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Yu W, Cai S, Zhao J, Hu S, Zang C, Xu J, Hu L. Beyond genome: Advanced omics progress of Panax ginseng. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112022. [PMID: 38311250 DOI: 10.1016/j.plantsci.2024.112022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Ginseng is a perennial herb of the genus Panax in the family Araliaceae as one of the most important traditional medicine. Genomic studies of ginseng assist in the systematic discovery of genes related to bioactive ginsenosides biosynthesis and resistance to stress, which are of great significance in the conservation of genetic resources and variety improvement. The transcriptome reflects the difference and consistency of gene expression, and transcriptomics studies of ginseng assist in screening ginseng differentially expressed genes to further explore the powerful gene source of ginseng. Protein is the ultimate bearer of ginseng life activities, and proteomic studies of ginseng assist in exploring the biosynthesis and regulation of secondary metabolites like ginsenosides and the molecular mechanism of ginseng adversity adaptation at the overall level. In this review, we summarize the current status of ginseng research in genomics, transcriptomics and proteomics, respectively. We also discuss and look forward to the development of ginseng genome allele mapping, ginseng spatiotemporal, single-cell transcriptome, as well as ginseng post-translational modification proteome. We hope that this review will contribute to the in-depth study of ginseng and provide a reference for future analysis of ginseng from a systems biology perspective.
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Affiliation(s)
- Wenjing Yu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Siyuan Cai
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiali Zhao
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Shuhan Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China
| | - Chen Zang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun, China.
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Lee SH, Kim J, Park HS, Koo H, Waminal NE, Pellerin RJ, Shim H, Lee HO, Kim E, Park JY, Yu HS, Kim HH, Lee J, Yang TJ. Genome structure and diversity among Cynanchum wilfordii accessions. BMC PLANT BIOLOGY 2022; 22:4. [PMID: 34979940 PMCID: PMC8722063 DOI: 10.1186/s12870-021-03390-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/06/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Cynanchum wilfordii (Cw) and Cynanchum auriculatum (Ca) have long been used in traditional medicine and as functional food in Korea and China, respectively. They have diverse medicinal functions, and many studies have been conducted, including pharmaceutical efficiency and metabolites. Especially, Cw is regarded as the most famous medicinal herb in Korea due to its menopausal symptoms relieving effect. Despite the high demand for Cw in the market, both species are cultivated using wild resources with rare genomic information. RESULTS We collected 160 Cw germplasm from local areas of Korea and analyzed their morphological diversity. Five Cw and one Ca of them, which were morphologically diverse, were sequenced, and nuclear ribosomal DNA (nrDNA) and complete plastid genome (plastome) sequences were assembled and annotated. We investigated the genomic characteristics of Cw as well as the genetic diversity of plastomes and nrDNA of Cw and Ca. The Cw haploid nuclear genome was approximately 178 Mbp. Karyotyping revealed the juxtaposition of 45S and 5S nrDNA on one of 11 chromosomes. Plastome sequences revealed 1226 interspecies polymorphisms and 11 Cw intraspecies polymorphisms. The 160 Cw accessions were grouped into 21 haplotypes based on seven plastome markers and into 108 haplotypes based on seven nuclear markers. Nuclear genotypes did not coincide with plastome haplotypes that reflect the frequent natural outcrossing events. CONCLUSIONS Cw germplasm had a huge morphological diversity, and their wide range of genetic diversity was revealed through the investigation with 14 molecular markers. The morphological and genomic diversity, chromosome structure, and genome size provide fundamental genomic information for breeding of undomesticated Cw plants.
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Affiliation(s)
- Sae Hyun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiseok Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - HyunJin Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Remnyl Joyce Pellerin
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun-Oh Lee
- Phyzen Genomics Institute, Seongnam, 13558, Republic of Korea
| | - Eunbi Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hong Seob Yu
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Jeonghoon Lee
- National Institute of Horticultural and Herbal Science, RDA, Eumseong, 27709, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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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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Abstract
Background Panax ginseng is one of the most valuable medicinal plants in Korea. However, deciphering its full genome sequence information for crop improvement has been hampered due to its complex genomic, genetic, and growth characteristics. Many efforts have been made in the past decade to overcome these limitations and understand the genome structure and the evolutionary history of P. ginseng. Methods This review aims to discuss the current status of genomic studies on P. ginseng and related species, and the experimental clues suggesting phylogenetic classification and evolutionary history of the genus Panax. Conclusion The development of sequencing technologies made genome sequencing of the large P. ginseng genome possible, providing fundamental information to deciphering the evolutionary history of P. ginseng and related species. P. ginseng went through two rounds of whole genome duplication events after diverging from the closest family Apiaceae, which was unveiled from complete whole genome sequences. Further in-depth comparative genome analysis with other related species and genera will uncover the evolutionary history as well as important morphological and ecological characteristics of Panax species.
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Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T. Centromeres of Cucumis melo L. comprise Cmcent and two novel repeats, CmSat162 and CmSat189. PLoS One 2020; 15:e0227578. [PMID: 31945109 PMCID: PMC6964814 DOI: 10.1371/journal.pone.0227578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/20/2019] [Indexed: 12/29/2022] Open
Abstract
Centromeres are prerequisite for accurate segregation and are landmarks of primary constrictions of metaphase chromosomes in eukaryotes. In melon, high-copy-number satellite DNAs (SatDNAs) were found at various chromosomal locations such as centromeric, pericentromeric, and subtelomeric regions. In the present study, utilizing the published draft genome sequence of melon, two new SatDNAs (CmSat162 and CmSat189) of melon were identified and their chromosomal distributions were confirmed using fluorescence in situ hybridization. DNA probes prepared from these SatDNAs were successfully hybridized to melon somatic and meiotic chromosomes. CmSat162 was located on 12 pairs of melon chromosomes and co-localized with the centromeric repeat, Cmcent, at the centromeric regions. In contrast, CmSat189 was found to be located not only on centromeric regions but also on specific regions of the chromosomes, allowing the characterization of individual chromosomes of melon. It was also shown that these SatDNAs were transcribed in melon. These results suggest that CmSat162 and CmSat189 might have some functions at the centromeric regions.
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Affiliation(s)
- Agus Budi Setiawan
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Chee How Teo
- Center for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - Shinji Kikuchi
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Hidenori Sassa
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, Kita-ku, Okayama, Japan
| | - Takato Koba
- Laboratory of Genetics and Plant Breeding, Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- * E-mail:
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Jang W, Jang Y, Kim NH, Waminal NE, Kim YC, Lee JW, Yang TJ. Genetic diversity among cultivated and wild Panax ginseng populations revealed by high-resolution microsatellite markers. J Ginseng Res 2019; 44:637-643. [PMID: 32617044 PMCID: PMC7322750 DOI: 10.1016/j.jgr.2019.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/26/2019] [Accepted: 05/20/2019] [Indexed: 11/25/2022] Open
Abstract
Background Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. Methods We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. Results Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (He) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. Conclusion Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.
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Affiliation(s)
- Woojong Jang
- 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, Republic of Korea
| | - Yeeun Jang
- 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, Republic of Korea
| | - Nam-Hoon Kim
- Phyzen Genomics Institute, Seongnam, Republic of Korea
| | - Nomar Espinosa Waminal
- 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, Republic of Korea.,Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, Republic of Korea
| | - Young Chang Kim
- Ginseng Research Division, National Institution of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Republic of Korea
| | - Jung Woo Lee
- Ginseng Research Division, National Institution of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 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, Republic of Korea
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Zhou HC, Pellerin RJ, Waminal NE, Yang TJ, Kim HH. Pre-labelled oligo probe-FISH karyotype analyses of four Araliaceae species using rDNA and telomeric repeat. Genes Genomics 2019; 41:839-847. [PMID: 30903554 DOI: 10.1007/s13258-019-00786-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/08/2019] [Indexed: 11/24/2022]
Abstract
BACKGROUND The family Araliaceae contains many medicinal species including ginseng of which the whole genome sequencing analyses have been going on these days. OBJECTIVE To characterize the chromosomal distribution of 5S and 45S rDNAs and telomeric repeat in four ginseng related species of Aralia elata (Miq.) Seem., Dendropanax morbiferus H. Lév., Eleutherococcus sessiliflorus (Rupr. Et Maxim.) Seem., Kalopanax septemlobus (Thunb. ex A.Murr.) Koidz. METHOD Pre-labelled oligoprobe (PLOP)-fluorescence in situ hybridization (FISH) was carried out. RESULTS The chromosome number of A. elata was 2n = 24, whereas that of the other three species of D. morbiferus, E. sessiliflorus, and K. septemlobus was 2n = 48, corresponding to diploid and tetraploid, respectively, based on the basic chromosome number x = 12 in Araliaceae. In all four species, one pair of 5S signals were detected in the proximal regions of the short arms of chromosome 3, whereas in K. septemlobus, the 5S rDNA signals localized in the subtelomeric region of short arm of chromosome 3, while all the 45S rDNA signals localized at the paracentromeric region of the short arm of chromosome 1. And the telomeric repeat signals were detected at the telomeric region of both short and long arms of most chromosomes. CONCLUSION The PLOP-FISH was very effective compared with conventional FISH method. These results provide useful comparative cytogenetic information to better understand the genome structure of each species and will be useful to trace the history of ginseng genomic constitution.
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Affiliation(s)
- Hui Chao Zhou
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Remnyl Joyce Pellerin
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea.
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Kim N, Jayakodi M, Lee S, Choi B, Jang W, Lee J, Kim HH, Waminal NE, Lakshmanan M, van Nguyen B, Lee YS, Park H, Koo HJ, Park JY, Perumal S, Joh HJ, Lee H, Kim J, Kim IS, Kim K, Koduru L, Kang KB, Sung SH, Yu Y, Park DS, Choi D, Seo E, Kim S, Kim Y, Hyun DY, Park Y, Kim C, Lee T, Kim HU, Soh MS, Lee Y, In JG, Kim H, Kim Y, Yang D, Wing RA, Lee D, Paterson AH, Yang T. Genome and evolution of the shade-requiring medicinal herb Panax ginseng. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1904-1917. [PMID: 29604169 PMCID: PMC6181221 DOI: 10.1111/pbi.12926] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/19/2018] [Accepted: 03/18/2018] [Indexed: 05/19/2023]
Abstract
Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.
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Affiliation(s)
- Nam‐Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sang‐Choon Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | | | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hyun Hee Kim
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoulKorea
| | - Nomar E. Waminal
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Department of Life ScienceChromosome Research InstituteSahmyook UniversitySeoulKorea
| | - Meiyappan Lakshmanan
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR)Singapore CitySingapore
| | - Binh van Nguyen
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hyun‐Seung Park
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hyun Jo Koo
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Hana Lee
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Jinkyung Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - In Seo Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Lokanand Koduru
- School of Chemical EngineeringSungkyunkwan UniversityJangan‐gu, Suwon, Gyeonggi‐doKorea
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical ScienceSeoul National UniversitySeoulKorea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical ScienceSeoul National UniversitySeoulKorea
| | - Yeisoo Yu
- Phyzen Genomics InstituteSeongnamGyeonggi‐doKorea
| | - Daniel S. Park
- Department of Organismic and Evolutionary BiologyHarvard University HerbariaCambridgeMAUSA
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Young‐Chang Kim
- Planning and Coordination DivisionNIHS, RDAWanju‐gunJeollabuk‐doKorea
| | - Dong Yun Hyun
- Ginseng Research DivisionNational Institute of Horticultural & Herbal Science, RDAEumseongChungcheongbuk‐doKorea
| | - Youn‐Il Park
- Department of Biological SciencesChungnam National UniversityDaejeonKorea
| | - Changsoo Kim
- Department of Crop ScienceChungnam National UniversityDaejeonKorea
| | - Tae‐Ho Lee
- Genomics DivisionNational Institute of Agricultural SciencesJeonjuJeollabuk‐doKorea
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource EngineeringPlant Engineering Research InstituteSejong UniversitySeoulKorea
| | - Moon Soo Soh
- Division of Integrative Bioscience and BiotechnologySejong UniversitySeoulKorea
| | - Yi Lee
- Department of Industrial Plant Science & TechnologyChungbuk National UniversityCheongjuChungcheongbuk‐doKorea
| | - Jun Gyo In
- Laboratory of Resource and AnalysisR&D HeadquartersKorea Ginseng CorporationDaejeonKorea
| | - Heui‐Soo Kim
- Department of Biological SciencesCollege of Natural SciencesPusan National UniversityBusanKorea
| | - Yong‐Min Kim
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeonKorea
| | - Deok‐Chun Yang
- Graduate School of Biotechnology and Ginseng BankKyung Hee UniversityYonginGyeonggi‐doKorea
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesThe University of ArizonaTucsonAZUSA
| | - Dong‐Yup Lee
- Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR)Singapore CitySingapore
- School of Chemical EngineeringSungkyunkwan UniversityJangan‐gu, Suwon, Gyeonggi‐doKorea
| | - Andrew H. Paterson
- Plant Genome Mapping LaboratoryCollege of Agricultural and Environmental Sciences and Franklin College of Arts and SciencesUniversity of GeorgiaAthensGAUSA
| | - Tae‐Jin Yang
- Department of Plant Science, Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
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9
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Waminal NE, Pellerin RJ, Kim NS, Jayakodi M, Park JY, Yang TJ, Kim HH. Rapid and Efficient FISH using Pre-Labeled Oligomer Probes. Sci Rep 2018; 8:8224. [PMID: 29844509 PMCID: PMC5974128 DOI: 10.1038/s41598-018-26667-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/17/2018] [Indexed: 12/29/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1-2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats. The 16 developed rDNA PLOPs can be universally applied to plants and animals. The telomere PLOPs can be utilized in most plants with Arabidopsis-type telomeres. The ginseng-specific PLOP can be used to distinguish P. ginseng from related Panax species. Differential labeling of PLOPs allowed us to simultaneously visualize different target loci while reducing the FISH hybridization time from ~16 h to 5 min. PLOP-FISH is efficient, reliable, and rapid, making it ideal for routine analysis, especially of newly sequenced genomes using either universal or specific targets, such as novel tandem repeats identified from whole-genome sequencing data.
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Affiliation(s)
- Nomar Espinosa Waminal
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.,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, 08826, Korea
| | - Remnyl Joyce Pellerin
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea
| | - Nam-Soo Kim
- Department of Molecular Biosciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Murukarthick Jayakodi
- 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, 08826, Korea
| | - 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, 08826, 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, 08826, Korea.
| | - Hyun Hee Kim
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.
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10
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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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