Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China
Abstract Background Ginkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the...
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2025-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-05977-7 |
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| author | Liyun Nie Fangling Liu Meixia Wang Zhuying Jiang Jiali Kong Luke R. Tembrock Shenglong Kan Penghao Wang Jie Wang Zhiqiang Wu Xiaoli Liu |
| author_facet | Liyun Nie Fangling Liu Meixia Wang Zhuying Jiang Jiali Kong Luke R. Tembrock Shenglong Kan Penghao Wang Jie Wang Zhiqiang Wu Xiaoli Liu |
| author_sort | Liyun Nie |
| collection | DOAJ |
| description | Abstract Background Ginkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the Sichuan Basin - a potential glacial refugium that may have played a crucial role in Ginkgo’s persistence. Results Analysis of 227 complete plastomes, including 81 newly sampled individuals from the Sichuan Basin, revealed three distinct maternal lineages differing from known nuclear genome patterns. We identified 170 sequence variants and extensive RNA editing (235 sites) with a bias toward hydrophobic amino acid conversions, suggesting active molecular evolution. A previously undocumented haplotype (IIA2), predominant in western Sichuan Basin populations, showed close genetic affinity with rare refugial haplotypes. Western populations exhibited higher haplotypic diversity and distinctive genetic structure, supporting the basin’s role as both glacial refugium and corridor for population expansion. Ancient trees (314–784 years) provided evidence for interaction between natural processes and historical human dispersal in shaping current genetic patterns. Conclusions Our findings demonstrate substantial genetic diversity within Sichuan Basin Ginkgo populations and reveal dynamic molecular evolution through plastome variation and RNA editing patterns, challenging the notion of evolutionary stasis in this living fossil. This study provides crucial genomic resources for understanding Ginkgo’s evolution and informs conservation strategies for this endangered species. |
| format | Article |
| id | doaj-art-b750daa29f984902b7d9264ed56f6bb1 |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-b750daa29f984902b7d9264ed56f6bb12025-01-19T12:16:37ZengBMCBMC Plant Biology1471-22292025-01-0125111410.1186/s12870-024-05977-7Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of ChinaLiyun Nie0Fangling Liu1Meixia Wang2Zhuying Jiang3Jiali Kong4Luke R. Tembrock5Shenglong Kan6Penghao Wang7Jie Wang8Zhiqiang Wu9Xiaoli Liu10Chengdu Botanical Garden, Chengdu Park Urban Plant Science Research InstituteChengdu Botanical Garden, Chengdu Park Urban Plant Science Research InstituteJiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural UniversityChengdu Botanical Garden, Chengdu Park Urban Plant Science Research InstituteShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesDepartment of Agricultural Biology, Colorado State UniversityShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesSchool of Medical, Molecular and Forensic Sciences, Murdoch UniversityShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesChengdu Botanical Garden, Chengdu Park Urban Plant Science Research InstituteAbstract Background Ginkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the Sichuan Basin - a potential glacial refugium that may have played a crucial role in Ginkgo’s persistence. Results Analysis of 227 complete plastomes, including 81 newly sampled individuals from the Sichuan Basin, revealed three distinct maternal lineages differing from known nuclear genome patterns. We identified 170 sequence variants and extensive RNA editing (235 sites) with a bias toward hydrophobic amino acid conversions, suggesting active molecular evolution. A previously undocumented haplotype (IIA2), predominant in western Sichuan Basin populations, showed close genetic affinity with rare refugial haplotypes. Western populations exhibited higher haplotypic diversity and distinctive genetic structure, supporting the basin’s role as both glacial refugium and corridor for population expansion. Ancient trees (314–784 years) provided evidence for interaction between natural processes and historical human dispersal in shaping current genetic patterns. Conclusions Our findings demonstrate substantial genetic diversity within Sichuan Basin Ginkgo populations and reveal dynamic molecular evolution through plastome variation and RNA editing patterns, challenging the notion of evolutionary stasis in this living fossil. This study provides crucial genomic resources for understanding Ginkgo’s evolution and informs conservation strategies for this endangered species.https://doi.org/10.1186/s12870-024-05977-7Living fossil evolutionGinkgo bilobaPlastome diversityGlacial refugiaPopulation geneticsConservation |
| spellingShingle | Liyun Nie Fangling Liu Meixia Wang Zhuying Jiang Jiali Kong Luke R. Tembrock Shenglong Kan Penghao Wang Jie Wang Zhiqiang Wu Xiaoli Liu Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China BMC Plant Biology Living fossil evolution Ginkgo biloba Plastome diversity Glacial refugia Population genetics Conservation |
| title | Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China |
| title_full | Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China |
| title_fullStr | Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China |
| title_full_unstemmed | Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China |
| title_short | Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China |
| title_sort | plastome data provides new insights into population differentiation and evolution of ginkgo in the sichuan basin of china |
| topic | Living fossil evolution Ginkgo biloba Plastome diversity Glacial refugia Population genetics Conservation |
| url | https://doi.org/10.1186/s12870-024-05977-7 |
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