Chromosome-Level Genome Assembly of Red Sea Bream (Pagrus major) Reveals Integration of Heterospecific Sperm-Derived Genetic Material in Artificial Gynogenesis

Artificially induced gynogenesis, a technique that utilizes UV-irradiated sperm to activate eggs while excluding paternal genetic contribution, has been instrumental in the genetic improvement of aquaculture species. Although the allo-sperm effect has been observed in some freshwater fish and suggests the integration of paternal DNA, its occurrence and mechanisms in marine fish remain unclear. In this study, a 795.23 Mb chromosome-level genome assembly for red sea bream (<i>Pagrus major</i>) was presented, with a scaffold N50 of 32.03 Mb, encompassing 29,083 protein-coding genes. Furthermore, the allo-sperm effect was investigated on the artificial gynogenesis of Japanese flounder (<i>Paralichthys olivaceus</i>) induced by UV-irradiated <i>P. major</i> sperm. Whole-genome sequencing of gynogenetic and normal fertilized offspring revealed eight representative genomic sequences with >96.88% nucleotide identity to <i>P. major</i>, including six Sparidae-specific centromeric satellite DNA sequences. PCR validation and Sanger sequencing confirmed that these sequences were present exclusively in gynogenetic groups and absent in normally fertilized offspring, providing direct evidence of the allo-sperm effect. Our findings extend the allo-sperm effect to marine fish and demonstrate its potential across taxonomically distant taxa, <i>P. olivaceus</i> (Pleuronectiformes) × <i>P. major</i> (Spariformes). These results offer valuable genomic information for <i>P. major</i>, and provide important insights for future genetic breeding programs in aquaculture.