Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies
Abstract Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive un...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-03-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04800-8 |
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| author | Tiezhu Yang Liangjie Zhao Chaoqun Su Xusheng Guo Xinliang Peng Shijie Yang Gaoyou Yao |
| author_facet | Tiezhu Yang Liangjie Zhao Chaoqun Su Xusheng Guo Xinliang Peng Shijie Yang Gaoyou Yao |
| author_sort | Tiezhu Yang |
| collection | DOAJ |
| description | Abstract Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement. |
| format | Article |
| id | doaj-art-12e186c6381d4a32ba03c8dd1a7c54e7 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-12e186c6381d4a32ba03c8dd1a7c54e72025-08-20T03:41:39ZengNature PortfolioScientific Data2052-44632025-03-0112111110.1038/s41597-025-04800-8Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologiesTiezhu Yang0Liangjie Zhao1Chaoqun Su2Xusheng Guo3Xinliang Peng4Shijie Yang5Gaoyou Yao6College of Fisheries, Xinyang Agriculture and Forestry UniversityCollege of Fisheries, Xinyang Agriculture and Forestry UniversityCollege of Fisheries, Xinyang Agriculture and Forestry UniversityCollege of Fisheries, Xinyang Agriculture and Forestry UniversityCollege of Fisheries, Xinyang Agriculture and Forestry UniversityXinyang Nanwan Reservoir Affairs CenterCollege of Fisheries, Xinyang Agriculture and Forestry UniversityAbstract Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement.https://doi.org/10.1038/s41597-025-04800-8 |
| spellingShingle | Tiezhu Yang Liangjie Zhao Chaoqun Su Xusheng Guo Xinliang Peng Shijie Yang Gaoyou Yao Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies Scientific Data |
| title | Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies |
| title_full | Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies |
| title_fullStr | Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies |
| title_full_unstemmed | Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies |
| title_short | Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies |
| title_sort | chromosome scale assembly of the xenocypris davidi using pacbio hifi reads and hi c technologies |
| url | https://doi.org/10.1038/s41597-025-04800-8 |
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