A Chromosome-Level Genome Assembly Identifies the Origin of Neo-Y Chromosome to the Unique X 1 X 2 Y System

The barred knifejaw, Oplegnathus fasciatus (Teleostei: Centrarchiformes Oplegnathidae), is an important species in marine cage culture and fish stocking for marine ranching in East Asia. The males of Oplegnathidae (O. fasciatus and O. punctatus) species are characterized by an X1X2Y system with a neo-Y chromosome based on male karyotype analyses. Release of the chromosome-level reference genome of female O. fasciatus has facilitated insights into the origin of the unique X1X2Y system of male O. fasciatus. In the present study, we applied PacBio long-read sequencing and high-throughput chromosome interaction mapping (Hi-C) to assemble a chromosome-level genome of male O. fasciatus. A highly contiguous genome with a size of 795 Mb, 2,295 contigs, and a contig N50 of 2.13 Mb was obtained. The 1,355 ordered contigs combined with the draft genome were further assembled into 23 chromosomes approximately 762 Mb in length with a contig N50 of 2.18 Mb and a scaffold N50 of 32.43 Mb. A large neo-chromosome (Ch9) of 94.2 Mb was assembled from 444 contigs, and found to be more than three times larger than the rest chromosomes of male O. fasciatus. In addition, 63.4 Mb of the Ch9 sequences of male O. fasciatus had high identity (~99.0%) to the Ch8 (31.4 Mb/37.5 Mb) and Ch10 (32.0 Mb/35.3 Mb) sequences of female O. fasciatus based on a whole-genome synteny analysis, showing that the neo-Y chromosome shared significant homology with Ch8 and Ch10 based on male/female genome comparison. Significant fission tracks at the terminal point of the chromosomes were also identified between Ch9 and Ch8/Ch10 using synteny analyses, which showed chromosome rearrangements events had happened in the neo-chromosome Ch9. Our present results accurately demonstrated that the X1X2Y system of male O. fasciatus originated from the fusions of the non-homologous chromosomes Ch8 and Ch10. According to the synteny analyses and previous karyotypes results, which characterized acrocentric chromosomes, we suggested that a centric fusion of Ch8 and Ch10 was responsible for the formation of the X1X2Y system of male O. fasciatus.