{"title":"利用纳米孔和Hi-C技术组装青鱼的染色体水平基因组。","authors":"Yuxuan Zhang, Yanwen Shao, Xudong Liu, Liang Zhong, Zhaoyan Zhong, Weiwei Zeng, Jiping Zhang, Wenlong Cai, Runsheng Li","doi":"10.1038/s41597-025-04421-1","DOIUrl":null,"url":null,"abstract":"<p><p>Black carp (Mylopharyngodon piceus) is one of the \"four famous domestic fishes\" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies. The final genome assembly was 848.70 Mb in length, with a contig N50 of 3.37 Mb and a scaffold N50 of 34.13 Mb. The genome was anchored onto 24 chromosomes by Hi-C technology. The BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of the genome assembly is 97.6% when compared to the Actinopterygii_odb10 database. In total, 203.54 Mb of repeat sequences and 37,418 protein-coding genes were predicted in the genome assembly. Taken together, our study provides a chromosome-level genome assembly, which can serve as a valuable genetic resource to support further biological studies and breeding efforts of black carp.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"145"},"PeriodicalIF":6.9000,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11763064/pdf/","citationCount":"0","resultStr":"{\"title\":\"Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies.\",\"authors\":\"Yuxuan Zhang, Yanwen Shao, Xudong Liu, Liang Zhong, Zhaoyan Zhong, Weiwei Zeng, Jiping Zhang, Wenlong Cai, Runsheng Li\",\"doi\":\"10.1038/s41597-025-04421-1\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Black carp (Mylopharyngodon piceus) is one of the \\\"four famous domestic fishes\\\" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies. The final genome assembly was 848.70 Mb in length, with a contig N50 of 3.37 Mb and a scaffold N50 of 34.13 Mb. The genome was anchored onto 24 chromosomes by Hi-C technology. The BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of the genome assembly is 97.6% when compared to the Actinopterygii_odb10 database. In total, 203.54 Mb of repeat sequences and 37,418 protein-coding genes were predicted in the genome assembly. Taken together, our study provides a chromosome-level genome assembly, which can serve as a valuable genetic resource to support further biological studies and breeding efforts of black carp.</p>\",\"PeriodicalId\":21597,\"journal\":{\"name\":\"Scientific Data\",\"volume\":\"12 1\",\"pages\":\"145\"},\"PeriodicalIF\":6.9000,\"publicationDate\":\"2025-01-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11763064/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Scientific Data\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1038/s41597-025-04421-1\",\"RegionNum\":2,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Scientific Data","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1038/s41597-025-04421-1","RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Chromosome-level genome assembly of black carp Mylopharyngodon piceus using Nanopore and Hi-C technologies.
Black carp (Mylopharyngodon piceus) is one of the "four famous domestic fishes" in China and an important economic fish in freshwater aquaculture. A high-quality genome is essential for advancing future biological research and breeding programs for this species. In this study, we aimed to generate a high-quality chromosome-level genome assembly of black carp using Nanopore and Hi-C technologies. The final genome assembly was 848.70 Mb in length, with a contig N50 of 3.37 Mb and a scaffold N50 of 34.13 Mb. The genome was anchored onto 24 chromosomes by Hi-C technology. The BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness score of the genome assembly is 97.6% when compared to the Actinopterygii_odb10 database. In total, 203.54 Mb of repeat sequences and 37,418 protein-coding genes were predicted in the genome assembly. Taken together, our study provides a chromosome-level genome assembly, which can serve as a valuable genetic resource to support further biological studies and breeding efforts of black carp.
期刊介绍：
Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data.
The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.
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