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| Main Authors: | , , , , , , , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
Scientific data
2025
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| Online Access: | https://pubmed.ncbi.nlm.nih.gov/40346083/ |
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| _version_ | 1868266206555799552 |
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| author | Kon, Tetsuo Kon-Nanjo, Koto Handayani, Kiki Syaputri Zang, Liqing Fahrurrozi, Fahrurrozi Simakov, Oleg Gultom, Victor David Nico Shimada, Yasuhito |
| author_facet | Kon, Tetsuo Kon-Nanjo, Koto Handayani, Kiki Syaputri Zang, Liqing Fahrurrozi, Fahrurrozi Simakov, Oleg Gultom, Victor David Nico Shimada, Yasuhito Kon, Tetsuo Kon-Nanjo, Koto Handayani, Kiki Syaputri Zang, Liqing Fahrurrozi, Fahrurrozi Simakov, Oleg Gultom, Victor David Nico Shimada, Yasuhito |
| collection | PubMed - marine biology |
| contents | Chromosome-level genome assembly of the doctor fish (Garra rufa). Kon, Tetsuo Kon-Nanjo, Koto Handayani, Kiki Syaputri Zang, Liqing Fahrurrozi, Fahrurrozi Simakov, Oleg Gultom, Victor David Nico Shimada, Yasuhito Animals Genome Cyprinidae Chromosomes Phylogeny Molecular Sequence Annotation Garra rufa, or doctor fish, is a small cyprinid known for its high-temperature tolerance and its use in ichthyotherapy. Recently, this trait has gained interest as a model for human diseases, including infections and cancer xenografts, though limited genomic resources hinder experimental use. In this study, we have generated a high-quality, chromosome-level genome assembly of G. rufa using PacBio HiFi long-read sequencing and Hi-C technology. The genome is 1.38 Gb in size, with 25 chromosomes and a scaffold N50 of 49.3 Mb. Approximately 59% of the genome consists of repetitive elements, while 27,352 protein-coding genes were annotated, with 98.3% being functionally characterized. BUSCO analysis revealed 94.5% and 94.7% completeness for the genome assembly and annotated protein sequences, respectively. Notably, we identified two heat shock transcription factor (HSF) genes, 239 heat shock protein (HSP)-related genes, and 1,036 heat shock elements (HSEs) in regulatory regions. Phylogenetic analysis supports the placement of G. rufa within the Labeoninae subfamily. This genome assembly provides a valuable resource for advancing G. rufa as a model organism. |
| format | Artículo científico |
| id | pubmed_40346083 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Scientific data |
| record_format | pubmed |
| spellingShingle | Chromosome-level genome assembly of the doctor fish (Garra rufa). Kon, Tetsuo Kon-Nanjo, Koto Handayani, Kiki Syaputri Zang, Liqing Fahrurrozi, Fahrurrozi Simakov, Oleg Gultom, Victor David Nico Shimada, Yasuhito Animals Genome Cyprinidae Chromosomes Phylogeny Molecular Sequence Annotation Chromosome-level genome assembly of the doctor fish (Garra rufa). Kon, Tetsuo Kon-Nanjo, Koto Handayani, Kiki Syaputri Zang, Liqing Fahrurrozi, Fahrurrozi Simakov, Oleg Gultom, Victor David Nico Shimada, Yasuhito Animals Genome Cyprinidae Chromosomes Phylogeny Molecular Sequence Annotation Garra rufa, or doctor fish, is a small cyprinid known for its high-temperature tolerance and its use in ichthyotherapy. Recently, this trait has gained interest as a model for human diseases, including infections and cancer xenografts, though limited genomic resources hinder experimental use. In this study, we have generated a high-quality, chromosome-level genome assembly of G. rufa using PacBio HiFi long-read sequencing and Hi-C technology. The genome is 1.38 Gb in size, with 25 chromosomes and a scaffold N50 of 49.3 Mb. Approximately 59% of the genome consists of repetitive elements, while 27,352 protein-coding genes were annotated, with 98.3% being functionally characterized. BUSCO analysis revealed 94.5% and 94.7% completeness for the genome assembly and annotated protein sequences, respectively. Notably, we identified two heat shock transcription factor (HSF) genes, 239 heat shock protein (HSP)-related genes, and 1,036 heat shock elements (HSEs) in regulatory regions. Phylogenetic analysis supports the placement of G. rufa within the Labeoninae subfamily. This genome assembly provides a valuable resource for advancing G. rufa as a model organism. |
| title | Chromosome-level genome assembly of the doctor fish (Garra rufa). |
| topic | Animals Genome Cyprinidae Chromosomes Phylogeny Molecular Sequence Annotation |
| url | https://pubmed.ncbi.nlm.nih.gov/40346083/ |