{"title":"Chromosome-scale genome assembly and annotation of Xenocypris argentea.","authors":"Yidi Wu, Hang Sha, Hongwei Liang","doi":"10.1038/s41597-025-04916-x","DOIUrl":null,"url":null,"abstract":"<p><p>Xenocypris argentea is a small to medium-sized freshwater cyprinid fish. It distributes widely in the rivers and lakes of China, and is often used as a tool fish for water quality improvement and optimizing aquaculture structures. In recent years, natural populations of X. argentea have decreased rapidly due to human activities, yet little is known about the genetics and genomics of this fish. In the present work, we reported a chromosome-level reference genome of X. argentea based on PacBio HiFi, Hi-C and Illumina paired-end sequencing technologies. The assembled genome was 984.96 Mb in length, with a contig N50 of 36.02 Mb. Using Hi-C interaction information, 99.47% of the contigs were anchored onto 24 chromosomes, and 18 of the chromosomes were gap-free. Further analysis identified 560.27 Mb of repeat sequences and 28,533 protein-coding genes in the genome, of which, 95.62% (27,284) genes were functionally annotated. This high-quality genome offers an invaluable resource for population genetics and phylogeny, comparative genomics, adaptive evolution and functional exploration of X. argentea.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"573"},"PeriodicalIF":5.8000,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Scientific Data","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1038/s41597-025-04916-x","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}
引用次数: 0
Abstract
Xenocypris argentea is a small to medium-sized freshwater cyprinid fish. It distributes widely in the rivers and lakes of China, and is often used as a tool fish for water quality improvement and optimizing aquaculture structures. In recent years, natural populations of X. argentea have decreased rapidly due to human activities, yet little is known about the genetics and genomics of this fish. In the present work, we reported a chromosome-level reference genome of X. argentea based on PacBio HiFi, Hi-C and Illumina paired-end sequencing technologies. The assembled genome was 984.96 Mb in length, with a contig N50 of 36.02 Mb. Using Hi-C interaction information, 99.47% of the contigs were anchored onto 24 chromosomes, and 18 of the chromosomes were gap-free. Further analysis identified 560.27 Mb of repeat sequences and 28,533 protein-coding genes in the genome, of which, 95.62% (27,284) genes were functionally annotated. This high-quality genome offers an invaluable resource for population genetics and phylogeny, comparative genomics, adaptive evolution and functional exploration of X. argentea.
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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