Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus)
Abstract The gold barb (Barbodes semifasciolatus), a member of the Cyprinidae family, exhibits remarkable adaptability to highly acidic environments, making it an ideal model for studying extreme environmental adaptation. However, its genome has not been previously characterized. To address this, we...
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Nature Portfolio
2025-05-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05178-3 |
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| author | Weitao Chen Chao Li Rong Yang Yuefei Li Baosheng Wu Jie Li |
| author_facet | Weitao Chen Chao Li Rong Yang Yuefei Li Baosheng Wu Jie Li |
| author_sort | Weitao Chen |
| collection | DOAJ |
| description | Abstract The gold barb (Barbodes semifasciolatus), a member of the Cyprinidae family, exhibits remarkable adaptability to highly acidic environments, making it an ideal model for studying extreme environmental adaptation. However, its genome has not been previously characterized. To address this, we assembled a high-quality chromosome-scale genome for B. semifasciolatus using High-Fidelity (HiFi) sequencing and Hi-C technology. The resulting haplotype-resolved assemblies, spanning 776 Mb and 779 Mb across 25 chromosomes, achieved genome coverages of 99.5% and 99.7%, respectively, and included four gap-free chromosomes. Genome quality assessment using BUSCO indicated a high completeness score of 98.2% for haplotype1 and 98.3% for haplotype2, further validated by strong synteny with the zebrafish (Danio rerio), confirming the assembly’s integrity and continuity. Through integration of full-length transcriptome data, RNA sequencing, and homology-based annotation, we identified 26,057 protein-coding genes with 2,087 pseudogenes in haplotype 2, and 25,622 protein-coding genes with 2,101 pseudogenes in haplotype 1. This high-resolution genome assembly is a crucial resource for advancing research in the Cyprinidae, particularly for understanding adaptive evolution in extreme environments. |
| format | Article |
| id | doaj-art-49718ca690a64c88bfcc3526a40a1237 |
| institution | OA Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-49718ca690a64c88bfcc3526a40a12372025-08-20T02:39:02ZengNature PortfolioScientific Data2052-44632025-05-011211710.1038/s41597-025-05178-3Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus)Weitao Chen0Chao Li1Rong Yang2Yuefei Li3Baosheng Wu4Jie Li5Pearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Engineering Technology Research Center for Environmentally, Friendly Aquaculture, School of Life Sciences, South China Normal UniversityGuangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Engineering Technology Research Center for Environmentally, Friendly Aquaculture, School of Life Sciences, South China Normal UniversityPearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesGuangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of SciencesPearl River Fisheries Research Institute, Chinese Academy of Fishery SciencesAbstract The gold barb (Barbodes semifasciolatus), a member of the Cyprinidae family, exhibits remarkable adaptability to highly acidic environments, making it an ideal model for studying extreme environmental adaptation. However, its genome has not been previously characterized. To address this, we assembled a high-quality chromosome-scale genome for B. semifasciolatus using High-Fidelity (HiFi) sequencing and Hi-C technology. The resulting haplotype-resolved assemblies, spanning 776 Mb and 779 Mb across 25 chromosomes, achieved genome coverages of 99.5% and 99.7%, respectively, and included four gap-free chromosomes. Genome quality assessment using BUSCO indicated a high completeness score of 98.2% for haplotype1 and 98.3% for haplotype2, further validated by strong synteny with the zebrafish (Danio rerio), confirming the assembly’s integrity and continuity. Through integration of full-length transcriptome data, RNA sequencing, and homology-based annotation, we identified 26,057 protein-coding genes with 2,087 pseudogenes in haplotype 2, and 25,622 protein-coding genes with 2,101 pseudogenes in haplotype 1. This high-resolution genome assembly is a crucial resource for advancing research in the Cyprinidae, particularly for understanding adaptive evolution in extreme environments.https://doi.org/10.1038/s41597-025-05178-3 |
| spellingShingle | Weitao Chen Chao Li Rong Yang Yuefei Li Baosheng Wu Jie Li Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus) Scientific Data |
| title | Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus) |
| title_full | Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus) |
| title_fullStr | Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus) |
| title_full_unstemmed | Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus) |
| title_short | Haplotype resolved chromosome-level genome assembly of the gold barb (Barbodes semifasciolatus) |
| title_sort | haplotype resolved chromosome level genome assembly of the gold barb barbodes semifasciolatus |
| url | https://doi.org/10.1038/s41597-025-05178-3 |
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