Chromosome-level genome assembly of masu salmon (Oncorhynchus masou masou)

Whole-genome duplication is a major evolutionary force, with salmonids providing a key model system. In this study, we generated a high-quality masu salmon genome using PacBio HiFi, ONT ultra-long and Hi-C sequencing technologies. The final phased assembly includes two haplotypes: HAP1 (2.5 Gb) and HAP2 (2.4 Gb). The contiguity of the assembly is excellent, with scaffold N50 values of 99.28 Mb (HAP1) and 98.82 Mb (HAP2). Notably, the 33 largest scaffolds in each haplotype cover over 99.6% of the genome, approaching chromosome-level scale. The genomic completeness was assessed at 98.3% (HAP1) and 97.7% (HAP2) via BUSCO analysis. Finally, we identified 41,858 and 40,970 protein-coding genes for HAP1 and HAP2, respectively. Furthermore, to enable research into reproductive strategies, we generated 90 transcriptome datasets from the semelparous masu salmon across key post-spawning time points, alongside a comparative dataset of 60 transcriptomes from the iteroparous rainbow trout. Together, these high-quality genomic and transcriptomic resources offer a powerful platform for investigating both post-WGD genome evolution and the molecular basis of semelparity in salmonids.