Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti)
Abstract Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques....
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| Format: | Article |
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Nature Portfolio
2025-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04416-y |
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| author | Xuemei Li Xingbing Wu Yongjiu Zhu Xiaoli Li Zihao Meng Nian Wei Miao Xiang Deguo Yang Tingbing Zhu |
| author_facet | Xuemei Li Xingbing Wu Yongjiu Zhu Xiaoli Li Zihao Meng Nian Wei Miao Xiang Deguo Yang Tingbing Zhu |
| author_sort | Xuemei Li |
| collection | DOAJ |
| description | Abstract Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques. According to the PacBio sequencing, C. guichenoti genome was successfully assembled to 1100.1 Mb size, with a Contig N50 size of 25.0 Mb, and containing 731.0 Mb of repeats. Hi-C sequencing data was utilized for chromosome assembly and 25 chromosome sequences were ultimately yielded, with a total length of 1076.8 Mb. Moreover, a total of 22,506 protein-coding genes were predicted with average intron length of 2293 bp. Evolutionary analysis and divergence time prediction revealed that C. guichenoti was closely related to C. heterodon and they phylogenetically diverged from common ancestor ~20.7 million years ago (Mya), following the separation of Cyprinidae at 28.3 Mya. In the future, the utilization of comparative genomics research is important in elucidating the molecular mechanisms of Ichthyophthirius disease and ensuring the conservation of biological resources. |
| format | Article |
| id | doaj-art-eab89c566b6d4b1e81652e2a4307b4c1 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Scientific Data |
| spelling | doaj-art-eab89c566b6d4b1e81652e2a4307b4c12025-01-19T12:10:02ZengNature PortfolioScientific Data2052-44632025-01-011211810.1038/s41597-025-04416-yChromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti)Xuemei Li0Xingbing Wu1Yongjiu Zhu2Xiaoli Li3Zihao Meng4Nian Wei5Miao Xiang6Deguo Yang7Tingbing Zhu8Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesKey Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery SciencesAbstract Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques. According to the PacBio sequencing, C. guichenoti genome was successfully assembled to 1100.1 Mb size, with a Contig N50 size of 25.0 Mb, and containing 731.0 Mb of repeats. Hi-C sequencing data was utilized for chromosome assembly and 25 chromosome sequences were ultimately yielded, with a total length of 1076.8 Mb. Moreover, a total of 22,506 protein-coding genes were predicted with average intron length of 2293 bp. Evolutionary analysis and divergence time prediction revealed that C. guichenoti was closely related to C. heterodon and they phylogenetically diverged from common ancestor ~20.7 million years ago (Mya), following the separation of Cyprinidae at 28.3 Mya. In the future, the utilization of comparative genomics research is important in elucidating the molecular mechanisms of Ichthyophthirius disease and ensuring the conservation of biological resources.https://doi.org/10.1038/s41597-025-04416-y |
| spellingShingle | Xuemei Li Xingbing Wu Yongjiu Zhu Xiaoli Li Zihao Meng Nian Wei Miao Xiang Deguo Yang Tingbing Zhu Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) Scientific Data |
| title | Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) |
| title_full | Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) |
| title_fullStr | Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) |
| title_full_unstemmed | Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) |
| title_short | Chromosome-level genome assembly and annotation of largemouth bronze gudgeon (Coreius guichenoti) |
| title_sort | chromosome level genome assembly and annotation of largemouth bronze gudgeon coreius guichenoti |
| url | https://doi.org/10.1038/s41597-025-04416-y |
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