银杏性染色体进化阶段的确定及进化驱动力研究

性别决定机制和性染色体进化是进化生物学的核心研究主题，重组抑制和基因退化是性染色体早中期进化的关键过程。植物性染色体起源时间跨度较大，多数较年轻，更适合研究其早期进化和时序过程。但植物性染色体研究案例仍极少且集中于被子植物中进化初期阶段的性系统，缺少起源更早的性系统进化机制的研究。本项目在前期鉴定了银杏X染色体上性别决定区域和3个进化断层且起源时间至少72mya的基础上，拟采用双亲本PacBio HiFi测序+F1代雄株stLFR测序的策略，获得高质量雄性基因组，评估重组抑制规模和基因退化程度，确定进化阶段；通过检验背景选择、米勒齿轮效应、遗传漂移、垃圾里的红宝石假说，阐明银杏Y染色体退化机制。本研究不仅可增进对银杏和裸子植物性染色体进化和性别决定机制的理解，还为陆地植物性系统进化提供了起源较早的案例，是连接被子植物与苔类植物的关键一环，从而促进植物性系统进化时序过程和平行进化机制的比较。

Sex determination mechanisms and sex chromosome evolution are central themes of evolutionary biology. Recombination suppression and gene degeneration play key roles in the origin and early evolution of sex chromosomes. Unlike animals, whose sex-determination systems have been well-studied and are known to be ancient, plants appear to have sex-determination systems evolved independently at different evolutionary times, allowing study of the time course of events in the evolution of sex chromosomes. However, hitherto limited empirical studies on plant sex chromosome evolution were focused on initial and early stages when recombination has not massively developed let alone gene degeneration. In our previous study, a ~4 Mb sex-determination region with three evolutionary strata were identified on the X chromosome of Ginkgo biloba, which was originated at least 72 mya older than all known ages of plant chromosomes. We propose to address recombination suppression and gene degeneration of ginkgo's sex chromosomes based on assembling a high-quality Y chromosome genome using on the strategy of Trio binning, i.e., sequencing parents using the PacBio HiFi platform and sequencing male F1 hybrid using the stLFR approach. Four hypotheses, i.e., background selection, Muller rachet, genetic hitchhiking and “a ruby in the rubbish”, will be statistically tested to elucidate the evolutionary forces driving gene degeneration. Our results will not only gain novel insights into sex chromosome evolution of ginkgo and gymnosperm, but provide a key node on the tree of sex linking both older and younger sexual system, as well as linking both angiosperms and liverworts. Such a comparison will ultimately lead to a comprehensive understanding of the time course and convergence of sex chromosome evolution in plants.