DISSERTATION RESEARCH: The genomic basis of dioecy in Asparagus (Asparagaceae)

植物种群由单独的雄性和雌性个体组成，估计在6%的开花植物物种中发生，并不断进化。在至少39个物种和17个开花植物科中，异源染色体的进化与称为异源染色体的特化染色体的进化有关。然而，人们对导致植物中异源体进化的基因组变化或这些染色体形成后发生的基因组变化知之甚少。 这项研究将调查花园芦笋（芦笋）在1- 200万年的分化过程中异染色体的起源以及随后的基因组变化。通过跟踪相关芦笋物种中等同染色体上基因的进化，这项研究将阐明异源染色体是如何进化的，以及这个过程如何导致异源染色体对中一条染色体的退化。 该研究将导致一名研究生在不同的系统方法的培训，并指导本科生在下一代测序方法，荧光显微镜和生物信息学。 这项研究产生的计算机代码和分析管道将通过开放访问的网站向研究人员广泛和免费传播。该项目还将为芦笋育种者提供分子标记，从而可能导致显著的作物改良。芦笋是研究影响从祖先常染色体进化为异染色体的因素的理想物种。理论预测，植物中的异源体的起源涉及选择停止至少两个基因之间的重组：一个抑制雌蕊的形成，另一个促进雄蕊的形成。然而，这一预测尚未得到实证检验。最近的工作已经确定了非重组的Y-连锁区的花园芦笋基因组，并暗示在这个区域内的一个单一的Y-连锁基因作为抑制雌蕊发育雄花。这项研究将使用有针对性的序列捕获来调查该基因在超过一半的芦笋物种中的进化，包括两性和雌雄异株的类群。与此同时，将采用合并的方法，使用单拷贝基因重建芦笋属的分子遗传学。由此产生的同源性将提供一个历史背景下的比较基因组分析，旨在重建基因内容的祖先的异体染色体和测试的预测，促进雄蕊发育的基因突变有助于常染色体的起源。

Dioecy -- where plant populations are comprised of separate male and female individuals -- occurs in an estimated 6% of flowering plant species and has evolved repeatedly. In at least 39 species and 17 flowering plant families, the evolution of dioecy is linked to the evolution of specialized chromosomes called allosomes. However, little is known about the genomic changes that result in the evolution of allosomes in plants, or the genomic changes that occur after the formation of these chromosomes. This research will investigate the origin of allosomes and the subsequent genomic changes during 1-2 million years of divergence in garden asparagus (Asparagus officinalis). By tracking the evolution of genes on equivalent chromosomes in related Asparagus species, this research will elucidate how allosomes have evolved, and how this process may be contributing to the degeneration of one chromosome within the allosome pair. The research will result in the training of one graduate student in diverse systematic methods, and the mentoring of undergraduate students in next-generation sequencing methods, fluorescent microscopy, and bioinformatics. Computer code and analysis pipelines resulting from this research will be disseminated broadly and freely to researchers through open-access websites. The project will also provide asparagus breeders with molecular markers that could lead to significant crop improvements.Asparagus officinalis is an ideal species to investigate factors influencing the evolution of allosomes from ancestral autosomes. Theory predicts that the origin of allosomes in plants involves selection for cessation of recombination between at least two genes: one suppressing the formation of pistils and another promoting the formation of stamens. This prediction, however, has not yet been empirically tested. Recent work has identified non-recombining Y-linked regions of the garden asparagus genome and implicated a single Y-linked gene within this region as a suppressor of pistil development in male flowers. This research will use targeted sequence capture to investigate the evolution of this gene across more than half of Asparagus species, including both hermaphroditic and dioecious taxa. At the same time, coalescent methods will be employed to reconstruct a molecular phylogeny for the Asparagus genus using single copy genes. The resulting phylogeny will provide a historical context for comparative genomic analyses aimed at reconstructing gene content in the ancestral allosomes and testing the prediction that mutations in genes promoting stamen development contributed to the origin of autosomes.