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Nguyen DH, Tran QH, Le LT, Nguyen HHT, Tran HT, Do TP, Ho AN, Tran QH, Thu HTN, Bui VN, Chu HH, Pham NB. Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12.1C. Microb Biotechnol 2024; 17:e70007. [PMID: 39235571 PMCID: PMC11376216 DOI: 10.1111/1751-7915.70007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/15/2024] [Indexed: 09/06/2024] Open
Abstract
Previous studies have reported the functional role, biochemical features and synthesis pathway of podophyllotoxin (PTOX) in plants. In this study, we employed combined morphological and molecular techniques to identify an endophytic fungus and extract PTOX derivatives. Based on the analysis of ITS sequences and the phylogenetic tree, the isolate was classified as Penicillium herquei HGN12.1C, with a sequence identity of 98.58%. Morphologically, the HGN12.1C strain exhibits white colonies, short-branched mycelia and densely packed hyphae. Using PacBio sequencing at an average read depth of 195×, we obtained a high-quality genome for the HGN12.1C strain, which is 34.9 Mb in size, containing eight chromosomes, one mitochondrial genome and a GC content of 46.5%. Genome analysis revealed 10 genes potentially involved in PTOX biosynthesis. These genes include VdtD, Pinoresinollariciresinol reductase (PLR), Secoisolariciresinol dehydrogenase (SDH), CYP719A23, CYP71BE54, O-methyltransferase 1 (OMT1), O-methyltransferase 3 (OMT3), 2-ODD, CYP71CU and CYP82D61. Notably, the VdtD gene in fungi shares functional similarities with the DIR gene found in plants. Additionally, we identified peltatin, a PTOX derivative, in the HGN12.1C extract. Docking analysis suggests a potential role for the 2-ODD enzyme in converting yatein to deoxypodophyllotoxin. These findings offer invaluable insights into the synthesis mechanism of PTOX in fungi, shedding light on the relationship between host plants and endophytes.
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Affiliation(s)
- Duong Huy Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Quang Ho Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), VAST, Hanoi, Vietnam
| | - Lam Tung Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Ha Hong Thi Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Hoa Thi Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), VAST, Hanoi, Vietnam
| | - Thuy Phuong Do
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Anh Ngoc Ho
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), VAST, Hanoi, Vietnam
| | - Quang Hong Tran
- Institute of Marine Biochemistry (IMBC), VAST, Hanoi, Vietnam
| | - Hien Thi Nguyen Thu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Van Ngoc Bui
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), VAST, Hanoi, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), VAST, Hanoi, Vietnam
| | - Ngoc Bich Pham
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), VAST, Hanoi, Vietnam
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Zhu Z, Chen D, Sun M, Xiao M, Huang P, Ren D, Yang Y, Zhang Z, Zhao Q, Li R. Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae). BMC Genomics 2024; 25:421. [PMID: 38684979 PMCID: PMC11059704 DOI: 10.1186/s12864-024-10306-1] [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: 01/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum. RESULTS The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters. CONCLUSION These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.
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Affiliation(s)
- Ziwei Zhu
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- Institute for Advanced Study, Chengdu University, 610106, Chengdu, China
| | - Daihan Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Min Sun
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- Institute for Advanced Study, Chengdu University, 610106, Chengdu, China
| | - Maotao Xiao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Peng Huang
- Tibet Rhodiola Pharmaceutical Holding Company, 850000, Lhasa, China
| | - Dongsheng Ren
- Tibet Rhodiola Pharmaceutical Holding Company, 850000, Lhasa, China
| | - Yixi Yang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Zhen Zhang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Qi Zhao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China.
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China.
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China.
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China.
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Fu H, Guo C, Peng J, Shao F, Sheng S, Wang S. Transcriptomic Insights and Cytochrome P450 Gene Analysis in Kadsura coccinea for Lignan Biosynthesis. Genes (Basel) 2024; 15:270. [PMID: 38540329 PMCID: PMC10969973 DOI: 10.3390/genes15030270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 06/15/2024] Open
Abstract
Kadsura coccinea is a medicinal plant from the Schisandraceae family that is native to China and has great pharmacological potential due to its lignans. However, there are significant knowledge gaps regarding the genetic and molecular mechanisms of lignans. We used transcriptome sequencing technology to analyze root, stem, and leaf samples, focusing on the identification and phylogenetic analysis of Cytochrome P450 (CYP) genes. High-quality data containing 158,385 transcripts and 68,978 unigenes were obtained. In addition, 36,293 unigenes in at least one database, and 23,335 across five databases (Nr, KEGG, KOG, TrEMBL, and SwissProt) were successfully annotated. The KEGG pathway classification and annotation of these unigenes identified 10,825 categorized into major metabolic pathways, notably phenylpropanoid biosynthesis, which is essential for lignan synthesis. A key focus was the identification and phylogenetic analysis of 233 Cytochrome P450 (CYP) genes, revealing their distribution across 38 families in eight clans, with roots showing specific CYP gene expression patterns indicative of their role in lignan biosynthesis. Sequence alignment identified 22 homologous single genes of these CYPs, with 6 homologous genes of CYP719As and 1 of CYP81Qs highly expressed in roots. Our study significantly advances the understanding of the biosynthesis of dibenzocyclooctadiene lignans, offering valuable insights for future pharmacological research and development.
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Affiliation(s)
- Hanyu Fu
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
| | - Chuan Guo
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
| | - Jiqing Peng
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
| | - Fengxia Shao
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
| | - Song Sheng
- Yuelushan Laboratory, Qiushi Building, Hunan Agricultural University, Furong District, Changsha 410128, China
| | - Sen Wang
- College of Forestry, Central South University of Forestry & Technology, 498 South Shaoshan Road, Changsha 410004, China; (H.F.); (C.G.); (J.P.); (F.S.)
- The Belt and Road International Union Research Center for Tropical Arid Non-Wood Forest in Hunan Province, 498 South Shaoshan Road, Changsha 410004, China
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Lee HJ, Lee Y, Lee SC, Kim CK, Kang JN, Kwon SJ, Kang SH. Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica. FRONTIERS IN PLANT SCIENCE 2023; 14:1183406. [PMID: 37469771 PMCID: PMC10352487 DOI: 10.3389/fpls.2023.1183406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023]
Abstract
The family Schisandraceae is a basal angiosperm plant group distributed in East and Southeast Asia and includes many medicinal plant species such as Schisandra chinensis. In this study, mitochondrial genomes (mitogenomes) of two species, Schisandra repanda and Kadsura japonica, in the family were characterized through de novo assembly using sequencing data obtained with Oxford Nanopore and Illumina sequencing technologies. The mitogenomes of S. repanda were assembled into one circular contig (571,107 bp) and four linear contigs (10,898-607,430 bp), with a total of 60 genes: 38 protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The mitogenomes of K. japonica were assembled into five circular contigs (211,474-973,503 bp) and three linear contigs (8,010-72,712 bp), with a total of 66 genes: 44 PCGs, 19 tRNA genes, and 3 rRNA genes. The mitogenomes of the two species had complex structural features with high repeat numbers and chloroplast-derived sequences, as observed in other plant mitogenomes. Phylogenetic analysis based on PCGs revealed the taxonomical relationships of S. repanda and K. japonica with other species from Schisandraceae. Finally, molecular markers were developed to distinguish between S. repanda, K. japonica, and S. chinensis on the basis of InDel polymorphisms present in the mitogenomes. The mitogenomes of S. repanda and K. japonica will be valuable resources for molecular and taxonomic studies of plant species that belong to the family Schisandraceae.
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Affiliation(s)
- Hyo Ju Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea
| | | | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea
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Stimulation of Lignan Production in Schisandra rubriflora In Vitro Cultures by Elicitation. Molecules 2022; 27:molecules27196681. [PMID: 36235218 PMCID: PMC9572178 DOI: 10.3390/molecules27196681] [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: 08/22/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022] Open
Abstract
The study investigated the effect of elicitation with: chitosan (CH) (200 mg/L), yeast extract (YeE) (3000 mg/L), ethephon (ETH) (25 µM/L), and methyl jasmonate (MeJA) (50 µM/L), on lignan accumulation in agitated and bioreactor (Plantform temporary immersion systems) microshoot cultures of female (F) and male (M) Schisandra rubriflora Rehd. et Wils. (Schisandraceae) lines. The elicitors were supplemented on the 10th day of culture. Biomasses were collected at 24 h and 48 h, and 4, 6, and 8 days after the addition of each elicitor. The 24 compounds from the dibenzocyclooctadiene, aryltetralin, dibenzylbutane, and tetrahydrofuran lignans and neolignans were determined qualitatively and quantitatively in biomass extracts using the UHPLC–MS/MS method. The highest total contents [mg/100 g DW] of lignans were: for CH-95.00 (F, day 6) and 323.30 (M, 48 h); for YeE 104.30 (F, day 8) and 353.17 (M, day 4); for ETH 124.50 (F, 48 h) and 334.90 (M, day 4); and for MeJA 89.70 (F, 48 h) and 368.50 (M, 24 h). In the biomass extracts of M cultures grown in bioreactors, the highest total lignan content was obtained after MeJA elicitation (153.20 mg/100 g DW). The maximum total lignan contents in the biomass extracts from agitated and bioreactor cultures were 3.29 and 1.13 times higher, respectively, than in the extracts from the non-elicited cultures. The poor understanding of the chemical composition and the lack of studies in the field of plant biotechnology of S. rubriflora emphasize the innovativeness of the research.
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Lu D, Wu Y, Pan Q, Zhang Y, Qi Y, Bao W. Identification of key genes controlling L-ascorbic acid during Jujube ( Ziziphus jujuba Mill.) fruit development by integrating transcriptome and metabolome analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:950103. [PMID: 35991405 PMCID: PMC9386341 DOI: 10.3389/fpls.2022.950103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Chinese jujube (Ziziphus jujuba) is a vital economic tree native to China. Jujube fruit with abundant L-Ascorbic Acid (AsA) is an ideal material for studying the mechanism of AsA biosynthesis and metabolism. However, the key transcription factors regulating AsA anabolism in jujube have not been reported. Here, we used jujube variety "Mazao" as the experimental material, conducted an integrative analysis of transcriptome and metabolome to investigate changes in differential genes and metabolites, and find the key genes regulating AsA during jujube fruit growth. The results showed that AsA was mostly synthesized in the young stage and enlargement stage, ZjMDHAR gene takes an important part in the AsA recycling. Three gene networks/modules were highly correlated with AsA, among them, three genes were identified as candidates controlling AsA, including ZjERF17 (LOC107404975), ZjbZIP9 (LOC107406320), and ZjGBF4 (LOC107421670). These results provide new directions and insights for further study on the regulation mechanism of AsA in jujube.
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Hong CP, Kim CK, Lee DJ, Jeong HJ, Lee Y, Park SG, Kim HJ, Kang JN, Ryu H, Kwon SJ, Kang SH. Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis. BMC Genomics 2022; 23:17. [PMID: 34996357 PMCID: PMC8742460 DOI: 10.1186/s12864-021-08253-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/14/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Schisandra chinensis, an ancient member of the most basal angiosperm lineage which is known as the ANITA, is a fruit-bearing vine with the pharmacological effects of a multidrug system, such as antioxidant, anti-inflammatory, cardioprotective, neuroprotective, anti-osteoporosis effects. Its major bioactive compound is represented by lignans such as schisandrin. Molecular characterization of lignan biosynthesis in S. chinensis is of great importance for improving the production of this class of active compound. However, the biosynthetic mechanism of schisandrin remains largely unknown. RESULTS To understand the potential key catalytic steps and their regulation of schisandrin biosynthesis, we generated genome-wide transcriptome data from three different tissues of S. chinensis cultivar Cheongsoon, including leaf, root, and fruit, via long- and short-read sequencing technologies. A total of 132,856 assembled transcripts were generated with an average length of 1.9 kb and high assembly completeness. Overall, our data presented effective, accurate gene annotation in the prediction of functional pathways. In particular, the annotation revealed the abundance of transcripts related to phenylpropanoid biosynthesis. Remarkably, transcriptome profiling during fruit development of S. chinensis cultivar Cheongsoon revealed that the phenylpropanoid biosynthetic pathway, specific to coniferyl alcohol biosynthesis, showed a tendency to be upregulated at the postfruit development stage. Further the analysis also revealed that the pathway forms a transcriptional network with fruit ripening-related genes, especially the ABA signaling-related pathway. Finally, candidate unigenes homologous to isoeugenol synthase 1 (IGS1) and dirigent-like protein (DIR), which are subsequently activated by phenylpropanoid biosynthesis and thus catalyze key upstream steps in schisandrin biosynthesis, were identified. Their expression was increased at the postfruit development stage, suggesting that they may be involved in the regulation of schisandrin biosynthesis in S. chinensis. CONCLUSIONS Our results provide new insights into the production and accumulation of schisandrin in S. chinensis berries and will be utilized as a valuable transcriptomic resource for improving the schisandrin content.
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Affiliation(s)
- Chang Pyo Hong
- Theragen Bio Co., Ltd., Suwon, 16229, Republic of Korea.
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Dong Jin Lee
- Theragen Bio Co., Ltd., Suwon, 16229, Republic of Korea
| | - Hee Jeong Jeong
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yi Lee
- Department of Industrial Plant Science & Technology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Sin-Gi Park
- Theragen Bio Co., Ltd., Suwon, 16229, Republic of Korea
| | - Hyo-Jin Kim
- Jeollabukdo ARES Medicinal Resource Research Institute, Jinan, 55440, Republic of Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea.
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