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

论文研究：芦笋（天门冬科）雌雄异体的基因组基础

• 批准号: 1501589
• 负责人: James Leebens-Mack
• 金额: $ 1.93万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2016-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1501589&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; genomic; basis; dioecy

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.

雌雄异株——植物种群由不同的雄性和雌性个体组成——估计有 6% 的开花植物物种存在，并且已经反复进化。在至少 39 个物种和 17 个开花植物科中，雌雄异体的进化与称为异体的特殊染色体的进化有关。然而，人们对导致植物异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 (Asparagus officinalis) 在 1-200 万年的分化过程中异体的起源以及随后的基因组变化。通过追踪相关芦笋物种中等效染色体上基因的进化，这项研究将阐明异体是如何进化的，以及这个过程如何导致异体对中一条染色体的退化。 该研究将对一名研究生进行多种系统方法的培训，并在下一代测序方法、荧光显微镜和生物信息学方面指导本科生。 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免费地传播给研究人员。该项目还将为芦笋育种者提供可能导致作物显着改良的分子标记。芦笋是研究影响祖先常染色体异体进化因素的理想物种。理论预测，植物中异体的起源涉及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。这项研究将使用靶向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的分类群。同时，将采用合并方法使用单拷贝基因重建芦笋属的分子系统发育。由此产生的系统发育将为比较基因组分析提供历史背景，该分析旨在重建祖先异体中的基因内容，并测试促进雄蕊发育的基因突变促成常染色体起源的预测。