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Chetri BK, Senapati A, Shelke RG, Mitra S, Rangan L. Phylogenetic exploration, codon usage bias, and genomic divergence in Hydrocotyle: a comparative plastome study across different geographical locations. Genetica 2024:10.1007/s10709-024-00213-4. [PMID: 39327345 DOI: 10.1007/s10709-024-00213-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
Hydrocotyle himalaica from Bhutan, a perennial herb that thrives from 1500 to 2600 m, possesses both ecological importance and medicinal properties. The plastome analysis revealed a length of 153,383 bp, showing variation from conspecific taxa in China. Its standard structure comprises two IR regions (18,336 bp IRa and 18,336 bp IRb), an LSC region of 97,944 bp, and an SSC region of 18,767 bp, with a GC content of 37.63%. Non-coding regions showed higher mutation susceptibility, with Pi values from 0.006 to 0.107. An AT-rich codon bias was consistent across all 18 Hydrocotyle species. Nucleotide composition and GC% in coding sequences differed among the species. The codon preference in Hydrocotyle is shaped by multiple factors, with natural selection being the primary influence, as indicated by the ENC-plot, PR2-plot, and Neutrality-plot. Codon usage patterns varied, with RSCU values from 0 to 2.23. Codons ending in A or U had RSCU > 1, while those ending in C or G had RSCU < 1. GC2 content surpassed GC3 and GC1 in most genes. The phylogenetic analysis placed H. himalaica, sourced from Kanglung, Bhutan, within the monophyly of the Hydrocotyloideae subfamily. However, the species showed weaker bootstrap support (BS < 50) with H. javanica and H. hookeri subsp., a deviation from a prior report on the same species from Jiangkou, Guizhou, China. This analysis highlighted the genomic characteristics and evolutionary relationships of H. himalaica from Bhutan, underscoring the need for a comprehensive phylogenetic, ecological, and botanical characterization to confirm intra-specific variation within Hydrocotyle species.
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Affiliation(s)
- Bimal K Chetri
- School of Agro and Rural Technology, Indian Institute of Technology, Guwahati, Assam, 781 039, India
- Department of Environment and Life Sciences, Sherubtse College, Royal University of Bhutan, 42002, Kanglung, Bhutan
| | - Alok Senapati
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Assam, 781 039, India
| | - Rahul G Shelke
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Assam, 781 039, India
| | - Sudip Mitra
- School of Agro and Rural Technology, Indian Institute of Technology, Guwahati, Assam, 781 039, India
| | - Latha Rangan
- School of Agro and Rural Technology, Indian Institute of Technology, Guwahati, Assam, 781 039, India.
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Assam, 781 039, India.
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Tonga SLK, Tchegnitegni BT, Siwe-Noundou X, Tsopmene UJ, Ponou BK, Dzoyem JP, Poka M, Demana PH, Tapondjou LA, Beukes DR, Antunes EM, Teponno RB. Manniosides G-J, New Ursane- and Lupane-Type Saponins from Schefflera mannii (Hook.f.) Harms. Molecules 2024; 29:3447. [PMID: 39124853 PMCID: PMC11313943 DOI: 10.3390/molecules29153447] [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: 06/29/2024] [Revised: 07/20/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024] Open
Abstract
Four previously unreported triterpenoid saponins named 3β-hydroxy-23-oxours-12-en-28-oic acid 28-O-β-D-glucopyranosyl ester (mannioside G) (1), 23-O-acetyl-3β-hydroxyurs-12-en-28-oic acid 28-O-β-D-glucopyranosyl ester (mannioside H) (2), ursolic acid 28-O-[α-L-rhamnopyranosyl-(1→4)-β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyl] ester (mannioside I) (3), and 3β-hydroxy-23-oxolup-20(29)-en-28-oic acid 28-O-β-D-glucopyranosyl ester (mannioside J) (4) were isolated as minor constituents from the EtOAc soluble fraction of the MeOH extract of the leaves of Schefflera mannii along with the known compounds 23-hydroxyursolic acid 28-O-β-D-glucopyranosyl ester (5), ursolic acid 28-O-β-D-glucopyranosyl ester (6), pulsatimmoside B (7) betulinic acid 28-O-[α-L-rhamnopyranosyl-(1→4)-β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyl] ester (8), 23-hydroxy-3-oxo-urs-12-en-28-oic acid (9), hederagenin (10), ursolic acid (11), betulinic acid (12), and lupeol (13). Their structures were elucidated by a combination of 1D and 2D NMR analysis and mass spectrometry. The MeOH extract, the EtOAc and n-BuOH fractions, and some of the isolated compounds were evaluated for their antibacterial activity against four bacteria: Staphylococcus aureus ATCC1026, Staphylococcus epidermidis ATCC 35984, Escherichia coli ATCC10536, and Klepsiella pnemoniae ATCC13882. They were also screened for their antioxidant properties, but no significant results were obtained.
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Affiliation(s)
- Simionne Lapoupée Kuitcha Tonga
- Research Unit of Environmental and Applied Chemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (S.L.K.T.); (B.T.T.); (B.K.P.); (L.A.T.)
| | - Billy Toussie Tchegnitegni
- Research Unit of Environmental and Applied Chemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (S.L.K.T.); (B.T.T.); (B.K.P.); (L.A.T.)
- School of Pharmacy, University of the Western Cape, Bellville 7535, South Africa;
- Department of Chemistry, University of the Western Cape, Bellville 7535, South Africa
| | - Xavier Siwe-Noundou
- Department of Pharmaceutical Sciences, School of Pharmacy, Sefako Makgatho Health Sciences University, P.O. Box 218, Pretoria 0208, South Africa; (M.P.); (P.H.D.)
| | - Ulrich Joël Tsopmene
- Research Unit of Microbiology and Antimicrobial Substances, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (U.J.T.); (J.P.D.)
| | - Beaudelaire Kemvoufo Ponou
- Research Unit of Environmental and Applied Chemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (S.L.K.T.); (B.T.T.); (B.K.P.); (L.A.T.)
| | - Jean Paul Dzoyem
- Research Unit of Microbiology and Antimicrobial Substances, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (U.J.T.); (J.P.D.)
| | - Madan Poka
- Department of Pharmaceutical Sciences, School of Pharmacy, Sefako Makgatho Health Sciences University, P.O. Box 218, Pretoria 0208, South Africa; (M.P.); (P.H.D.)
| | - Patrick H. Demana
- Department of Pharmaceutical Sciences, School of Pharmacy, Sefako Makgatho Health Sciences University, P.O. Box 218, Pretoria 0208, South Africa; (M.P.); (P.H.D.)
| | - Léon Azefack Tapondjou
- Research Unit of Environmental and Applied Chemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (S.L.K.T.); (B.T.T.); (B.K.P.); (L.A.T.)
| | - Denzil R. Beukes
- School of Pharmacy, University of the Western Cape, Bellville 7535, South Africa;
| | - Edith M. Antunes
- Department of Chemistry, University of the Western Cape, Bellville 7535, South Africa
| | - Rémy Bertrand Teponno
- Research Unit of Environmental and Applied Chemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon; (S.L.K.T.); (B.T.T.); (B.K.P.); (L.A.T.)
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Yang H, Ni Y, Zhang X, Li J, Chen H, Liu C. The mitochondrial genomes of Panax notoginseng reveal recombination mediated by repeats associated with DNA replication. Int J Biol Macromol 2023; 252:126359. [PMID: 37619687 DOI: 10.1016/j.ijbiomac.2023.126359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Abstract
Panax notoginseng is one of the most valuable medicinal species. However, its mitochondrial genome has not been reported yet. We aimed to determine the mitogenome sequence of P. notoginseng. We de novo assembled the mitogenome with Illumina short reads and Nanopore long reads. The mitochondrial genome of P. notoginseng has a multipartite structure consisting of interconversion between a "master circle" and numerous "subgenomic circles" through recombinations mediated by 64 pairs of repetitive sequences. Among the multipartite structure, seven subgenomic circles were best supported. Six of the seven subgenomic circles shared an 852 bp conserved fragment. The complete mitogenome of P. notoginseng was 662,479 bp long including 34 mitochondrial protein-coding genes (PCGs), three rRNA, and 19 tRNA genes. We identified 166 microsatellite repeats and 26 long-tandem repeats. Phylogenetic analysis resolved a tree that was mostly congruent with the phylogeny of Apiales species described in the APG IV system and the tree built with the chloroplast genome sequences. A total of 12 mitochondrial plastid DNA fragments were identified. Lastly, we predicted 591C-to-U RNA editing sites in the coding regions of mitochondrial PCGs. The mitochondrial genome will lay the foundation for understanding the evolution of Panax species.
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Affiliation(s)
- Heyu Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
| | - Xinyi Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
| | - Jingling Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China.
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Yan R, Gu L, Qu L, Wang X, Hu G. New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes. Int J Mol Sci 2023; 24:16629. [PMID: 38068952 PMCID: PMC10706649 DOI: 10.3390/ijms242316629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), a small single-copy (SSC) region (18,585-18,768 bp), and a pair of inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.
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Affiliation(s)
- Rongrong Yan
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Li Gu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Lu Qu
- Institute of Medicinal Plant Development Yunnan Branch, Chinese Academy of Medical Sciences, Jinghong 666100, China;
| | - Xiaoyu Wang
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Guoxiong Hu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
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Lin N, Liu R, Wang Y, Guo P, Wang Y, Liu Y, Shang F. The complete chloroplast genome of Ulmus mianzhuensis with insights into structural variations, adaptive evolution, and phylogenetic relationships of Ulmus (Ulmaceae). BMC Genomics 2023; 24:366. [PMID: 37386355 PMCID: PMC10308733 DOI: 10.1186/s12864-023-09430-1] [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: 03/23/2023] [Accepted: 06/06/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Ulmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species. RESULTS Our results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 - 88,408 bp, a small single copy (SSC) region of 18,650 - 19,038 bp and an inverted repeat (IR) region of 26,288 - 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections. CONCLUSIONS Features of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.
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Affiliation(s)
- Nan Lin
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Rui Liu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Yakun Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Peng Guo
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Yihan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China
| | - Yanpei Liu
- College of Life Science, Henan Agricultural University, Zhengzhou, China.
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China.
| | - Fude Shang
- College of Life Science, Henan Agricultural University, Zhengzhou, China.
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, China.
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Gan J, Li Y, Tang D, Guo B, Li D, Cao F, Sun C, Yu L, Yan Z. The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus. Genes (Basel) 2023; 14:genes14040929. [PMID: 37107687 PMCID: PMC10138119 DOI: 10.3390/genes14040929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The chloroplast genomes of seven species of the genus Gynostemma were sequenced and annotated, of which the genomes of Gynostemma simplicifolium, Gynostemma guangxiense and Gynostemma laxum were sequenced and annotated for the first time. The chloroplast genomes ranged from 157,419 bp (Gynostemma compressum) to 157,840 bp (G. simplicifolium) in length, including 133 identical genes: 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. Phylogenetic analysis showed that the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum. The highly variable regions of atpH-atpL, rpl32-trnL, and ccsA-ndhD, the repeat unilts of AAG/CTT and ATC/ATG in simple sequence repeats (SSRs) and the length of overlapping regions between rps19 and inverted repeats(IRb) and between ycf1 and small single-copy (SSC) were found to be consistent with the phylogeny. Observations of fruit morphology of the genus Gynostemma revealed that transitional state species have independent morphological characteristics, such as oblate fruit and inferior ovaries. In conclusion, both molecular and morphological results showed consistency with those of phylogenetic analysis.
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Affiliation(s)
- Jiaxia Gan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Ying Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Deying Tang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong 666100, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Doudou Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Feng Cao
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Liying Yu
- Guangxi Botanical Garden of Medicinal Plant, Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Nanning 530023, China
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Ramadan AM, Mohammed T, Al-Ghamdi KM, Alghamdi AJ, Atef A. The first report describes features of the chloroplast genome of Withania frutescens. Saudi J Biol Sci 2023; 30:103600. [PMID: 36874202 PMCID: PMC9975694 DOI: 10.1016/j.sjbs.2023.103600] [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] [Received: 01/04/2023] [Revised: 01/29/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Genomic studies not only help researcher not only to identify genomic features in organisms, but also facilitate understanding of evolutionary relationships. Species in the Withania genus have medicinal benefits, and one of them is Withania frutescens, which is used to treat various diseases. This report investigates the nucleotides and genic features of chloroplast genome of Withania frutescens and trying to clarify the evolutionary relationship with Withania sp and family Solanaceae. We found that the total size of Withania frutescens chloroplast genome was 153.771 kb (the smallest chloroplast genome in genus Withania). A large single-copy region (91.285 kb), a small single-copy region (18.373 kb) form the genomic region, and are distinct from each other by a large inverted repeat (22.056 kb). 137 chloroplast genes are found including 4 rRNAs, 38 tRNAs and 83 protein-coding genes. The Withania frutescens chloroplast genome as well as four closest relatives was compared for features such as structure, nucleotide composition, simple sequence repeats (SSRs) and codon bias. Compared to other Withania species, Withania frutescens has unique characteristics. It has the smallest chloroplast genome of any Withania species, isoleucine is the major amino acid, and tryptophan is the minor, In addition, there are no ycf3 and ycf4 genes, fourth, there are only fifteen replicative genes, while in most other species there are more. Using fast minimum evolution and neighbor joining, we have reconstructed the trees to confirm the relationship with other Solanacaea species. The Withania frutescens chloroplast genome is submitted under accession no. ON153173.
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Affiliation(s)
- Ahmed M Ramadan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
- Plant Molecular Biology Department, Agricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypt
- Corresponding author at: Department of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabia.
| | - Taimyiah Mohammed
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid M Al-Ghamdi
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdullah J Alghamdi
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Atef
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Najla bint Saud Al-Saud Center for Excellence Research in Biotechnology, King Abdulaziz University, Jeddah, Saudi Arabia
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Park HS, Jeon JH, Cho W, Lee Y, Park JY, Kim J, Park YS, Koo HJ, Kang JH, Lee TJ, Kim SH, Kim JB, Kwon HY, Kim SH, Paek NC, Jang G, Suh JY, Yang TJ. High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants. HORTICULTURE RESEARCH 2022; 10:uhac246. [PMID: 36643742 PMCID: PMC9832966 DOI: 10.1093/hr/uhac246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/26/2022] [Indexed: 06/17/2023]
Abstract
Chimeric plants composed of green and albino tissues have great ornamental value. To unveil the functional genes responsible for albino phenotypes in chimeric plants, we inspected the complete plastid genomes (plastomes) in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species, including monocots, dicots, and gymnosperms. In nine chimeric plants, plastomes were identical between green and albino tissues. Meanwhile, another 14 chimeric plants were heteroplasmic, showing a mutation between green and albino tissues. We identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase (rpo) or photosystems which caused albinism in the chimeric plants. Among them, 12 were deleterious mutations in the target genes, in which early termination appeared due to small deletion-mediated frameshift or single nucleotide substitution. Another was single nucleotide substitution in an intron of the ycf3 and the other was a missense mutation in coding region of the rpoC2 gene. We inspected chlorophyll structure, protein functional model of the rpoC2, and expression levels of the related genes in green and albino tissues of Reynoutria japonica. A single amino acid change, histidine-to-proline substitution, in the rpoC2 protein may destabilize the peripheral helix of plastid-encoded RNA polymerase, impairing the biosynthesis of the photosynthesis system in the albino tissue of R. japonica chimera plant.
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Affiliation(s)
| | | | | | | | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jiseok Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun Jo Koo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jung Hwa Kang
- Hantaek Botanical Garden, Yongin, Gyeonggi-do, 17183, Republic of Korea
| | - Taek Joo Lee
- Hantaek Botanical Garden, Yongin, Gyeonggi-do, 17183, Republic of Korea
| | - Sang Hoon Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea
| | - Jin-Baek Kim
- Radiation Breeding Research Team, Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Korea
| | - Hae-Yun Kwon
- Special Forest Resources Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Suk-Hwan Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nam-Chon Paek
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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9
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Park YS, Kang JS, Park JY, Shim H, Yang HO, Kang JH, Yang TJ. Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution. PLoS One 2022; 17:e0275590. [PMID: 36197898 PMCID: PMC9534445 DOI: 10.1371/journal.pone.0275590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.
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Affiliation(s)
- Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyun Ok Yang
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea
| | | | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
- * E-mail:
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10
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Zhang G, Wei F, Chen Z, Wang Y, Jiao S, Yang J, Chen Y, Liu C, Huang Z, Dong L, Chen S. Evidence for saponin diversity-mycobiome links and conservatism of plant-fungi interaction patterns across Holarctic disjunct Panax species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154583. [PMID: 35304141 DOI: 10.1016/j.scitotenv.2022.154583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/25/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Although interplays between plant and coevolved microorganisms are believed to drive landscape formation and ecosystem services, the relationships between the mycobiome and phytochemical evolution and the evolutionary characteristics of plant-mycobiome interaction patterns are still unclear. The present study explored fungal communities from 405 multiniche samples of three Holarctic disjunct Panax species. The overall mycobiomes showed compartment-dominated variations and dynamic universality. Neutral models were fitted for each compartment at the Panax genus (I) and species (II) levels to infer the community assembly mechanism and identify fungal subgroups potentially representing different plant-fungi interaction results, i.e., the potentially selected, opposed, and neutral taxa. Selection contributed more to the endosphere than to external compartments. The nonneutral taxa showed significant phylogenetic clustering. In Model I, the opposed subgroups could best reflect Panax saponin diversities (r = 0.69), and genera with highly positive correlations to specific saponins were identified using machine learning. Although mycobiomes in the three species differed significantly, subgroups in Model II were phylogenetically clustered based on potential interaction type rather than plant species, indicating potentially conservative plant-fungi interactions. In summary, the finding of strong links between invaders and saponin diversity can help explore the underlying mechanisms of saponin biosynthesis evolution from microbial insights, which is important to understanding the formation of the current landscape. The potential conservatism of plant-fungi interaction patterns suggests that the related genetic modules and selection pressures were convergent across Panax species, advancing our understanding of plant interplay with biotic environments.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co, Ltd., Wenshan 663000, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A & F University, Yangling 712100, China.
| | - JiaYing Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yongzhong Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Congsheng Liu
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Zhixin Huang
- Zhangzhou Pianzihuang Pharmaceutical Co., Ltd., Fujian 363099, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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11
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Yan L, Wang H, Huang X, Li Y, Yue Y, Wang Z, Tang S. Chloroplast Genomes of Genus Tilia: Comparative Genomics and Molecular Evolution. Front Genet 2022; 13:925726. [PMID: 35873491 PMCID: PMC9305825 DOI: 10.3389/fgene.2022.925726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022] Open
Abstract
Tilia is a complex genus in the family Malvaceae that has high ecological and economical values. Owing to the lack of sufficient distinguishable morphological and molecular characteristics, interspecific relationships in this genus are not clear. Chloroplast (cp) genomes are small, meanwhile most angiosperms usually undergo matrilineal inheritance. Consequently, they can be used in molecular systematics and phylogenetic analyses. Here, we sequenced and assembled cp genomes from T. endochrysea, T. tomentosa, T. miqueliana, T. americana and T. cordata, and compared them with those of seven previously reported Tilia species. Similar gene contents, gene orders and GC contents existed among the 12 cp genomes, which ranged from 162,564 to 162,855 bp and encoded 113 unique genes. Abundant simple sequence repeats (119–127) and dispersed repeats (97–135) were detected in Tilia cp genomes. In total, 11 hypervariable regions were identified that could be suitable for species identification and phylogenetic studies. A phylogenetic analysis of Malvaceae based on 5 hypervariable genes (matK + ndhF + rpoB + rpoC2+ycf1) revealed that all eight subfamilies were monophyletic groups. Additionally, the genus Tilia was divided into three groups on the basis of all 521 molecular variation loci. The current study provides valuable insights into the genomic evolution of the genus Tilia.
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Affiliation(s)
- Linjun Yan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Huanli Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Xi Huang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Yingchao Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuanhao Yue
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Zhongwei Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
| | - Shijie Tang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Memorial Sun Yat-Sen, Nanjing, China
- *Correspondence: Shijie Tang,
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12
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Dong Z, Zhang R, Shi M, Song Y, Xin Y, Li F, Ma J, Xin P. The complete plastid genome of the endangered shrub Brassaiopsis angustifolia (Araliaceae): Comparative genetic and phylogenetic analysis. PLoS One 2022; 17:e0269819. [PMID: 35771795 PMCID: PMC9246242 DOI: 10.1371/journal.pone.0269819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022] Open
Abstract
Brassaiopsis angustifolia K.M. Feng belongs to the family Araliaceae, and is an endangered shrub species in southwest China. Despite the importance of this species, the plastid genome has not been sequenced and analyzed. In this study, the complete plastid genome of B. angustifolia was sequenced, analyzed, and compared to the eight species in the Araliaceae family. Our study reveals that the complete plastid genome of B. angustifolia is 156,534 bp long, with an overall GC content of 37.9%. The chloroplast genome (cp) encodes 133 genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. All protein-coding genes consisted of 21,582 codons. Among the nine species of Araliaceae, simple sequence repeats (SSRs) and five large repeat sequences were identified with total numbers ranging from 37 to 46 and 66 to 78, respectively. Five highly divergent regions were successfully identified that could be used as potential genetic markers of Brassaiopsis and Asian Palmate group. Phylogenetic analysis of 47 plastomes, representing 19 genera of Araliaceae and two related families, was performed to reconstruct highly supported relationships for the Araliaceae, which highlight four well-supported clades of the Hydrocotyle group, Greater Raukaua group, Aralia-Panax group, and Asian Palmate group. The genus Brassaiopsis can be divided into four groups using internal transcribed spacer (ITS) data. The results indicate that plastome and ITS data can contribute to investigations of the taxonomy, and phylogeny of B. angustifolia. This study provides a theoretical basis for species identification and future biological research on resources of the genus Brassaiopsis.
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Affiliation(s)
- Zhanghong Dong
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Ruli Zhang
- Sympodial Bamboos Technological and Engineering Research Center, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Ming Shi
- Sympodial Bamboos Technological and Engineering Research Center, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, China
| | - Yaxuan Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Feng Li
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Jianzhong Ma
- Yunnan Academy of Forestry and Grassland, Kunming, China
- * E-mail: (JM); (PX)
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
- * E-mail: (JM); (PX)
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13
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Wang Y, Zhang H, Ri HC, An Z, Wang X, Zhou JN, Zheng D, Wu H, Wang P, Yang J, Liu DK, Zhang D, Tsai WC, Xue Z, Xu Z, Zhang P, Liu ZJ, Shen H, Li Y. Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. Nat Commun 2022; 13:2224. [PMID: 35468919 PMCID: PMC9038795 DOI: 10.1038/s41467-022-29908-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
Araliaceae species produce various classes of triterpene and triterpenoid saponins, such as the oleanane-type triterpenoids in Aralia species and dammarane-type saponins in Panax, valued for their medicinal properties. The lack of genome sequences of Panax relatives has hindered mechanistic insight into the divergence of triterpene saponins in Araliaceae. Here, we report a chromosome-level genome of Aralia elata with a total length of 1.05 Gb. The loss of 12 exons in the dammarenediol synthase (DDS)-encoding gene in A. elata after divergence from Panax might have caused the lack of dammarane-type saponin production, and a complementation assay shows that overexpression of the PgDDS gene from Panax ginseng in callus of A. elata recovers the accumulation of dammarane-type saponins. Tandem duplication events of triterpene biosynthetic genes are common in the A. elata genome, especially for AeCYP72As, AeCSLMs, and AeUGT73s, which function as tailoring enzymes of oleanane-type saponins and aralosides. More than 13 aralosides are de novo synthesized in Saccharomyces cerevisiae by overexpression of these genes in combination. This study sheds light on the diversity of saponins biosynthetic pathway in Araliaceae and will facilitate heterologous bioproduction of aralosides.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - He Zhang
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China
| | - Hyok Chol Ri
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Biochemistry Institute, University of Science, Pyongyang, 999093, Democratic People's Republic of Korea
| | - Zeyu An
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Xin Wang
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jia-Nan Zhou
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Dongran Zheng
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Hao Wu
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Pengchao Wang
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Jianfei Yang
- School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Ding-Kun Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan, China
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan, China
| | - Zheyong Xue
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Zhichao Xu
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, 150040, China
| | - Peng Zhang
- School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Hailong Shen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
- School of Forestry, Northeast Forestry University, Harbin, 150040, China.
| | - Yuhua Li
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China.
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14
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El-Hagrassi AM, Osman AF, El-Naggar ME, Mowaad NA, Khalil S, Hamed MA. Phytochemical constituents and protective efficacy of Schefflera arboricola L. leaves extract against thioacetamide-induced hepatic encephalopathy in rats. Biomarkers 2022; 27:375-394. [PMID: 35234557 DOI: 10.1080/1354750x.2022.2048892] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Context: Hepatic encephalopathy (HE) is a severe neuropsychiatric syndrome resulting from liver failure. Objective: To evaluate the protective effect of Schefflera arboricola L. leaves methanol extract against thioacetamide (TAA) induced HE in rats. Materials and methods: GC/MS, LC-ESI-MS and the total phenolic and flavonoid contents were determined. The methanol extract was orally administrated (100 and 200 mg/kg) for 21 days. TAA (200 mg/kg) was given intraperitoneally on day 19 and continued for three days. The evaluation was done by measuring alanine aminotransferases (ALT), alkaline phosphatase (ALP), ammonia, reduced glutathione (GSH), malondialdehyde (MDA), nitric oxide (NO) alpha tumor necrotic factor (TNFα), toll like receptor (TLR4), interleukin 1 beta (IL-1β), interlukin 6 (IL-6), cyclooxygenase 2(COX2), B cell lymphoma (BCL2), alpha smooth muscle actin (α-SMA) and cluster of differentiation 163 (CD163). The histological features of liver and brain were conducted. Results: Forty five compounds were identified from the n-hexane fraction, while twenty nine phenolic compounds were determined from the methanol extract. Pretreatment with the plant extract returned most of the measurements under investigation to nearly normal. Conclusion: Due to its richness with bioactive compounds, Schefflera arboricola L. leaves extract succeeded to exert anti-fibrotic, anti-inflammatory and antioxidants properties in TAA-induced HE in rats with more efficacy to its high protective dose.
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Affiliation(s)
- Ali M El-Hagrassi
- Phytochemistry and Plant Systematics Department, National Research Centre, Dokki, Giza, Egypt
| | - Abeer F Osman
- Chemistry of Natural Compounds Department, National Research Centre, Dokki, Giza, Egypt
| | - Mostafa E El-Naggar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Sadat City, Menoufia, Egypt
| | - Noha A Mowaad
- Department of Narcotics, Ergogenic Acids and Poisons, National Research Centre, Dokki, Giza, Egypt
| | - Sahar Khalil
- Department of Histology & Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Manal A Hamed
- Department of Therapeutic Chemistry, National Research Centre, Dokki, Giza, Egypt
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15
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Ruang-Areerate P, Yoocha T, Kongkachana W, Phetchawang P, Maknual C, Meepol W, Jiumjamrassil D, Pootakham W, Tangphatsornruang S. Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests. BIOLOGY 2022; 11:383. [PMID: 35336757 PMCID: PMC8945693 DOI: 10.3390/biology11030383] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/19/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023]
Abstract
Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.
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Affiliation(s)
- Panthita Ruang-Areerate
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Phakamas Phetchawang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, Thailand
| | - Wijarn Meepol
- Department of Marine and Coastal Resources, Ranong Mangrove Forest Research Center, Tambon Ngao, Muang District, Ranong 85000, Thailand
| | - Darunee Jiumjamrassil
- Marine and Coastal Resources Office 5, 199/6 Khanom, Khanom, Nakhon Si Thammarat 80210, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
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16
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Gu L, Hou Y, Wang G, Liu Q, Ding W, Weng Q. Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae. PLoS One 2022; 17:e0262813. [PMID: 35077482 PMCID: PMC8789150 DOI: 10.1371/journal.pone.0262813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/05/2022] [Indexed: 11/19/2022] Open
Abstract
Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.
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Affiliation(s)
- Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunyan Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Guangyi Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Ding
- Colleage of plant protection, Southwest University, Chongqing, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
- * E-mail:
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17
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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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18
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Chu LL, Bae H. Bacterial endophytes from ginseng and their biotechnological application. J Ginseng Res 2022; 46:1-10. [PMID: 35035239 PMCID: PMC8753428 DOI: 10.1016/j.jgr.2021.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 12/19/2022] Open
Abstract
Ginseng has been well-known as a medicinal plant for thousands of years. Bacterial endophytes ubiquitously colonize the inside tissues of ginseng without any disease symptoms. The identification of bacterial endophytes is conducted through either the internal transcribed spacer region combined with ribosomal sequences or metagenomics. Bacterial endophyte communities differ in their diversity and composition profile, depending on the geographical location, cultivation condition, and tissue, age, and species of ginseng. Bacterial endophytes have a significant effect on the growth of ginseng through indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and nitrogen fixation. Moreover, bacterial endophytes can protect ginseng by acting as biocontrol agents. Interestingly, bacterial endophytes isolated from Panax species have the potential to produce ginsenosides and bioactive metabolites, which can be used in the production of food and medicine. The ability of bacterial endophytes to transform major ginsenosides into minor ginsenosides using β-glucosidase is gaining increasing attention as a promising biotechnology. Recently, metabolic engineering has accelerated the possibilities for potential applications of bacterial endophytes in producing beneficial secondary metabolites.
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Affiliation(s)
- Luan Luong Chu
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi, Viet Nam
- Bioresource Research Center, Phenikaa University, Hanoi, Viet Nam
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
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19
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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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20
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Song JH, Kim H, Jeong M, Kong MJ, Choi HK, Jun W, Kim Y, Choi KC. In Vivo Evaluation of Dendropanax morbifera Leaf Extract for Anti-Obesity and Cholesterol-Lowering Activity in Mice. Nutrients 2021; 13:1424. [PMID: 33922621 PMCID: PMC8146056 DOI: 10.3390/nu13051424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 12/31/2022] Open
Abstract
Metabolic syndrome is a worldwide health problem, and obesity is closely related to type 2 diabetes, cardiovascular disease, hypertension, and cancer. According to WHO in 2018, the prevalence of obesity in 2016 tripled compared to 1975. D. morbifera reduces bad cholesterol and triglycerides levels in the blood and provides various antioxidant nutrients and germicidal sub-stances, as well as selenium, which helps to remove active oxygen. Moreover, D. morbifera is useful for treating cardiovascular diseases, hypertension, hyperlipidemia, and diabetes. Therefore, we study in vivo efficacy of D. morbifera to investigate the prevention effect of obesity and cholesterol. The weight and body fat were effectively reduced by D. morbifera water (DLW) extract administration to high-fat diet-fed C57BL/6 mice compared to those of control mice. The group treated with DLW 500 mg∙kg-1∙d-1 had significantly lower body weights compared to the control group. In addition, High-density lipoprotein (HDL) cholesterol increased in the group treated with DLW 500 mg∙kg-1∙d-1. The effect of DLW on the serum lipid profile could be helpful to prevent obesity. DLW suppresses lipid formation in adipocytes and decreases body fat. In conclusion, DLW can be applied to develop anti-obesity functional foods and other products to reduce body fat.
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Affiliation(s)
- Ji-Hye Song
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (J.-H.S.); (H.K.); (M.J.); (M.J.K.)
| | - Hyunhee Kim
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (J.-H.S.); (H.K.); (M.J.); (M.J.K.)
| | - Minseok Jeong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (J.-H.S.); (H.K.); (M.J.); (M.J.K.)
| | - Min Jung Kong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (J.-H.S.); (H.K.); (M.J.); (M.J.K.)
| | | | - Woojin Jun
- Division of Food and Nutrition, Chonnam National University, Gwangju 61186, Korea;
| | - Yongjae Kim
- SDC Research Institute, Jeollanam-do 57309, Korea;
| | - Kyung-Chul Choi
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea; (J.-H.S.); (H.K.); (M.J.); (M.J.K.)
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21
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Park YS, Park JY, Kang JH, Lee WH, Yang TJ. Diversity and authentication of Rubus accessions revealed by complete plastid genome and rDNA sequences. Mitochondrial DNA B Resour 2021; 6:1454-1459. [PMID: 33969195 PMCID: PMC8079122 DOI: 10.1080/23802359.2021.1911712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/26/2021] [Indexed: 11/06/2022] Open
Abstract
Complete plastid genome (plastome) and ribosomal DNA (rDNA) sequences of three Rubus accessions (two Rubus longisepalus and one R. hirsutus) were newly assembled using Illumina whole-genome sequences. Rubus longisepalus Nakai and R. longisepalus var. tozawai, described as different varieties, have identical plastomes and rDNA sequences. The plastomes are 155,957 bp and 156,005 bp and the 45S rDNA transcription unit sizes are 5809 bp and 5811 bp in R. longisepalus and R. hirsutus, respectively. The 5S rDNA transcription unit is an identical 121 bp in three Rubus accessions. We developed three DNA markers to authenticate R. longisepalus and R. hirsutus based on plastome diversity. Phylogenomic analysis revealed that the Rubus species classified as two clades and R. longisepalus, R. hirsutus, and R. chingii are the most closely related species in clade 1.
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Affiliation(s)
- Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | | | | | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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22
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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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23
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Park HS, Lee WK, Lee SC, Lee HO, Joh HJ, Park JY, Kim S, Song K, Yang TJ. Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F 1 hybrid combinations. Sci Rep 2021; 11:2506. [PMID: 33510273 PMCID: PMC7843999 DOI: 10.1038/s41598-021-81988-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 01/13/2021] [Indexed: 11/19/2022] Open
Abstract
Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.
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Affiliation(s)
- Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Won Kyung Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sang-Choon Lee
- Phyzen Genomics Institute, Seongnam, Gyeonggi-do, 13558, Republic of Korea
| | - Hyun Oh Lee
- Phyzen Genomics Institute, Seongnam, Gyeonggi-do, 13558, Republic of Korea
| | - Ho Jun Joh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and 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 and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kihwan Song
- Department of Bioresources Engineering, College of Life Sciences, Sejong University, Seoul, 05006, Republic of Korea.
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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24
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Lee YS, Kim J, Woo S, Park JY, Park HS, Shim H, Choi HI, Kang JH, Lee TJ, Sung SH, Yang TJ, Kang KB. Assessing the genetic and chemical diversity of Taraxacum species in the Korean Peninsula. PHYTOCHEMISTRY 2021; 181:112576. [PMID: 33166748 DOI: 10.1016/j.phytochem.2020.112576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/19/2020] [Accepted: 10/24/2020] [Indexed: 05/12/2023]
Abstract
The genetic relationship between Taraxacum species, also known as the dandelion, is complicated because of asexual and mixed sexual apomictic reproduction. The usage of Taraxacum species in traditional medicines make their specialized metabolism important, but interspecific chemical difference has rarely been reported for the genus. In this study, we assembled the chloroplast genome and 45S rDNA of six Taraxacum species that occur in Korea (T. campylodes, T. coreanum, T. erythrospermum, T. mongolicum, T. platycarpum, and T. ussuriense), and performed a comparative analysis, which revealed their phylogenetic relationships and possible natural hybridity. We also performed a liquid chromatography-mass spectrometry-based phytochemical analysis to reveal interspecific chemical diversity. The comparative metabolomics analysis revealed that Taraxacum species could be separated into three chemotypes according to their major defensive specialized metabolites, which were the sesquiterpene lactones, the phenolic inositols, and chlorogenic acid derivatives. The CP DNA- and 45S rDNA-based phylogenetic trees showed a tangled relationship, which supports the notion of ongoing hybridization of wild Taraxacum species. The untargeted LC-MS analysis revealed that each Taraxacum plant exhibits species-specific defensive specialized metabolism. Moreover, 45S rDNA-based phylogenetic tree correlated with the hierarchical cluster relied on metabolite compositions. Given the coincidence between these analyses, we represented that 45S rDNA could well reflect overall nuclear genome variation in Taraxacum species.
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Affiliation(s)
- Yun Sun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinkyung Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sunmin Woo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jung Hwa Kang
- Hantaek Botanical Garden, Yongin, 17183, Republic of Korea
| | - Taek Joo Lee
- Hantaek Botanical Garden, Yongin, 17183, Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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25
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Balakrishnan R, Cho DY, Su-Kim I, Choi DK. Dendropanax Morbiferus and Other Species from the Genus Dendropanax: Therapeutic Potential of Its Traditional Uses, Phytochemistry, and Pharmacology. Antioxidants (Basel) 2020; 9:antiox9100962. [PMID: 33049991 PMCID: PMC7601828 DOI: 10.3390/antiox9100962] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
The Dendropanax genus is a kind of flowering plant in the family of Araliaceae that encompasses approximately 91 to 95 species. Several Dendropanax species are used as traditional medicinal plants, extensively used Korea and South America and other parts of the world. Almost every part of the plant, including the leaves, bark, roots, and stems, can be used as traditional medicine for the prevention and management of a broad spectrum of health disorders. This paper sought to summarizes the ethnopharmacological benefits, biological activities, and phytochemical investigations of plants from the genus Dendropanax, and perhaps to subsequently elucidate potential new perspectives for future pharmacological research to consider. Modern scientific literature suggests that plants of the Dendropanax genus, together with active compounds isolated from it, possess a wide range of therapeutic and pharmacological applications, including antifungal, anti-complement, antioxidant, antibacterial, insect antifeedant, cytotoxic, anti-inflammatory, neuroprotective, anti-diabetic, anti-cancer, and anti-hypouricemic properties. The botanical descriptions of approximately six to 10 species are provided by different scientific web sources. However, only six species, namely, D. morbiferus, D. gonatopodus, D. dentiger, D. capillaris, D. chevalieri, and D. arboreus, were included in the present investigation to undergo phytochemical evaluation, due to the unavailability of data for the remaining species. Among these plant species, a high concentration of variable bioactive ingredients was identified. In particular, D. morbifera is a traditional medicinal plant used for the multiple treatment purposes and management of several human diseases or health conditions. Previous experimental evidence supports that the D. morbifera species could be used to treat various inflammatory disorders, diarrhea, diabetes, cancer, and some microbial infections. It has recently been reported, by our group and other researchers, that D. morbifera possesses a neuroprotective and memory-enhancing agent. A total of 259 compounds have been identified among six species, with 78 sourced from five of these species reported to be bioactive. However, there is no up-to-date information concerning the D. morbifera, its different biological properties, or its prospective benefits in the enhancement of human health. In the present study, we set out to conduct a comprehensive analysis of the botany, traditional medicinal history, and medicinal resources of species of the Dendropanax genus. In addition, we explore several phytochemical constituents identified in different species of the Dendropanax genus and their biological properties. Finally, we offer comprehensive analysis findings of the phytochemistry, medicinal uses, pharmacological actions, and a toxicity and safety evaluation of the D. morbifera species and its main bioactive ingredients for future consideration.
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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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27
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Jia G, Wang H, Yu P, Li P. The complete chloroplast genome of the Lonicera maackii (Caprifoliaceae), an ornamental plant. Mitochondrial DNA B Resour 2020; 5:560-561. [PMID: 33366646 PMCID: PMC7748521 DOI: 10.1080/23802359.2019.1710288] [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] [Indexed: 10/31/2022] Open
Abstract
Lonicera maackii, is scattered in west and northeast China as well as adjacent Korea, Japan and the Soviet union. Here, we assembled and characterized the complete chloroplast (cp) genome of L. maackii using Illumina sequencing data for the first time. The complete cp genome was 155,337 bp in length, consisting of a pair of inverted repeats of 23,718 bp, a large single-copy region of 89,221 bp and a small single-copy region of 18,680 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 25 complete cp genome sequences indicated that L. maackii is closely related to Lonicera sachalinensis and Lonicera insularis.
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Affiliation(s)
- Guolun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi’an, People’s Republic of China
| | - Huan Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi’an, People’s Republic of China
| | - Pei Yu
- Xi’an International University, Xi’an, People’s Republic of China
| | - Peng Li
- Xi’an International University, Xi’an, People’s Republic of China
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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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Li YH, Li HR, Yang CT, Tian K, Yang C, Sun JX, Wang W, Huang XZ. Three new diterpenoids from Aralia dumetorum. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2019; 21:308-315. [PMID: 30829053 DOI: 10.1080/10286020.2019.1567503] [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: 09/29/2018] [Revised: 01/05/2019] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
Three new diterpenoids, dumetoranes A (1) and B (2), melanocane B (3), together with four known ones including melanocane A (4), ent-15S,16-dihydroxypimar-8(14)-en-19-oic acid (5), ent-pimara-8(14),15-diene-19-oic acid (6), and ent-pimara-8(14),15-diene-19-ol (7) were obtained from the ethanol extract of the roots of Aralia dumetorum. Their structure elucidation was achieved by the methods of spectroscopic HRMS, IR, NMR, and by comparison with literature. The cytotoxicities of compounds 1-3 and 5 were assayed by in vitro MTT methods.
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Affiliation(s)
- Yan-Hong Li
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Hong-Rui Li
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Chun-Tao Yang
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Kai Tian
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Cui Yang
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Jing-Xian Sun
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Wei Wang
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
| | - Xiang-Zhong Huang
- a Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy , Yunnan Minzu University , Kunming 650504 , China
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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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31
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Yu P, Yang X, Zhou W, Yang W, Zhou L, Liu X, Wan Q, Zhang J. Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae). Genetica 2019; 147:165-176. [PMID: 30887216 DOI: 10.1007/s10709-019-00059-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.
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Affiliation(s)
- Peng Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Weishang Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Wentao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xuan Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Quan Wan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China. .,Mingguang Modern Agricultural Science and Technology Cooperation Promotion Service Center, Mingguang, 239400, China.
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32
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Jeon JH, Park HS, Park JY, Kang TS, Kwon K, Kim YB, Han JW, Kim SH, Sung SH, Yang TJ. Two complete chloroplast genome sequences and intra-species diversity for Rehmannia glutinosa (Orobanchaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1545529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jae-Hyeon Jeon
- 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
| | - Hyun-Seung 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, Republic of 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, Republic of Korea
| | - Tae Sun Kang
- New Hazardous Substances Team, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Ohsong, Republic of Korea
| | - Kisung Kwon
- New Hazardous Substances Team, Food Safety Evaluation Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Ohsong, Republic of Korea
| | - Yeon Bok Kim
- Department of Medicinal & Industrial Crops, Korea National College of Agriculture and Fisheries, Jeonju, Republic of Korea
| | - Jong-Won Han
- Herbal Crop Research Division, Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Eumseong, Republic of Korea
| | - Seung Hyun Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 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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33
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Kang SJ, Park JY, Jang W, Koo HJ, Lee DY, Kim MS, Han SI, Sung SH, Yang TJ. The complete chloroplast genome sequence of an invasive plant Lonicera Maackii (Caprifoliaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1524722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Shin-Jae Kang
- 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
| | - 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, Republic of Korea
| | - 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
| | - Hyun Jo Koo
- 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
| | - Dong Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, Republic of Korea
| | - Mi Song Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, Republic of Korea
| | - Sang Il Han
- Medicinal Plant Garden, College of Pharmacy, Seoul National University, Koyang, Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Science, Seoul National University, Seoul, 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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Kang KB, Kang SJ, Kim MS, Lee DY, Han SI, Kim TB, Park JY, Kim J, Yang TJ, Sung SH. Chemical and genomic diversity of six Lonicera species occurring in Korea. PHYTOCHEMISTRY 2018; 155:126-135. [PMID: 30121427 DOI: 10.1016/j.phytochem.2018.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 07/15/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Lonicera spp. (Caprifoliaceae) are important not only as a common medicinal herb in East Asia but also as one of the most problematic invasive species in North America. In the present study, we performed a systemic analysis of genomic and chemical diversity among six Lonicera species occurring in Korea, L. japonica, L. maackii, L. insularis, L. sachalinensis, L. praeflorens, and L. vesicaria, using chloroplast DNA whole genome shotgun (WGS) sequencing and LC-MS analyses. The phylogenetic and phylochemical relationships did not coincide with each other, but partial consistency could be found among them. InDel-based cDNA marker for authentication was developed based on the genome sequences. Flavonoids, iridoids, and organic acids were identified in the LC-MS analyses, and their inter-species distribution and localization were also revealed.
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Affiliation(s)
- Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Shin-Jae Kang
- 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, 08826, Republic of Korea
| | - Mi Song Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Il Han
- Medicinal Plant Garden, College of Pharmacy, Seoul National University, Koyang, 12045, Republic of Korea
| | - Tae Bum Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jee Young 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, 08826, Republic of Korea
| | - Jinwoong Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Medicinal Plant Garden, College of Pharmacy, Seoul National University, Koyang, 12045, 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, 08826, Republic of Korea.
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
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35
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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: 101] [Impact Index Per Article: 16.8] [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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Jayakodi M, Choi BS, Lee SC, Kim NH, Park JY, Jang W, Lakshmanan M, Mohan SVG, Lee DY, Yang TJ. Ginseng Genome Database: an open-access platform for genomics of Panax ginseng. BMC PLANT BIOLOGY 2018; 18:62. [PMID: 29649979 PMCID: PMC5898050 DOI: 10.1186/s12870-018-1282-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. DESCRIPTION The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. CONCLUSION This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.
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Affiliation(s)
- Murukarthick Jayakodi
- 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
| | - Beom-Soon Choi
- Phyzen Genome Institute, Seongnam-si, Gyeonggi-do 13558 Republic of Korea
| | - Sang-Choon Lee
- 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
| | - Nam-Hoon Kim
- 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
| | - Jee Young Park
- 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
| | - Woojong Jang
- 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
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute; Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668 Singapore
| | - Shobhana V. G. Mohan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Argricultural University, Coimbatore - 03, India
| | - Dong-Yup Lee
- Bioprocessing Technology Institute; Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, Singapore, 138668 Singapore
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 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
- Crop Biotechnology Institute, Green Bio Science and Technology, Seoul National University, Pyeongchang, 232-916 Republic of Korea
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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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Lee J, Waminal NE, Choi HI, Perumal S, Lee SC, Nguyen VB, Jang W, Kim NH, Gao LZ, Yang TJ. Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax. Sci Rep 2017; 7:9045. [PMID: 28831052 PMCID: PMC5567358 DOI: 10.1038/s41598-017-08194-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/05/2017] [Indexed: 01/08/2023] Open
Abstract
Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8-4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39-52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23-35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.
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Affiliation(s)
- Junki 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, 08826, 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, 08826, Republic of Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sampath Perumal
- 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, Republic of Korea
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - 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, 08826, 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, 08826, Republic of Korea
| | - 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, 08826, Republic of Korea
| | - Nam-Hoon 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, 08826, Republic of Korea
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - 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, Republic of Korea.
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
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Nguyen VB, Park HS, Lee SC, Lee J, Park JY, Yang TJ. Authentication Markers for Five Major Panax Species Developed via Comparative Analysis of Complete Chloroplast Genome Sequences. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6298-6306. [PMID: 28530408 DOI: 10.1021/acs.jafc.7b00925] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ginseng represents a set of high-value medicinal plants of different species: Panax ginseng (Asian ginseng), Panax quinquefolius (American ginseng), Panax notoginseng (Chinese ginseng), Panax japonicus (Bamboo ginseng), and Panax vietnamensis (Vietnamese ginseng). Each species is pharmacologically and economically important, with differences in efficacy and price. Accordingly, an authentication system is needed to combat economically motivated adulteration of Panax products. We conducted comparative analysis of the chloroplast genome sequences of these five species, identifying 34-124 InDels and 141-560 SNPs. Fourteen InDel markers were developed to authenticate the Panax species. Among these, eight were species-unique markers that successfully differentiated one species from the others. We generated at least one species-unique marker for each of the five species, and any of the species can be authenticated by selection among these markers. The markers are reliable, easily detectable, and valuable for applications in the ginseng industry as well as in related research.
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Affiliation(s)
- 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
| | - Hyun-Seung 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
| | - Junki 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
| | - 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
| | - 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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