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| Natura: | Artículo científico |
| Lingua: | en |
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Biology
2025
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| Accesso online: | https://pubmed.ncbi.nlm.nih.gov/41300277/ |
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| _version_ | 1868266119914061825 |
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| author | Chen, Jieming Zhang, Xinhui Li, Yanping Lv, Yunyun You, Xinxin Shi, Qiong Wen, Zhengyong |
| author_facet | Chen, Jieming Zhang, Xinhui Li, Yanping Lv, Yunyun You, Xinxin Shi, Qiong Wen, Zhengyong Chen, Jieming Zhang, Xinhui Li, Yanping Lv, Yunyun You, Xinxin Shi, Qiong Wen, Zhengyong |
| collection | PubMed - marine biology |
| contents | Chromosome-Scale Genome Assembly and Genome-Wide Identification of Antimicrobial Peptide-Containing Genes in the Endangered Long-Finned Gudgeon Fish (). Chen, Jieming Zhang, Xinhui Li, Yanping Lv, Yunyun You, Xinxin Shi, Qiong Wen, Zhengyong As an economically important species endemic to the upper tributaries of Yangtze River in China, long-finned gudgeon fish () has been classified as endangered due to habitat destruction and population decline. In this study, we constructed a chromosome-level genome assembly of by integration of MGI, PacBio and Hi-C sequencing technologies. The final genome assembly was 1015.9 Mb in length (contig N50: 25.91 Mb; scaffold N50: 39.99 Mb), and 97.19% of the haplotypic genome sequences were anchored onto 25 chromosomes. Repetitive elements accounted for 51.00% of the entire genome assembly. A total of 23,220 protein-coding genes were predicted for the assembled genome, of which 99.79% were functionally annotated. Genome evaluation revealed 99.72% completeness for the genome assembly. Through genome-wide prediction of antimicrobial peptides (AMPs), we identified and localized 561 putative AMP-containing genes in the genome. These genes were further classified into 185 distinct functional categories based on public databases, with the top ten components of Penetratin (21.74%), Histone (5.70%), E6AP (4.09%), Scolopendin 1 (2.67%), D38 (2.31%), WBp-1 (2.13%), Defensin (2.13%), Claudin 1 (1.96%), Azurocidin (AZU1, 1.78%), and Ubiquitin (1.60%). Our data presented here provide a potential genetic resource for promoting fundamental research and wild population conservation of this endangered fish species. |
| format | Artículo científico |
| id | pubmed_41300277 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Biology |
| record_format | pubmed |
| spellingShingle | Chromosome-Scale Genome Assembly and Genome-Wide Identification of Antimicrobial Peptide-Containing Genes in the Endangered Long-Finned Gudgeon Fish (). Chen, Jieming Zhang, Xinhui Li, Yanping Lv, Yunyun You, Xinxin Shi, Qiong Wen, Zhengyong Chromosome-Scale Genome Assembly and Genome-Wide Identification of Antimicrobial Peptide-Containing Genes in the Endangered Long-Finned Gudgeon Fish (). Chen, Jieming Zhang, Xinhui Li, Yanping Lv, Yunyun You, Xinxin Shi, Qiong Wen, Zhengyong As an economically important species endemic to the upper tributaries of Yangtze River in China, long-finned gudgeon fish () has been classified as endangered due to habitat destruction and population decline. In this study, we constructed a chromosome-level genome assembly of by integration of MGI, PacBio and Hi-C sequencing technologies. The final genome assembly was 1015.9 Mb in length (contig N50: 25.91 Mb; scaffold N50: 39.99 Mb), and 97.19% of the haplotypic genome sequences were anchored onto 25 chromosomes. Repetitive elements accounted for 51.00% of the entire genome assembly. A total of 23,220 protein-coding genes were predicted for the assembled genome, of which 99.79% were functionally annotated. Genome evaluation revealed 99.72% completeness for the genome assembly. Through genome-wide prediction of antimicrobial peptides (AMPs), we identified and localized 561 putative AMP-containing genes in the genome. These genes were further classified into 185 distinct functional categories based on public databases, with the top ten components of Penetratin (21.74%), Histone (5.70%), E6AP (4.09%), Scolopendin 1 (2.67%), D38 (2.31%), WBp-1 (2.13%), Defensin (2.13%), Claudin 1 (1.96%), Azurocidin (AZU1, 1.78%), and Ubiquitin (1.60%). Our data presented here provide a potential genetic resource for promoting fundamental research and wild population conservation of this endangered fish species. |
| title | Chromosome-Scale Genome Assembly and Genome-Wide Identification of Antimicrobial Peptide-Containing Genes in the Endangered Long-Finned Gudgeon Fish (). |
| url | https://pubmed.ncbi.nlm.nih.gov/41300277/ |