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<p><i>Garra rufa</i>, 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 <i>G. rufa</i> using PacBio HiFi long-read sequencing and Hi-C technology. The genome is 1.38 Gb&#xa0;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 <i>G. rufa</i> within the Labeoninae subfamily. This genome assembly provides a valuable resource for advancing <i>G. rufa</i> as a model organism.</p>

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Chromosome-level genome assembly of the doctor fish (Garra rufa)

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年5月9日

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  • Tetsuo Kon,
  • Koto Kon-Nanjo,
  • Kiki Syaputri Handayani,
  • Liqing Zang,
  • Fahrurrozi Fahrurrozi,
  • Oleg Simakov,
  • Victor David Nico Gultom,
  • Yasuhito Shimada

摘要

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.