Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra
Abstract Licorice (Glycyrrhiza L.), a medicinally and economically significant genus in the Fabaceae, is known for synthesizing glycyrrhizin. Here, we present a newly assembled genome of Glycyrrhiza uralensis, a key species distributed across Central and East Asia. Using Oxford Nanopore, Hi-C, and I...
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Nature Portfolio
2025-03-01
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| Online Access: | https://doi.org/10.1038/s41598-025-92115-4 |
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| author | Jungeun Kim Jeonghoon Lee Jong-Soo Kang Hyeonah Shim Daewon Kang Sae Hyun Lee Jae-Pil Choi Hui-Su Kim Min Sun Kim Yong Il Kim Yunji Lee Zafarjon Ziyaev Yong Kook Shin Jong Bhak Tae-Jin Yang |
| author_facet | Jungeun Kim Jeonghoon Lee Jong-Soo Kang Hyeonah Shim Daewon Kang Sae Hyun Lee Jae-Pil Choi Hui-Su Kim Min Sun Kim Yong Il Kim Yunji Lee Zafarjon Ziyaev Yong Kook Shin Jong Bhak Tae-Jin Yang |
| author_sort | Jungeun Kim |
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| description | Abstract Licorice (Glycyrrhiza L.), a medicinally and economically significant genus in the Fabaceae, is known for synthesizing glycyrrhizin. Here, we present a newly assembled genome of Glycyrrhiza uralensis, a key species distributed across Central and East Asia. Using Oxford Nanopore, Hi-C, and Illumina sequencing, we assembled a 415 Mbp genome with an N50 of 47 Mbp. While the genome structure was similar to previously reported assemblies, structural variations were observed across all eight chromosomes. Re-sequencing data from 29 individuals, including G. uralensis, G. glabra, and their hybrids, revealed significant genetic diversity, population structure, and hybridization events. Phylogenomic analyses using nuclear and plastid genomes demonstrated phylogenetic incongruence, supporting hybridization between G. uralensis and G. glabra. Our species network and gene flow test identified hybrid groups (Ggu1, Ggu2, and Gug) acting as genetic bridges between the species. Demographic history inferred via PSMC showed Glycyrrhiza species thrived during the Middle Pleistocene, with population size fluctuations in G. uralensis and hybrids. Current low heterozygosity and high genetic differentiation suggest long-term geographic and ecological isolation, reducing gene flow. Our findings advance the understanding of evolutionary history in Glycyrrhiza species and help conservation and molecular breeding of these species. |
| format | Article |
| id | doaj-art-eb0948a7c4044a71830472b9f5179caa |
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| language | English |
| publishDate | 2025-03-01 |
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| spelling | doaj-art-eb0948a7c4044a71830472b9f5179caa2025-08-20T01:47:32ZengNature PortfolioScientific Reports2045-23222025-03-0115111310.1038/s41598-025-92115-4Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabraJungeun Kim0Jeonghoon Lee1Jong-Soo Kang2Hyeonah Shim3Daewon Kang4Sae Hyun Lee5Jae-Pil Choi6Hui-Su Kim7Min Sun Kim8Yong Il Kim9Yunji Lee10Zafarjon Ziyaev11Yong Kook Shin12Jong Bhak13Tae-Jin Yang14Personal Genomics Institute, Genome Research FoundationNational Institute of Horticultural and Herbal Science, RDADepartment of Agriculture, Forestry and Bioresources, College of Agriculture & Life Sciences, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, College of Agriculture & Life Sciences, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, College of Agriculture & Life Sciences, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Seoul National UniversityDepartment of Agriculture, Forestry and Bioresources, College of Agriculture & Life Sciences, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Seoul National UniversityNational Institute of Horticultural and Herbal Science, RDAKorean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST)Personal Genomics Institute, Genome Research FoundationNational Institute of Horticultural and Herbal Science, RDANational Institute of Horticultural and Herbal Science, RDAResearch Institute of Plant Genetic ResourcesSchool of Industrial Bio-pharmaceutical Science, Semyung UniversityPersonal Genomics Institute, Genome Research FoundationDepartment of Agriculture, Forestry and Bioresources, College of Agriculture & Life Sciences, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Seoul National UniversityAbstract Licorice (Glycyrrhiza L.), a medicinally and economically significant genus in the Fabaceae, is known for synthesizing glycyrrhizin. Here, we present a newly assembled genome of Glycyrrhiza uralensis, a key species distributed across Central and East Asia. Using Oxford Nanopore, Hi-C, and Illumina sequencing, we assembled a 415 Mbp genome with an N50 of 47 Mbp. While the genome structure was similar to previously reported assemblies, structural variations were observed across all eight chromosomes. Re-sequencing data from 29 individuals, including G. uralensis, G. glabra, and their hybrids, revealed significant genetic diversity, population structure, and hybridization events. Phylogenomic analyses using nuclear and plastid genomes demonstrated phylogenetic incongruence, supporting hybridization between G. uralensis and G. glabra. Our species network and gene flow test identified hybrid groups (Ggu1, Ggu2, and Gug) acting as genetic bridges between the species. Demographic history inferred via PSMC showed Glycyrrhiza species thrived during the Middle Pleistocene, with population size fluctuations in G. uralensis and hybrids. Current low heterozygosity and high genetic differentiation suggest long-term geographic and ecological isolation, reducing gene flow. Our findings advance the understanding of evolutionary history in Glycyrrhiza species and help conservation and molecular breeding of these species.https://doi.org/10.1038/s41598-025-92115-4 |
| spellingShingle | Jungeun Kim Jeonghoon Lee Jong-Soo Kang Hyeonah Shim Daewon Kang Sae Hyun Lee Jae-Pil Choi Hui-Su Kim Min Sun Kim Yong Il Kim Yunji Lee Zafarjon Ziyaev Yong Kook Shin Jong Bhak Tae-Jin Yang Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra Scientific Reports |
| title | Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra |
| title_full | Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra |
| title_fullStr | Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra |
| title_full_unstemmed | Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra |
| title_short | Contributions of interspecific hybrids to genetic variability in Glycyrrhiza uralensis and G. glabra |
| title_sort | contributions of interspecific hybrids to genetic variability in glycyrrhiza uralensis and g glabra |
| url | https://doi.org/10.1038/s41598-025-92115-4 |
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