A study of a Chromosome-level Genome Assembly and the Origin of Neo-Y Chromosome to the X1X2Y System in the Male Barred knifejaw Oplegnathus fasciatus. Xiao et al.

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 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 and scaffold N50 length of 2.18 and 32.43 Mb, respectively. 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 in O. fasciatus genome. In addition, 63.1 Mb of the Ch9 sequences of male O. fasciatus had high identity (~99.0%) to the Ch8 and Ch10 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 acrocentric chromosomes Ch8 and Ch10 was responsible for the formation of the X1X2Y system of male O. fasciatus.

条纹石鲷（*Oplegnathus fasciatus*，辐鳍鱼纲：日鲈目，石鲷科）是东亚地区海水网箱养殖与海洋牧场增殖放流的重要经济物种。石鲷科物种（包括条纹石鲷与斑石鲷*O. punctatus*）的雄性核型分析显示，其性别决定系统为X1X2Y型，且存在新Y染色体（neo-Y chromosome）。条纹石鲷雌性染色体水平参考基因组的发布，为解析雄性条纹石鲷X1X2Y性别决定系统的起源提供了重要支撑。

本研究采用PacBio长读长测序（PacBio long-read sequencing）与高通量染色体构象捕获（Hi-C）技术，组装获得了雄性条纹石鲷的染色体水平基因组。最终得到连续性极佳的组装结果：基因组总长度为795 Mb，包含2295条重叠群（contig），重叠群N50为2.13 Mb。随后将1355条已排序的重叠群与草图基因组进一步组装，获得了23条染色体，总长度约762 Mb，重叠群N50与支架（scaffold）N50分别为2.18 Mb与32.43 Mb。

研究组装得到一条长度为94.2 Mb的大型新染色体（Ch9），由444条重叠群构成，其长度约为条纹石鲷基因组中其余染色体的3倍以上。此外，全基因组共线性分析（synteny analysis）显示，雄性条纹石鲷Ch9序列中有63.1 Mb的区域与雌性条纹石鲷Ch8、Ch10序列的相似度高达约99.0%，表明通过雌雄基因组比对可知，该新Y染色体与Ch8、Ch10存在显著的同源性。同时，共线性分析还在Ch9与Ch8/Ch10之间的染色体末端区域发现了显著的断裂痕迹，证实新染色体Ch9发生了染色体重排事件。

本研究结果明确证实，雄性条纹石鲷的X1X2Y性别决定系统起源于非同源染色体Ch8与Ch10的融合。结合本次共线性分析结果与此前以近端着丝粒染色体（acrocentric chromosomes）为特征的核型研究结论，我们推测Ch8与Ch10这两条近端着丝粒染色体的着丝粒融合，是雄性条纹石鲷X1X2Y性别决定系统形成的根本原因。