Abstract
Troglonectes daqikongensis is an obligate cave-dwelling fish with a narrowly restricted distribution in southwestern China and pronounced troglomorphic traits. Despite its ecological and evolutionary significance, genomic resources for this species remain scarce. Here, we report a chromosome-level reference genome of Troglonectes daqikongensis, assembled using PacBio HiFi long reads, Hi-C data, and MGI T7 short reads. The final assembly spans 615.17 Mb across 47 scaffolds, with a contig N50 of 20.92 Mb and a scaffold N50 of 23.57 Mb. In total, 97.96% of the assembly was anchored to 25 pseudo-chromosomes. Repetitive elements comprise 276.51 Mb, accounting for 44.95% of the genome. A total of 24,652 protein-coding genes were predicted using a combination of de novo prediction, homology-based annotation, and transcriptome evidence, with 99.89% functionally annotated. BUSCO assessments indicated high completeness for both the genome assembly (96.6%) and gene annotation (95.5%). This high-quality genome provides a foundational resource for evolutionary and ecological research, including studies on the genetic basis of cave adaptation and the conservation of the microendemic species Troglonectes daqikongensis.