High-quality genome assembly and annotation of the white-cheeked goby, Rhinogobius duospilus (Herre, 1935)...

The white-cheeked goby (Rhinogobius duospilus) is a small stream-dwelling fish endemic to southern China and Vietnam. With a sucker-like modified pelvic fin that helps it cling to substrate in fast-flowing water and vibrant breeding colors in males, R. duospilus is particularly appealing to aquarium enthusiasts. To investigate its distribution patterns, evolutionary history, and molecular adaptations to local environments, a high-quality genome assembly is critically needed. By employing PacBio HiFi sequencing combined with Hi-C-assisted assembly technology, we successfully obtained a chromosome-level genome assembly of R. duospilus. The final assembly yielded a genome size of 1,031.61 Mb with a scaffold N50 of 45.55 Mb. Approximately 991.84 Mb of genomic sequence was anchored onto 22 chromosome pairs. Benchmarking Universal Single-Copy Orthologs assessment indicated high genome completeness at 96.14%. Through gene prediction and functional annotation, we identified 24,418 protein-coding genes, with 23,660 (96.8%) successfully annotated. This work presents the first high-quality reference genome for R. duospilus, creating an essential genomic resource for investigating population differentiation and adaptive evolution through comparative genomics. Additionally, this dataset provides valuable support for taxonomy, evolution, and conservation genetics of genus Rhinogobius.