Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius
Abstract Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly tota...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04419-9 |
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| author | Ruoyu Liu Ziyu Meng Yinan Mu Ran Zhang Hanhui Ma Jingjing Hu Yanan Wang Yuxin Shi Yanan Li Chaofeng Wang Weini Zhang Longshan Lin Ping Zheng Xinhua Chen |
| author_facet | Ruoyu Liu Ziyu Meng Yinan Mu Ran Zhang Hanhui Ma Jingjing Hu Yanan Wang Yuxin Shi Yanan Li Chaofeng Wang Weini Zhang Longshan Lin Ping Zheng Xinhua Chen |
| author_sort | Ruoyu Liu |
| collection | DOAJ |
| description | Abstract Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly totaled 739.07 Mb across 697 contigs, with a Contig N50 of 10.004 Mb. Hi-C mapping yielded 23 chromosomes, with a successful mapping rate of 90.53% and a Scaffold N50 of 30.20 Mb. Genome BUSCO integrity was 97.05%. Repetitive sequences accounted for 240.83 Mb (32.58%) of the genome. Non-coding RNA annotations included 4,928 rRNAs, 9,663 tRNAs, 347 snRNAs, and 21 snoRNAs. A total of 30,345 protein-coding genes were identified, encoding 46,603 proteins, with a BUSCO completeness of 94.98%. Molecular pathway related to the endocrine system, carbohydrate metabolism, folding, sorting, and degradation, signal transduction, and transport and catabolism contribute to A. medius adaptation to extreme Arctic environments. This high-quality genome provides valuable genetic resources for understanding Arctic adaptations and supporting polar ecological conservation and management. |
| format | Article |
| id | doaj-art-fac6007eec0f487cb7f706252bdff708 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-fac6007eec0f487cb7f706252bdff7082025-01-19T12:10:07ZengNature PortfolioScientific Data2052-44632025-01-0112111210.1038/s41597-025-04419-9Chromosome-level reference genome and annotation of the Arctic fish Anisarchus mediusRuoyu Liu0Ziyu Meng1Yinan Mu2Ran Zhang3Hanhui Ma4Jingjing Hu5Yanan Wang6Yuxin Shi7Yanan Li8Chaofeng Wang9Weini Zhang10Longshan Lin11Ping Zheng12Xinhua Chen13State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityLaboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural ResourcesState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityGuangzhou Key Laboratory of Aquatic Animal Diseases and Waterfowl Breeding, College of Animal Sciences and Technology, Zhongkai University of Agriculture and EngineeringState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityLaboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural ResourcesState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityState Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityAbstract Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly totaled 739.07 Mb across 697 contigs, with a Contig N50 of 10.004 Mb. Hi-C mapping yielded 23 chromosomes, with a successful mapping rate of 90.53% and a Scaffold N50 of 30.20 Mb. Genome BUSCO integrity was 97.05%. Repetitive sequences accounted for 240.83 Mb (32.58%) of the genome. Non-coding RNA annotations included 4,928 rRNAs, 9,663 tRNAs, 347 snRNAs, and 21 snoRNAs. A total of 30,345 protein-coding genes were identified, encoding 46,603 proteins, with a BUSCO completeness of 94.98%. Molecular pathway related to the endocrine system, carbohydrate metabolism, folding, sorting, and degradation, signal transduction, and transport and catabolism contribute to A. medius adaptation to extreme Arctic environments. This high-quality genome provides valuable genetic resources for understanding Arctic adaptations and supporting polar ecological conservation and management.https://doi.org/10.1038/s41597-025-04419-9 |
| spellingShingle | Ruoyu Liu Ziyu Meng Yinan Mu Ran Zhang Hanhui Ma Jingjing Hu Yanan Wang Yuxin Shi Yanan Li Chaofeng Wang Weini Zhang Longshan Lin Ping Zheng Xinhua Chen Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius Scientific Data |
| title | Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius |
| title_full | Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius |
| title_fullStr | Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius |
| title_full_unstemmed | Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius |
| title_short | Chromosome-level reference genome and annotation of the Arctic fish Anisarchus medius |
| title_sort | chromosome level reference genome and annotation of the arctic fish anisarchus medius |
| url | https://doi.org/10.1038/s41597-025-04419-9 |
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