Genome Refinement in Pacific Bluefin Tuna (Thunnus orientalis): Chromosome-level Assembly Using Hybrid Linkage Data

Background: High-quality reference genomes are fundamental for selective breeding and genetic engineering for improving aquaculture productivity. Here, we report an improved chromosome-level genome assembly of Pacific bluefin tuna ( Thunnus orientalis ), a commercially valuable species consumed worldwide. By integrating genetic linkage information from interspecific hybrids of Euthynnus affinis and T. orientalis , we anchored and oriented T. orientalis scaffolds into 24 pseudochromosomes. Results: The updated assembly achieved a scaffold N50 of 34.19 Mb, representing a notable improvement from 13.3 Mb, and contained 22,640 predicted protein-coding genes. Conclusions: This resource provides a robust genomic foundation for future genetic and genomic studies aimed at advancing the selective breeding of T. orientalis in aquaculture.