Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species
Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutio...
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| Format: | Article |
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KeAi Communications Co., Ltd.
2025-01-01
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| Series: | Plant Diversity |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265924001252 |
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| author | Tian-Rui Wang Xin Ning Si-Si Zheng Yu Li Zi-Jia Lu Hong-Hu Meng Bin-Jie Ge Gregor Kozlowski Meng-Xiao Yan Yi-Gang Song |
| author_facet | Tian-Rui Wang Xin Ning Si-Si Zheng Yu Li Zi-Jia Lu Hong-Hu Meng Bin-Jie Ge Gregor Kozlowski Meng-Xiao Yan Yi-Gang Song |
| author_sort | Tian-Rui Wang |
| collection | DOAJ |
| description | Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses. |
| format | Article |
| id | doaj-art-17ec1a2990504399bfefa695ea824ca7 |
| institution | Kabale University |
| issn | 2468-2659 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj-art-17ec1a2990504399bfefa695ea824ca72025-02-12T05:31:31ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592025-01-014715367Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple speciesTian-Rui Wang0Xin Ning1Si-Si Zheng2Yu Li3Zi-Jia Lu4Hong-Hu Meng5Bin-Jie Ge6Gregor Kozlowski7Meng-Xiao Yan8Yi-Gang Song9Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, ChinaPlant Phylogenetics and Conservation Group, Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, ChinaEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Department of Biology and Botanic Garden, University of Fribourg, Fribourg, Switzerland; Natural History Museum Fribourg, Fribourg, SwitzerlandEastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; Corresponding author.Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China; Corresponding author. Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses.http://www.sciencedirect.com/science/article/pii/S2468265924001252QuercusEcological adaptationPhylogenomicsTranscriptomesFagaceae |
| spellingShingle | Tian-Rui Wang Xin Ning Si-Si Zheng Yu Li Zi-Jia Lu Hong-Hu Meng Bin-Jie Ge Gregor Kozlowski Meng-Xiao Yan Yi-Gang Song Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species Plant Diversity Quercus Ecological adaptation Phylogenomics Transcriptomes Fagaceae |
| title | Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species |
| title_full | Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species |
| title_fullStr | Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species |
| title_full_unstemmed | Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species |
| title_short | Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species |
| title_sort | genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species |
| topic | Quercus Ecological adaptation Phylogenomics Transcriptomes Fagaceae |
| url | http://www.sciencedirect.com/science/article/pii/S2468265924001252 |
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