A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)
Abstract Glass catfish (Kryptopterus vitreolus) is commonly distributed in several Asian countries, such as Thailand, Malaysia, and Indonesia. It is renowned for its near-transparent appearance, which has drawn considerable attention for biomedical research and the tropical ornamental fish industry....
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Nature Portfolio
2025-03-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04841-z |
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| author | Chao Bian Dahong Li Yiluan Wang Zhe He Wei-Ting Chen Cheong-Meng Chong Hongling Zhou Qiong Shi |
| author_facet | Chao Bian Dahong Li Yiluan Wang Zhe He Wei-Ting Chen Cheong-Meng Chong Hongling Zhou Qiong Shi |
| author_sort | Chao Bian |
| collection | DOAJ |
| description | Abstract Glass catfish (Kryptopterus vitreolus) is commonly distributed in several Asian countries, such as Thailand, Malaysia, and Indonesia. It is renowned for its near-transparent appearance, which has drawn considerable attention for biomedical research and the tropical ornamental fish industry. Here, we successfully constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish, by integration of PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies. The haplotypic assembly covers approximately 687.7 Mb in length, featuring a high contig N50 of 21.3 Mb. This assembly was then anchored into 32 chromosomes, presenting a complete set of 64 telomeres and 32 centromeres. It was predicted with 252.4 Mb of repetitive sequences and annotated with a total of 24,696 protein-coding genes. Subsequent BUSCO analysis revealed high genome completeness (up to 96.4%). This high-quality T2T genome assembly not only provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, but also supports in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important fish species. |
| format | Article |
| id | doaj-art-0682c0f4008a44bebb45b0a7fb1101c6 |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-0682c0f4008a44bebb45b0a7fb1101c62025-08-20T02:51:27ZengNature PortfolioScientific Data2052-44632025-03-011211810.1038/s41597-025-04841-zA telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)Chao Bian0Dahong Li1Yiluan Wang2Zhe He3Wei-Ting Chen4Cheong-Meng Chong5Hongling Zhou6Qiong Shi7Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversitySchool of Life Sciences, Jiaying UniversityState Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of MacauShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesLaboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen UniversityAbstract Glass catfish (Kryptopterus vitreolus) is commonly distributed in several Asian countries, such as Thailand, Malaysia, and Indonesia. It is renowned for its near-transparent appearance, which has drawn considerable attention for biomedical research and the tropical ornamental fish industry. Here, we successfully constructed the first telomere-to-telomere (T2T) chromosome-scale genome assembly for glass catfish, by integration of PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing technologies. The haplotypic assembly covers approximately 687.7 Mb in length, featuring a high contig N50 of 21.3 Mb. This assembly was then anchored into 32 chromosomes, presenting a complete set of 64 telomeres and 32 centromeres. It was predicted with 252.4 Mb of repetitive sequences and annotated with a total of 24,696 protein-coding genes. Subsequent BUSCO analysis revealed high genome completeness (up to 96.4%). This high-quality T2T genome assembly not only provides a valuable genetic resource for investigating the molecular mechanisms underlying transparency, but also supports in-depth studies on functional genomics, genetic diversity, and selective breeding for this economically important fish species.https://doi.org/10.1038/s41597-025-04841-z |
| spellingShingle | Chao Bian Dahong Li Yiluan Wang Zhe He Wei-Ting Chen Cheong-Meng Chong Hongling Zhou Qiong Shi A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus) Scientific Data |
| title | A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus) |
| title_full | A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus) |
| title_fullStr | A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus) |
| title_full_unstemmed | A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus) |
| title_short | A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus) |
| title_sort | telomere to telomere chromosome scale genome assembly of glass catfish kryptopterus vitreolus |
| url | https://doi.org/10.1038/s41597-025-04841-z |
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