A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)
Abstract Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-05137-x |
| _version_ | 1797774029222838272 |
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| author | Haoran Luo Xinrui Jiang Boping Li Jiahong Wu Jiexin Shen Zaoxu Xu Xiaoping Zhou Minghao Hou Zhen Huang Xiaobin Ou Luohao Xu |
| author_facet | Haoran Luo Xinrui Jiang Boping Li Jiahong Wu Jiexin Shen Zaoxu Xu Xiaoping Zhou Minghao Hou Zhen Huang Xiaobin Ou Luohao Xu |
| author_sort | Haoran Luo |
| collection | DOAJ |
| description | Abstract Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard. |
| first_indexed | 2024-03-12T22:15:00Z |
| format | Article |
| id | doaj.art-7d54d538f7ea400e9868a3332006bc70 |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-03-12T22:15:00Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-7d54d538f7ea400e9868a3332006bc702023-07-23T11:22:53ZengNature PortfolioCommunications Biology2399-36422023-07-016111110.1038/s42003-023-05137-xA high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)Haoran Luo0Xinrui Jiang1Boping Li2Jiahong Wu3Jiexin Shen4Zaoxu Xu5Xiaoping Zhou6Minghao Hou7Zhen Huang8Xiaobin Ou9Luohao Xu10MOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest UniversityMOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest UniversityGansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong UniversityMOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest UniversityMOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest UniversityGansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong UniversityKey Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen UniversityGansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong UniversityFujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese MedicineGansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Longdong UniversityMOE Key Laboratory of Freshwater Fish Reproduction and Development, Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest UniversityAbstract Conservation genomics often relies on non-invasive methods to obtain DNA fragments which limit the power of multi-omic analyses for threatened species. Here, we report multi-omic analyses based on a well-preserved great bustard individual (Otis tarda, Otidiformes) that was found dead in the mountainous region in Gansu, China. We generate a near-complete genome assembly containing only 18 gaps scattering in 8 out of the 40 assembled chromosomes. We characterize the DNA methylation landscape which is correlated with GC content and gene expression. Our phylogenomic analysis suggests Otidiformes and Musophagiformes are sister groups that diverged from each other 46.3 million years ago. The genetic diversity of great bustard is found the lowest among the four available Otidiformes genomes, possibly due to population declines during past glacial periods. As one of the heaviest migratory birds, great bustard possesses several expanded gene families related to cardiac contraction, actin contraction, calcium ion signaling transduction, as well as positively selected genes enriched for metabolism. Finally, we identify an extremely young evolutionary stratum on the sex chromosome, a rare case among birds. Together, our study provides insights into the conservation genomics, adaption and chromosome evolution of the great bustard.https://doi.org/10.1038/s42003-023-05137-x |
| spellingShingle | Haoran Luo Xinrui Jiang Boping Li Jiahong Wu Jiexin Shen Zaoxu Xu Xiaoping Zhou Minghao Hou Zhen Huang Xiaobin Ou Luohao Xu A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes) Communications Biology |
| title | A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes) |
| title_full | A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes) |
| title_fullStr | A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes) |
| title_full_unstemmed | A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes) |
| title_short | A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes) |
| title_sort | high quality genome assembly highlights the evolutionary history of the great bustard otis tarda otidiformes |
| url | https://doi.org/10.1038/s42003-023-05137-x |
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