginseng genus, Araliaceae), emphasizing its diversification processes in eastern Asia. Mol Phylogenet Evol 2017; 117:60-74. [PMID: 28743642 DOI: 10.1016/j.ympev.2017.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 06/08/2017] [Accepted: 06/20/2017] [Indexed: 12/01/2022]
Abstract
The intercontinental biogeography between eastern Asia and eastern North America has attracted much attention from evolutionary biologists. Further insights into understanding the evolution of the intercontinental disjunctions have been hampered by the lack of studies on the intracontinental biogeography in eastern Asia, a region with complex geology, geography, climates and habitats. Herein we studied the biogeographic history of the eastern Asian-eastern North American disjunct genus Panax with special emphasis on the investigation of its uneven diversification in Asia. This study reconstructs the diversification history of Panax and also emphasizes a large clade of Panax taxa, which has a wide distribution in eastern Asia, but was unresolved in previous studies. We examined the noncoding plastid DNA fragments of trnH-psbA, rps16, and psbM-trnD, the mitochondrial b/c intron of NAD1, and the nuclear ribosomal internal transcribed spacer (ITS) region of 356 samples from 47 populations. The results revealed the subtropical Northern Hemisphere origin (Asia or Asia and North America) of Panax in the Paleocene. Intercontinental disjunctions between eastern Asia and eastern North America formed twice in Panax, once estimated in early Eocene for the split of P. trifolius and another in mid-Miocene for the divergence of P. quinquefolius. Intercontinental diversifications in Panax showed temporal correlation with the increase of global temperature. The evolutionary radiation of the P. bipinnatifidus species complex occurred around the boundary of Oligocene and Miocene. Strong genetic structure among populations of the species complex was detected and the populations may be isolated by distance. The backbone network and the Bayesian clustering analysis revealed a major evolutionary radiation centered in the Hengduan Mountains of western China. Our results suggested that the evolutionary radiation of Panax was promoted by geographic barriers, including mountain ranges (Hengduan Mountains, Nanling Mountains and Wuyishan Mountains), oceans and altitudinal shifts, which further contribute to the knowledge of the uneven species diversification between eastern Asia and North America.
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Affiliation(s)
- Yun-Juan Zuo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences; Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Shi-Liang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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27
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Kim K, Nguyen VB, Dong J, Wang Y, Park JY, Lee SC, Yang TJ. Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species. Sci Rep 2017; 7:4917. [PMID: 28687778 PMCID: PMC5501832 DOI: 10.1038/s41598-017-05218-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
We produced complete sequences and conducted comparative analysis of the maternally inherited chloroplast (cp) genomes and bi-parentally inherited 45S nuclear ribosomal RNA genes (nrDNA) from ten Araliaceae species to elucidate the genetic diversity and evolution in that family. The cp genomes ranged from 155,993 bp to 156,730 bp with 97.1-99.6% similarity. Complete 45S nrDNA units were about 11 kb including a 5.8-kb 45S cistron. Among 79 cp protein-coding genes, 74 showed nucleotide variations among ten species, of which infA, rpl22, rps19 and ndhE genes showed the highest Ks values and atpF, atpE, ycf2 and rps15 genes showed the highest Ka/Ks values. Four genes, petN, psaJ, psbF, and psbN, related to photosynthesis and one gene, rpl23, related to the ribosomal large subunit remain conserved in all 10 Araliaceae species. Phylogenetic analysis revealed that the ten species could be resolved into two monophyletic lineages, the Panax-Aralia and the Eleutherococcus-Dendropanax groups, which diverged approximately 8.81-10.59 million years ago (MYA). The Panax genus divided into two groups, with diploid species including P. notoginseng, P. vietnamensis, and P. japonicus surviving in Southern Asia and a tetraploid group including P. ginseng and P. quinquefolius Northern Asia and North America 2.89-3.20 MYA.
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Affiliation(s)
- Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Van Binh Nguyen
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jingzhou Dong
- School of Forestry and Horticulture, Hubei University for Nationalities, Enshi, 445000, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, 510650, China
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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28
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Laurent S, Salamin N, Robinson-Rechavi M. No evidence for the radiation time lag model after whole genome duplications in Teleostei. PLoS One 2017; 12:e0176384. [PMID: 28426792 PMCID: PMC5398669 DOI: 10.1371/journal.pone.0176384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
The short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the species richness of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of new phenotypic traits, although the radiation of the lineage would not occur before a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed increase of the species number after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to taxonomic diversity in teleosts.
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Affiliation(s)
- Sacha Laurent
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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29
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Pan Y, Wang X, Sun G, Li F, Gong X. Application of RAD Sequencing for Evaluating the Genetic Diversity of Domesticated Panax notoginseng (Araliaceae). PLoS One 2016; 11:e0166419. [PMID: 27846268 PMCID: PMC5112861 DOI: 10.1371/journal.pone.0166419] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/29/2016] [Indexed: 11/19/2022] Open
Abstract
Panax notoginseng, a traditional Chinese medicinal plant, has been cultivated and domesticated for approximately 400 years, mainly in Yunnan and Guangxi, two provinces in southwest China. This species was named according to cultivated rather than wild individuals, and no wild populations had been found until now. The genetic resources available on farms are important for both breeding practices and resource conservation. In the present study, the recently developed technology RADseq, which is based on next-generation sequencing, was used to analyze the genetic variation and differentiation of P. notoginseng. The nucleotide diversity and heterozygosity results indicated that P. notoginseng had low genetic diversity at both the species and population levels. Almost no genetic differentiation has been detected, and all populations were genetically similar due to strong gene flow and insufficient splitting time. Although the genetic diversity of P. notoginseng was low at both species and population levels, several traditional plantations had relatively high genetic diversity, as revealed by the He and π values and by the private allele numbers. These valuable genetic resources should be protected as soon as possible to facilitate future breeding projects. The possible geographical origin of Sanqi domestication was discussed based on the results of the genetic diversity analysis.
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Affiliation(s)
- Yuezhi Pan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xueqin Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Guiling Sun
- Yunnan Key Laboratory for Wild Plant Resources, Kunming, China
| | - Fusheng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Jiang P, Shi FX, Li YL, Liu B, Li LF. Development of highly transferable microsatellites for Panax ginseng (Araliaceae) using whole-genome data. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600075. [PMID: 27843725 PMCID: PMC5104526 DOI: 10.3732/apps.1600075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/11/2016] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Highly transferable expressed sequence tag (EST) microsatellites were developed for Panax ginseng (Araliaceae), one of the most celebrated traditional Chinese medicines and an endangered species in East Asia, using whole-genome data. METHODS AND RESULTS Twenty-one EST microsatellites were characterized from next-generation sequencing and were composed of di- and trinucleotide repeats. Polymorphisms and genetic diversity were evaluated for 45 accessions of three ginseng landraces. The number of alleles for each locus ranged from one to five among the landraces, and the polymorphism information content varied from 0.0000 to 0.6450. These microsatellites were also tested for congeneric amplification with P. notoginseng, P. stipuleanatus, P. quinquefolius, P. bipinnatifidus, and the closely related species Aralia elata. CONCLUSIONS These novel EST-derived microsatellite markers will facilitate further population genetic studies of the genera Panax and Aralia.
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Affiliation(s)
- Peng Jiang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Feng-Xue Shi
- Museum of Natural History, Northeast Normal University, Changchun 130117, People’s Republic of China
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, People’s Republic of China
| | - Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, People’s Republic of China
- Department of Biology, Washington University, St. Louis, Missouri 63130 USA
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