A chromosome-level genome assembly of the scaly osman Diptychus maculatus

Diptychus maculatus, a rare cold-water cyprinid endemic to the high-altitude river systems of Xinjiang, China, has experienced range contraction and increasing conservation concern. However, the lack of a chromosome-level reference genome has limited downstream studies in conservation genomics and comparative genomics for this non-model species. Here, we present a chromosome-level genome assembly of D. maculatus generated using PacBio HiFi, Illumina short-read, and Hi-C data, with RNA-seq supporting gene annotation. The assembled genome totals 1.79 Gb with a scaffold N50 of 33.13 Mb, anchoring 90.68% (1.63 Gb) of the assembly onto 49 pseudo-chromosomes. BUSCO analysis indicates high completeness with a score of 99.30%, including 15.10% single-copy and 84.20% duplicated BUSCOs. The genome contains 44.55% (802.16 Mb) repetitive elements and encodes 60,481 predicted protein-coding genes, of which 85.66% are functionally annotated in at least one public database. Chromosome-scale synteny analysis reveals extensive collinearity between D. maculatus and Aspiorhynchus laticeps, supporting the utility of this assembly for comparative analyses within Cypriniformes. This genome assembly and associated annotations provide a valuable resource for future studies of genome evolution and conservation genomics in high-altitude freshwater fishes.