Programmed DNA elimination occurs during early gametogenesis in hybridogenetic hybrids from Hexagrammos genus.

Hybridogenesis is a unique type of reproduction found in hybrids, producing offspring that are partial (hemiclonal) genetic replicas of one parent. Along the southern coast of Hokkaido, Japan, two types of interspecies hybrids have been identified among three Hexagrammos species: Hexagrammos octogrammus (Hoc), H. otakii (Hot), and Hexagrammos agrammus (Hag). These hybrids are characterized by fertile females reproducing via hybridogenesis. During oogenesis of hybrids, the paternal haploid genome (Hag or Hot) is excluded, while only the maternal genome (Hoc) retains and transmits to gametes. This study investigates the mechanism of genome elimination in Hexagrammos hybrids through a comparative analysis of gonadal development in one-year-old juveniles and adult individuals of hybrids and their parental species. Comparative genomic hybridization on whole-mount gonads from Hoc/Hot and (Hoc/Hag) × Hag hybrids revealed gonocytes containing genomes of both parental species and gonocytes with only Hoc genome, suggesting that genome elimination occurs during early gametogenesis. In Hoc but not in Hot or Hag species, we observed heterochromatin foci enriched with H3K9me3 epigenetic histone modification. Similar foci were found in hybrids, confirming the presence of Hoc genome in their gonocytes. Furthermore, we detected micronuclei in the cytoplasm of gonocytes in parental species and hybrids. Although micronuclei were rare, their frequency was significantly higher in hybrids compared to parental species. Within micronuclei in Hoc/Hot and (Hoc/Hag) × Hag hybrids, we identified Hot and Hag chromosomes or their fragments, respectively. Thus, in Hexagrammos hybrids, genome elimination likely occurs during early gametogenic stages and is accompanied by micronuclei formation.