Chromosome-level genome assembly of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes)

Chirolophis japonicus is notable for its slender body and distinctive fringed head projections, features that help it camouflage among rocky reefs and make it an ecologically intriguing species in cold-temperate seas. Here, we report the first chromosome-level genome of C. japonicus by combining PacBio HiFi, Hi-C, and Illumina short reads. The genome size was 617.85 Mb, with repetitive content of 38.74% and contig N50 of 9.70 Mb. About 98.51% of genomic sequences were anchored onto 28 chromosomes, including six chromosomes with both telomeres and 17 chromosomes with one-end telomeres. A total of 22,165 protein-coding genes were predicted, of which 98.39% were functionally annotated. The genomic quality was further confirmed by Merqury with an average consensus quality value (QV) of 45.26 and the Benchmarking Universal Single-Copy Orthologs (BUSCO) value of 98.65%. The availability of the chromosome-level C. japonicus genome will provide a foundation for detailed analyses of population genetics, adaptation, and conservation biology, thereby filling a critical knowledge gap in the genomic resources for this species.