Chromosome-Level Genome Reveals the Origin of Neo-Y Chromosome in the Male Barred Knifejaw Oplegnathus fasciatus

The barred knifejaw, Oplegnathus fasciatus, is characterized by an X(1)X(2)Y system with a neo-Y chromosome for males. Here, a chromosome-level genome was assembled to investigate the origin of neo-Y chromosome to the male O. fasciatus. Twenty-three chromosomes corresponding to the male karyotypes were scaffolded to 762-Mb genome with a contig N50 length of 2.18 Mb. A large neo-Y chromosome (Ch9) in the male O. fasciatus genome was also assembled and exhibited high identity to those of the female chromosomes Ch8 and Ch10. Chromosome rearrangements events were detected in the neo-chromosome Ch9. Our results suggested that a centric fusion of acrocentric chromosomes Ch8 and Ch10 should be responsible for the formation of the X(1)X(2)Y system. The high-quality genome will not only provide a solid foundation for further sex-determining mechanism research in the X(1)X(2)Y system but also facilitate the artificial breeding aiming to improve the yield and disease resistance for Oplegnathus.