Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies
Abstract Triplophysa bombifrons, a species of bony fish localized in China, has largely been understudied genetically, with limited data available beyond its mitochondrial genome. This study introduces a chromosome-level genome assembly for T. bombifrons, achieved through the integration of PacBio l...
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Nature Portfolio
2024-12-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04340-7 |
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| author | Chengxin Wang Site Luo Yong Song Liting Yang Xinyue Wang Shengao Chen |
| author_facet | Chengxin Wang Site Luo Yong Song Liting Yang Xinyue Wang Shengao Chen |
| author_sort | Chengxin Wang |
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| description | Abstract Triplophysa bombifrons, a species of bony fish localized in China, has largely been understudied genetically, with limited data available beyond its mitochondrial genome. This study introduces a chromosome-level genome assembly for T. bombifrons, achieved through the integration of PacBio long-read sequencing and Hi-C chromatin interaction mapping. The assembly reveals a genome structure comprising 25 chromosomes and an overall size of 655.95 Mb. The quality of this assembly is demonstrated by a scaffold N50 length of 24.25 Mb, and a genome completeness evaluation via BUSCO, which shows that 97.4% of the Vertebrata Benchmarking Universal Single-Copy Orthologs are present. Gene prediction methods including de novo, homology-based, and transcript-based, identified 34,211 genes, with 34,151 being functionally annotated. These findings may provide valuable resources in conservation, functional genomics, and molecular breeding of T. bombifrons, as well as the molecular phylogenetics and evolutionary patterns in Triplophysa. |
| format | Article |
| id | doaj-art-c008d7ba5d5a46ce9faa705902207caa |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
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| series | Scientific Data |
| spelling | doaj-art-c008d7ba5d5a46ce9faa705902207caa2025-01-05T12:08:13ZengNature PortfolioScientific Data2052-44632024-12-011111810.1038/s41597-024-04340-7Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologiesChengxin Wang0Site Luo1Yong Song2Liting Yang3Xinyue Wang4Shengao Chen5College of Life Science and Technology/Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, Xinjiang Uygur Autonomous RegionSchool of Life Sciences, Xiamen UniversityCollege of Life Science and Technology/Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, Xinjiang Uygur Autonomous RegionCollege of Life Science and Technology/Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, Xinjiang Uygur Autonomous RegionCollege of Life Science and Technology/Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, Xinjiang Uygur Autonomous RegionCollege of Life Science and Technology/Tarim Research Center of Rare Fishes, Tarim University, CN-0997, Alar 843300, Xinjiang Uygur Autonomous RegionAbstract Triplophysa bombifrons, a species of bony fish localized in China, has largely been understudied genetically, with limited data available beyond its mitochondrial genome. This study introduces a chromosome-level genome assembly for T. bombifrons, achieved through the integration of PacBio long-read sequencing and Hi-C chromatin interaction mapping. The assembly reveals a genome structure comprising 25 chromosomes and an overall size of 655.95 Mb. The quality of this assembly is demonstrated by a scaffold N50 length of 24.25 Mb, and a genome completeness evaluation via BUSCO, which shows that 97.4% of the Vertebrata Benchmarking Universal Single-Copy Orthologs are present. Gene prediction methods including de novo, homology-based, and transcript-based, identified 34,211 genes, with 34,151 being functionally annotated. These findings may provide valuable resources in conservation, functional genomics, and molecular breeding of T. bombifrons, as well as the molecular phylogenetics and evolutionary patterns in Triplophysa.https://doi.org/10.1038/s41597-024-04340-7 |
| spellingShingle | Chengxin Wang Site Luo Yong Song Liting Yang Xinyue Wang Shengao Chen Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies Scientific Data |
| title | Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies |
| title_full | Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies |
| title_fullStr | Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies |
| title_full_unstemmed | Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies |
| title_short | Chromosome-level genome assembly of Triplophysa bombifrons using PacBio HiFi sequencing and Hi-C technologies |
| title_sort | chromosome level genome assembly of triplophysa bombifrons using pacbio hifi sequencing and hi c technologies |
| url | https://doi.org/10.1038/s41597-024-04340-7 |
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