A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum
Abstract Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collection...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-024-84540-8 |
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| author | Ho Jun Joh Young Sang Park Jong-Soo Kang Jin Tae Kim Jickerson P. Lado Sang Il Han Young-Won Chin Hyun-Seung Park Jee Young Park Tae-Jin Yang |
| author_facet | Ho Jun Joh Young Sang Park Jong-Soo Kang Jin Tae Kim Jickerson P. Lado Sang Il Han Young-Won Chin Hyun-Seung Park Jee Young Park Tae-Jin Yang |
| author_sort | Ho Jun Joh |
| collection | DOAJ |
| description | Abstract Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that the PJ accessions were monophyletic within the genus Peucedanum. However, ten plastomes were classified into two different groups according to their length of inverted repeat (IR) block, the short-type (S-type) plastome group containing the 18.6 kbp of the original IR and the long-type (L-type) plastome group containing the 35.7 kbp of expanded IR by duplication of the 17.1 kbp of the large single copy region. A total of nine single nucleotide polymorphisms and eight insertions or deletions were identified among the five L-type plastomes, whereas large variations were identified among the five S-type plastomes. Calculation of synonymous substitution rates and divergence time estimation suggested that the 17 kbp IR expansion occurred recently. Molecular markers were developed and validated to classify the 55 PJ germplasm according to their plastome types. Our study would be useful for unraveling the dynamic evolution of plastomes in the Apiaceae family and for the molecular breeding of PJ. |
| format | Article |
| id | doaj-art-3d41c5fbf994422e9718ea8e885ccda4 |
| institution | Kabale University |
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| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-3d41c5fbf994422e9718ea8e885ccda42025-01-05T12:23:31ZengNature PortfolioScientific Reports2045-23222025-01-0115111210.1038/s41598-024-84540-8A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicumHo Jun Joh0Young Sang Park1Jong-Soo Kang2Jin Tae Kim3Jickerson P. Lado4Sang Il Han5Young-Won Chin6Hyun-Seung Park7Jee Young Park8Tae-Jin Yang9Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityInterdisciplinary Program in Agricultural Genomics, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityMedicinal Plant Garden, College of Pharmacy, Seoul National UniversityCollege of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversityAbstract Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible and functional foods. In this study, we compared the plastid genomes (plastomes) and 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that the PJ accessions were monophyletic within the genus Peucedanum. However, ten plastomes were classified into two different groups according to their length of inverted repeat (IR) block, the short-type (S-type) plastome group containing the 18.6 kbp of the original IR and the long-type (L-type) plastome group containing the 35.7 kbp of expanded IR by duplication of the 17.1 kbp of the large single copy region. A total of nine single nucleotide polymorphisms and eight insertions or deletions were identified among the five L-type plastomes, whereas large variations were identified among the five S-type plastomes. Calculation of synonymous substitution rates and divergence time estimation suggested that the 17 kbp IR expansion occurred recently. Molecular markers were developed and validated to classify the 55 PJ germplasm according to their plastome types. Our study would be useful for unraveling the dynamic evolution of plastomes in the Apiaceae family and for the molecular breeding of PJ.https://doi.org/10.1038/s41598-024-84540-8Peucedanum japonicumPlastomePhylogenetic analysisIntra-species polymorphismInverted repeatKompetitive allele-specific PCR (KASP) |
| spellingShingle | Ho Jun Joh Young Sang Park Jong-Soo Kang Jin Tae Kim Jickerson P. Lado Sang Il Han Young-Won Chin Hyun-Seung Park Jee Young Park Tae-Jin Yang A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum Scientific Reports Peucedanum japonicum Plastome Phylogenetic analysis Intra-species polymorphism Inverted repeat Kompetitive allele-specific PCR (KASP) |
| title | A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum |
| title_full | A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum |
| title_fullStr | A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum |
| title_full_unstemmed | A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum |
| title_short | A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum |
| title_sort | recent large scale intraspecific ir expansion and evolutionary dynamics of the plastome of peucedanum japonicum |
| topic | Peucedanum japonicum Plastome Phylogenetic analysis Intra-species polymorphism Inverted repeat Kompetitive allele-specific PCR (KASP) |
| url | https://doi.org/10.1038/s41598-024-84540-8 |
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