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

Abstract

Garra rufa, commonly known as doctor fish, is a small freshwater cyprinid fish recognized for its high-temperature tolerance. G. rufa is primarily known for its role in ichthyotherapy, in which it helps remove keratinized skin from human hands and feet. However, in recent years, its high-temperature tolerance has attracted attention owing to its potential use as a model for human disease research, including infectious diseases and cancer xenograft models. Despite this interest, the genomic basis underlying high-temperature tolerance remains largely unexplored, primarily because of the limited availability of genomic resources, which hinders its development as an experimental model. In the present study, a high-quality chromosome-level genome assembly of G. rufa was generated using a combination of PacBio HiFi long-read sequencing and Hi-C technology. We generated a chromosome-level genome assembly with 25 chromosomes, 1.38 Gb in total length, and scaffold N50 of 49.3 Mb. Approximately 59% of the genome comprises repetitive elements, with DNA and LTR elements being particularly abundant. In total, 27,352 protein-coding genes were annotated, of which 26,900 genes (98.3%) were functionally annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark for genome assembly and gene annotation demonstrated 94.5% and 94.7% of complete BUSCOs, respectively. We identified two heat shock transcription factor (HSF) and 239 heat shock protein (HSP)-related genes. Heat shock elements, which are HSF-binding motifs, were present within 3 kb upstream of 944 genes, with statistically significant enrichment of HSP-related genes in this set. Furthermore, molecular phylogenetic analysis and whole-genome comparisons revealed that G. rufa is evolutionarily closely related to species in the Labeoninae subfamily of the Cyprinidae family. This chromosome-level reference genome provides a valuable resource for future research aimed at elucidating the molecular mechanisms underlying high-temperature tolerance in G. rufa and establishing it as a model organism for human biomedical studies.