A chromosome-level genome assembly of the East Asian fourfinger threadfin, Eleutheronema rhadinum (Jordan & Evermann, 1902).
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| Main Authors: | , , , , , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
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Scientific data
2025
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| _version_ | 1868266114419523584 |
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| author | Lu, Jingheng Zhang, Huijuan Liu, Weibin Wang, Linjuan Zheng, Anna Jin, Minxuan Zhang, Jiandong Tang, Baogui Wang, Bei Huang, Jiansheng Li, Jing Wang, Zhongliang |
| author_facet | Lu, Jingheng Zhang, Huijuan Liu, Weibin Wang, Linjuan Zheng, Anna Jin, Minxuan Zhang, Jiandong Tang, Baogui Wang, Bei Huang, Jiansheng Li, Jing Wang, Zhongliang Lu, Jingheng Zhang, Huijuan Liu, Weibin Wang, Linjuan Zheng, Anna Jin, Minxuan Zhang, Jiandong Tang, Baogui Wang, Bei Huang, Jiansheng Li, Jing Wang, Zhongliang |
| collection | PubMed - marine biology |
| contents | A chromosome-level genome assembly of the East Asian fourfinger threadfin, Eleutheronema rhadinum (Jordan & Evermann, 1902). Lu, Jingheng Zhang, Huijuan Liu, Weibin Wang, Linjuan Zheng, Anna Jin, Minxuan Zhang, Jiandong Tang, Baogui Wang, Bei Huang, Jiansheng Li, Jing Wang, Zhongliang Animals Genome Chromosomes Perciformes Whole Genome Sequencing Phylogeny The East Asian fourfinger threadfin (Eleutheronema rhadinum, Jordan & Evermann, 1902), an endemic species in East Asia, is distributed across coastal waters of China (including Taiwan Province), Japan, and northern Vietnam. Owing to its high market value, E. rhadinum is considered an economically important species in China and is widely targeted by gillnet, set net, and rod-and-reel fisheries in both coastal and inshore waters for commercial and recreational purposes. Despite its ecological and economic significance, the orthologous relationships and phylogenetic history of E. rhadinum remain largely un characterized. In this study, we performed whole-genome sequencing using PacBio SMRT and Hi-C technologies to generate a high-quality, chromosome-level genome assembly. The assembled genome size was 585.27 Mb, with a contig N50 of 24.22 Mb and 99.73% of sequences anchored to 26 chromosomes. A total of 23,090 protein-coding genes were predicted, and approximately 18.53% of the genome was identified as repetitive sequences. Specifically, DNA transposons, LINEs, SINEs, and LTR elements comprised about 12.83%, 6.24%, 0.47%, and 3.98% of the genome. We identified 657 miRNA, 1840 tRNA, 1576 rRNA and 899 snRNA in the E. rhadinum genome. This high-quality reference genome provides a valuable resource for future studies on the evolutionary biology, functional genomics, and genetic improvement of E. rhadinum and related threadfin species. |
| format | Artículo científico |
| id | pubmed_41381515 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Scientific data |
| record_format | pubmed |
| spellingShingle | A chromosome-level genome assembly of the East Asian fourfinger threadfin, Eleutheronema rhadinum (Jordan & Evermann, 1902). Lu, Jingheng Zhang, Huijuan Liu, Weibin Wang, Linjuan Zheng, Anna Jin, Minxuan Zhang, Jiandong Tang, Baogui Wang, Bei Huang, Jiansheng Li, Jing Wang, Zhongliang Animals Genome Chromosomes Perciformes Whole Genome Sequencing Phylogeny A chromosome-level genome assembly of the East Asian fourfinger threadfin, Eleutheronema rhadinum (Jordan & Evermann, 1902). Lu, Jingheng Zhang, Huijuan Liu, Weibin Wang, Linjuan Zheng, Anna Jin, Minxuan Zhang, Jiandong Tang, Baogui Wang, Bei Huang, Jiansheng Li, Jing Wang, Zhongliang Animals Genome Chromosomes Perciformes Whole Genome Sequencing Phylogeny The East Asian fourfinger threadfin (Eleutheronema rhadinum, Jordan & Evermann, 1902), an endemic species in East Asia, is distributed across coastal waters of China (including Taiwan Province), Japan, and northern Vietnam. Owing to its high market value, E. rhadinum is considered an economically important species in China and is widely targeted by gillnet, set net, and rod-and-reel fisheries in both coastal and inshore waters for commercial and recreational purposes. Despite its ecological and economic significance, the orthologous relationships and phylogenetic history of E. rhadinum remain largely un characterized. In this study, we performed whole-genome sequencing using PacBio SMRT and Hi-C technologies to generate a high-quality, chromosome-level genome assembly. The assembled genome size was 585.27 Mb, with a contig N50 of 24.22 Mb and 99.73% of sequences anchored to 26 chromosomes. A total of 23,090 protein-coding genes were predicted, and approximately 18.53% of the genome was identified as repetitive sequences. Specifically, DNA transposons, LINEs, SINEs, and LTR elements comprised about 12.83%, 6.24%, 0.47%, and 3.98% of the genome. We identified 657 miRNA, 1840 tRNA, 1576 rRNA and 899 snRNA in the E. rhadinum genome. This high-quality reference genome provides a valuable resource for future studies on the evolutionary biology, functional genomics, and genetic improvement of E. rhadinum and related threadfin species. |
| title | A chromosome-level genome assembly of the East Asian fourfinger threadfin, Eleutheronema rhadinum (Jordan & Evermann, 1902). |
| topic | Animals Genome Chromosomes Perciformes Whole Genome Sequencing Phylogeny |
| url | https://pubmed.ncbi.nlm.nih.gov/41381515/ |