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

雌雄异株——由单独的雄性和雌性个体组成的植物种群——发生在大约6%的开花植物物种中，并且已经反复进化。在至少39个物种和17个开花植物科中，雌雄异株的进化与称为同种异体的特殊染色体的进化有关。然而，对于导致植物同种异体进化的基因组变化，或者这些染色体形成后发生的基因组变化，人们知之甚少。本研究将探讨花园芦笋（asparagus officinalis）在1-2百万年的分化过程中同种异体的起源和随后的基因组变化。通过跟踪相关芦笋物种中等效染色体上基因的进化，本研究将阐明同种异体是如何进化的，以及这一过程如何可能导致同种异体对中一条染色体的退化。这项研究将训练一名研究生，学习不同的系统方法，并指导本科生学习下一代测序方法、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网站广泛而自由地传播给研究人员。该项目还将为芦笋育种者提供分子标记，从而显著改善作物。芦笋是研究异位体从祖先常染色体进化的影响因素的理想物种。理论预测，同种异体在植物中的起源涉及到至少两个基因之间重组停止的选择：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花园芦笋基因组的非重组y连锁区域，并暗示该区域内的单个y连锁基因是雄花雌蕊发育的抑制因子。本研究将使用目标序列捕获来研究该基因在超过一半的芦笋物种中的进化，包括雌雄同体和雌雄异株分类群。同时，利用单拷贝基因，利用聚结法重建芦笋属植物的分子系统发育。由此产生的系统发育将为旨在重建祖先同种异体基因含量的比较基因组分析提供历史背景，并验证促进雄蕊发育的基因突变有助于常染色体起源的预测。

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.