Chromosome-level Genome assembly and annotation of the Chirolophis japonicus

With the advancement of molecular biology and sequencing technologies, the genomes of an increasing number of fish species, ranging from model fish to many commercial species, have been sequenced and made publicly available. Thus, this has provided deep insights into accelerating our understanding of various aspects, including species evolution, parallel evolution, molecular regulatory mechanisms, and genetic breeding. Chirolophis japonicus is an economically important fish and is distributed in the cold waters of the northwest Pacific Ocean. This study provided a chromosome-level genome of C. japonicus using PacBio HiFi long-reads, Hi-C data and MGI short-reads. The C. japonicus genome was successfully assembled to a size of 623.67 Mb, with a contig N50 of 23.17 Mb, and a scaffold N50 of 23.77 Mb. It was anchored onto 28 chromosomes. The assembly completeness estimated by the BUSCO method was 99.42%. The repetitive elements accounted for 29.13% (118.67 Mb), primarily consisting of 26.64% transposable elements. We further predicted a total of 23,893 protein-coding genes, of which 23,550 were successfully annotated. In conclusion, the chromosome-level genome of Chirolophis japonicus will provide a valuable genomic resource for further aquaculture, genetic breeding and molecular mechanisms underlying its uniquely cold-tolerant traits.