The compact genome of torafugu (Takifugu rubripes) is a useful model for annotating the vertebrate genomes. However, the currently incomplete assembly of the torafugu genome has decreased its value for genetic and genomic analyses. This is partly due to the usage of naturally heterozygous diploid genome as a starting material. Therefore, we generated mito-gynogenetic torafugu using the eggs fertilized by UV-irradiated sperm, followed by cold shock treatment. After a preliminary confirmation of homozygosity by microsatellite genotyping in one mito-gynogenetic torafugu, genome-wide single nucleotide polymorphism (SNP) analyses were employed for an accurate assessment of whole-genome homozygosity levels. SNP genotyping results indicated that the torafugu obtained through mitotic gynogenesis induction was doubled haploid. We report the first instance of assessing homozygosity levels by genome-wide SNP analyses in mito-gynogenetic fishes.
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