Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies.
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| Autores principales: | , , , , , , |
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| Formato: | Artículo científico |
| Lenguaje: | en |
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Scientific data
2025
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| _version_ | 1868266125075152897 |
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| author | Hsu, Po-Cheng Lin, Chung-Yen Hsieh, Ping-Heng Chuang, Wei-Hsuan Lu, Mei-Yeh Chen, Chaolun Allen Chen, Shu-Hwa |
| author_facet | Hsu, Po-Cheng Lin, Chung-Yen Hsieh, Ping-Heng Chuang, Wei-Hsuan Lu, Mei-Yeh Chen, Chaolun Allen Chen, Shu-Hwa Hsu, Po-Cheng Lin, Chung-Yen Hsieh, Ping-Heng Chuang, Wei-Hsuan Lu, Mei-Yeh Chen, Chaolun Allen Chen, Shu-Hwa |
| collection | PubMed - marine biology |
| contents | Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies. Hsu, Po-Cheng Lin, Chung-Yen Hsieh, Ping-Heng Chuang, Wei-Hsuan Lu, Mei-Yeh Chen, Chaolun Allen Chen, Shu-Hwa Animals Genome, Mitochondrial Molecular Sequence Annotation Chromosomes Genome Cell Nucleus RNA, Untranslated Genomics Fishes The Japanese cutlassfish (Trichiurus japonicus) is a commercially important marine species across Asia. Here, we present a high-quality, chromosome-level genome assembly generated using PacBio HiFi, Hi-C, and Nanopore ONT reads. The nuclear genome comprised 24 chromosomes with 160 scaffolds totaling 1,138 Mb, with a scaffold N50 of 47.10 Mb and an average scaffold length of 6.18 Mb. A complete mitochondrial genome of 16,796 bp was also assembled, comprising 13 protein-coding and 23 non-coding RNA (ncRNA) genes, with 99.32% sequence identity to the reference in the NCBI database. The nuclear genome encodes 26,541 protein-coding genes (median length: 7,391 base pairs) and 16,383 non-coding RNA (ncRNA) genes. The ncRNA genes account for approximately 0.1694% of the genome's total length. BUSCO analysis indicated 99.4% and 99.2% completeness against the Actinopterygii ortholog set for the genome and proteome. Functional annotation covered 98.15% of genes. Recognized repeat elements and ncRNA regions accounted for 61.10% of the nuclear genome. With high mapping rates from external datasets, this assembly offers a valuable foundation for future sequencing-based studies. |
| format | Artículo científico |
| id | pubmed_41271797 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Scientific data |
| record_format | pubmed |
| spellingShingle | Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies. Hsu, Po-Cheng Lin, Chung-Yen Hsieh, Ping-Heng Chuang, Wei-Hsuan Lu, Mei-Yeh Chen, Chaolun Allen Chen, Shu-Hwa Animals Genome, Mitochondrial Molecular Sequence Annotation Chromosomes Genome Cell Nucleus RNA, Untranslated Genomics Fishes Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies. Hsu, Po-Cheng Lin, Chung-Yen Hsieh, Ping-Heng Chuang, Wei-Hsuan Lu, Mei-Yeh Chen, Chaolun Allen Chen, Shu-Hwa Animals Genome, Mitochondrial Molecular Sequence Annotation Chromosomes Genome Cell Nucleus RNA, Untranslated Genomics Fishes The Japanese cutlassfish (Trichiurus japonicus) is a commercially important marine species across Asia. Here, we present a high-quality, chromosome-level genome assembly generated using PacBio HiFi, Hi-C, and Nanopore ONT reads. The nuclear genome comprised 24 chromosomes with 160 scaffolds totaling 1,138 Mb, with a scaffold N50 of 47.10 Mb and an average scaffold length of 6.18 Mb. A complete mitochondrial genome of 16,796 bp was also assembled, comprising 13 protein-coding and 23 non-coding RNA (ncRNA) genes, with 99.32% sequence identity to the reference in the NCBI database. The nuclear genome encodes 26,541 protein-coding genes (median length: 7,391 base pairs) and 16,383 non-coding RNA (ncRNA) genes. The ncRNA genes account for approximately 0.1694% of the genome's total length. BUSCO analysis indicated 99.4% and 99.2% completeness against the Actinopterygii ortholog set for the genome and proteome. Functional annotation covered 98.15% of genes. Recognized repeat elements and ncRNA regions accounted for 61.10% of the nuclear genome. With high mapping rates from external datasets, this assembly offers a valuable foundation for future sequencing-based studies. |
| title | Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies. |
| topic | Animals Genome, Mitochondrial Molecular Sequence Annotation Chromosomes Genome Cell Nucleus RNA, Untranslated Genomics Fishes |
| url | https://pubmed.ncbi.nlm.nih.gov/41271797/ |