Chromosome-level genome assembly of Trichiurus japonicus resolves species boundaries and evolutionary history of cutlassfishes in Northwest Pacific.

Persistent taxonomic uncertainty has plagued the Trichiuridae family (hairtails), a group of ecologically and commercially significant fishes, a result of conflicting morphological criteria and historical misclassifications. While molecular approaches have advanced understanding their taxonomy, mitochondrial-based analyses and misapplied nomenclature have obscured species boundaries and population dynamics. Here, we integrate a chromosome-level genome assembly of Trichiurus japonicus with whole-genome resequencing of congeneric species to resolve the taxonomic ambiguity in Trichiurus. Combining phylogenomic, demographic, and population genetic analyses, we resolve taxonomic uncertainties by redefining species boundaries, reconstructing population dynamics, and identifying genomic divergence between populations. Our analyses suggest that T. japonicus and T. nanhaiensis are distinct species. Crucially, we identify a cryptic, genetically distinct lineage putatively derived from the Indian Ocean, misclassified as T. lepturus in previous studies, underscoring the impact of commercial trade on taxonomic confusion. Our analyses reveal low spatial genetic differentiation in T. japonicus across the sampled Northwest Pacific localities, consistent with weak population structure within our sampling frame. This study establishes a genomic framework of Trichiurus to resolve taxonomic conflicts in morphologically cryptic taxa and advances strategies for sustainable fisheries management under climate change.