Chromosome-level genome assembly and annotation of the schizothoracine fish Gymnodiptychus pachycheilus

Abstract Gymnodiptychus pachycheilus, a specialized schizothoracinae fish, exhibits remarkable morphological regression, such as near-complete scale loss, making it an important model for understanding the genomic basis of adaptation and phylogeny in this lineage. Here, we assembled a high-quality chromosome-level reference genome of G. pachycheilus by Illumina short reads, PacBio HiFi long reads, and Hi-C technologies. The final genome assembly spans 1.83 Gb, with 95.52% of the sequences anchored onto 25 pseudochromosomes, a contig N50 of 71.36 Mb, and a BUSCO completeness of 98.40%. Repetitive sequences accounted for 47.75% of this genome. We predicted 48,952 protein-coding genes, of which 92.51% were functionally annotated using multiple public databases, together with diverse classes of non-coding RNAs. This genome assembly represents the first high-quality reference for G. pachycheilus and provides a valuable resource for exploring genome evolution, rediploidization processes, and adaptive mechanisms of schizothoracinae fishes on the Qinghai-Tibet Plateau.