Sinocyclocheilus jii isolate:YN-Cave01 Genome sequencing

Sinocyclocheilus jii belongs to the genus Sinocyclocheilus (subfamily Barbinae). It is endemic to China and represents a typical cave-dwelling fish species. The genus Sinocyclocheilus exhibits remarkable species diversification, making it the largest genus within the family Cyprinidae in China and the most species-rich cavefish group globally. However, the lack of genomic resources has hindered our understanding of its genetic basis, phylogenetic position, and adaptive evolutionary strategies.Here, we assembled a chromosome-level reference genome for Sinocyclocheilus jii by integrating PacBio HiFi long-reads, Illumina short-reads, and Hi-C sequencing data. The genome size is 1.75 Gb, with a contig N50 of 35.0 Mb. Using Hi-C data, 99.3% of the assembled sequences were anchored onto 50 chromosomes. The current genome assembly contains 855.5 Mb of repetitive sequences and 52,867 protein-coding genes, of which 26,929 were functionally annotated.This study provides valuable insights into the phylogeny and evolutionary history of Sinocyclocheilus, as well as the genetic basis of adaptive strategies and specialized traits in Sinocyclocheilus jii.