Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing
Abstract Sinocyclocheilus jii, a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the...
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Nature Portfolio
2025-07-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05663-9 |
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| author | Jie Zhu Chunqing Li Longting Wu Yongkang You Ziheng Sheng Mengjiao Fu Heng Xiao Shanyuan Chen |
| author_facet | Jie Zhu Chunqing Li Longting Wu Yongkang You Ziheng Sheng Mengjiao Fu Heng Xiao Shanyuan Chen |
| author_sort | Jie Zhu |
| collection | DOAJ |
| description | Abstract Sinocyclocheilus jii, a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the most diverse group of cavefishes worldwide. However, the limited availability of genomic resources has limited investigations into the genetic basis of trait variations, phylogenetic relationships, and adaptive evolution in this genus. In this study, we assembled a chromosome-level reference genome for S. jii by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C sequencing data. Flow cytometry was used to estimate the genome size prior to assembly, providing a key step in technical validation. The final genome assembly spans 1.75 Gb with a contig N50 of 35.0 Mb. Using Hi-C sequencing data, the assembled scaffolds were successfully anchored to 50 chromosomes. The completeness of the chromosome-level assembly was estimated at 98.9% by BUSCO analysis. Genome annotation identified 855.5 Mb of repetitive sequences and predicted a total of 52,867 protein-coding genes, of which 51,932 genes were functionally annotated. This study presents a high-quality chromosome-level genome assembly and annotation of S. jii, providing a fundamental genomic resource for future phylogenetic and evolutionary studies. |
| format | Article |
| id | doaj-art-d4cc5d3c836c4c1689372573779feceb |
| institution | DOAJ |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-d4cc5d3c836c4c1689372573779feceb2025-08-20T03:04:18ZengNature PortfolioScientific Data2052-44632025-07-011211910.1038/s41597-025-05663-9Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencingJie Zhu0Chunqing Li1Longting Wu2Yongkang You3Ziheng Sheng4Mengjiao Fu5Heng Xiao6Shanyuan Chen7School of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversitySchool of Ecology and Environmental Science, Yunnan UniversityAbstract Sinocyclocheilus jii, a cavefish species endemic to China, belongs to the genus Sinocyclocheilus within the family Cyprinidae. Species within this genus exhibit significant morphological differentiation, making it not only the most species-rich genus within Cyprinidae in China but also the most diverse group of cavefishes worldwide. However, the limited availability of genomic resources has limited investigations into the genetic basis of trait variations, phylogenetic relationships, and adaptive evolution in this genus. In this study, we assembled a chromosome-level reference genome for S. jii by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C sequencing data. Flow cytometry was used to estimate the genome size prior to assembly, providing a key step in technical validation. The final genome assembly spans 1.75 Gb with a contig N50 of 35.0 Mb. Using Hi-C sequencing data, the assembled scaffolds were successfully anchored to 50 chromosomes. The completeness of the chromosome-level assembly was estimated at 98.9% by BUSCO analysis. Genome annotation identified 855.5 Mb of repetitive sequences and predicted a total of 52,867 protein-coding genes, of which 51,932 genes were functionally annotated. This study presents a high-quality chromosome-level genome assembly and annotation of S. jii, providing a fundamental genomic resource for future phylogenetic and evolutionary studies.https://doi.org/10.1038/s41597-025-05663-9 |
| spellingShingle | Jie Zhu Chunqing Li Longting Wu Yongkang You Ziheng Sheng Mengjiao Fu Heng Xiao Shanyuan Chen Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing Scientific Data |
| title | Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing |
| title_full | Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing |
| title_fullStr | Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing |
| title_full_unstemmed | Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing |
| title_short | Chromosome-level genome assembly of Sinocyclocheilus jii based on PacBio HiFi and Hi-C sequencing |
| title_sort | chromosome level genome assembly of sinocyclocheilus jii based on pacbio hifi and hi c sequencing |
| url | https://doi.org/10.1038/s41597-025-05663-9 |
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