Chromosome-Level Genome Assembly and Annotation of the Japanese Cutlassfish (Trichiurus japonicus): A High-Quality Genomic Resource Featuring Nuclear and Mitochondrial Completeness for Future Studies

The Japanese cutlassfish (Trichiurus japonicus) is a commercially important marine species across Asia. Here, we present a high-quality, chromosome-level genome assembly generated using PacBio HiFi, Hi-C, and Nanopore ONT reads. The nuclear genome comprised 24 chromosomes with 160 scaffolds totaling 1,138 Mb, with a scaffold N50 of 47.10 Mb and an average scaffold length of 6.18 Mb. A complete mitochondrial genome of 16,796 bp was also assembled, comprising 13 protein-coding and 23 non-coding RNA (ncRNA) genes, with 99.32% sequence identity to the reference in the NCBI database. The nuclear genome encodes 26,541 protein-coding genes (median length: 7,391 base pairs) and 16,383 non-coding RNA (ncRNA) genes. The ncRNA genes account for approximately 0.1694% of the genome's total length. BUSCO analysis indicated 99.4% and 99.2% completeness against the Actinopterygii ortholog set for the genome and proteome. Functional annotation covered 98.15% of genes. Recognized repeat elements and ncRNA regions accounted for 61.10% of the nuclear genome. With high mapping rates from external datasets, this assembly offers a valuable foundation for future sequencing-based studies.