Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae

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

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.

Comparative mitogenomic analysis of Chinese cavefish Triplophysa (Cypriniformes: Nemacheilidae): novel gene tandem duplication and evolutionary implications

BACKGROUND

Cavefish exhibit significant morphological changes that result in trade-offs in metabolic requirements and energy utilization in perpetual darkness. As cellular "powerhouses", mitochondria play crucial roles in energy metabolism, suggesting that mitochondrial genes have likely experienced selective pressures during cavefish evolution.

RESULTS

This study presents the first assembly of the complete mitogenome of Triplophysa yangi, a typical cavefish species in China. The mitogenome is 17,068 bp long, marking the longest recorded for the genus Triplophysa, and includes 13 protein-coding genes (PCGs), 2 rRNAs, 25 tRNAs, and a noncoding control region. An ~ 500 bp insertion between ND2 and WANCY regions was observed, comprising a large intact tandem repeat unit (A'-N'-OL'-C') flanked by two unannotated sequences (U1/U2). The evolutionary origin of this repeat unit may involve either in situ duplication events with subsequent functional divergence-where neofunctionalization, subfunctionalization, or pseudogenization drove differential mutation rates between paralogs-or alternatively, horizontal acquisition from exogenous genetic material that became functionally integrated into the ancestral T. yangi mitogenome through co-option mechanisms. Phylogenetic analyses revealed two major clades within Triplophysa-epigean and hypogean lineages-consistent with previous classifications, while cave-restricted species exhibited signs of parallel evolution within the hypogean lineage. Selective pressure analysis indicated that the hypogean lineage (cave-dwelling groups, II & III) have a significantly increased ratio of nonsynonymous to synonymous substitution rates (ω) compared to the epigean lineage (surface-dwelling group, I), suggesting a combination of adaptive selection and relaxed functional constraints in cave-dwelling species.

CONCLUSIONS

The duplication of tRNAs in T. yangi and the potential positive selection sites identified in Triplophysa cavefish further indicated adaptive evolution in mitochondrial PCGs in response to extreme subterranean conditions.

Potential of Garra rufa as a novel high-temperature resistant model fish: a review on current and future approaches

Garra rufa, commonly known as the "doctor fish", is a freshwater cyprinid native to warm regions of the Middle East. Since the late twentieth century, it has been widely utilized in spas for alternative therapeutics and fish pedicures (or manicures) for dermatological diseases such as psoriasis and eczema. Owing to its unique characteristics, there is growing interest in exploring various applications of G. rufa. This review provides a comprehensive summary of the phylogenetic position, ecology, biological characteristics, and breeding methods of G. rufa, and provides insights into its use as a therapeutic fish. Notably, the ability of G. rufa to thrive in high-temperature environments exceeding 37 °C distinguishes it from other cyprinids and suggests its potential as a model for human diseases, such as human infectious diseases, and in use in cancer xenograft models for high-throughput drug screening. The ongoing genome sequencing project for G. rufa aims to elucidate the mechanisms underlying its high-temperature tolerance and offers valuable genomic resources. These efforts have resulted in significant advances in fish aquaculture, species conservation, and biomedical research.

The Mitochondrial Genome of Linichthys laticeps (Cypriniformes: Cyprinidae): Characterization and Phylogeny

Mitochondrial genomes (mitogenomes) have been widely used in phylogenetic analysis and evolutionary biology. The Labeoninae is the largest subfamily of Cypriniformes and has great economic importance and ecological value. In this study, we sequenced, annotated, and characterized the complete mitogenome of Linichthys laticeps and then constructed the phylogenetic tree with previously published Labeoninae mitogenomes. The mitogenome of L. laticeps was 16,593 bp in length, with an A + T content of 57.1%. The mitogenome contained a standard set of 37 genes and a control region with the same order and orientation of genes as most fish mitogenomes. Each protein-coding gene (PCG) was initiated by an initial ATG codon, excluding COI, that began with a GTG codon. Furthermore, most of the PCGs were terminated by a conventional stop codon (TAA/TAG), while an incomplete termination codon (TA/T) was detected in 7 of the 13 PCGs. Most tRNA genes in L. laticeps were predicted to fold into the typical cloverleaf secondary structures. The Ka/Ks (ω) values for all PCGs were below one. The phylogenetic relationships of 96 Labeoninae mitogenomes indicated that Labeoninae was not a monophyletic group and L. laticeps was closely related to the genera Discogobio and Discocheilus. Overall, our study provided the first complete annotated mitogenome of L. laticeps, which filled a knowledge gap in Labeoninae and extended the understanding of the taxonomy and mitogenomic phylogeny of the subfamily Labeoninae.