Chromosome-level genome assembly and annotation of the Rhinogobio ventralis, an endangered endemic fish from the Yangtze River

Rhinogobio ventralis, a critically endangered freshwater fish endemic to the upper Yangtze River, holds significant ecological and economic value. Here, we present a high-quality chromosome-level genome assembly of R. ventralis. Using a combination of PacBio HiFi long-read sequencing (>99% single-read accuracy), DNBSEQ-T7 short-read sequencing (95.7% of bases ≥ Q30), and Hi-C scaffolding, we assembled a 1,039.34 Mb genome comprising 478 contigs with a contig N50 of 18.1 Mb. Hi-C data anchored 97.9% of the assembled sequence onto 25 chromosomes. The final assembly is highly complete (BUSCO completeness 96.6%) and accurate (QV 48.22). Repetitive elements account for 63.44% of the genome, with DNA transposons alone representing 42.31%. We predicted 23,246 protein-coding genes, of which 98.6% have functional annotations. This high-quality genome assembly provides a valuable resource for future studies on the genetics, adaptive evolution, and conservation of R. ventralis and other endangered freshwater fishes.