Transcriptome evolution and whole genome duplication

开花植物的基因组(总细胞DNA)，包括所有作物物种，经历了多轮全基因组复制(WGD，多倍体)。复制基因的可获得性，再加上WGD事件后广泛的基因组重塑，导致了一系列新的特征。显然，基因表达介导了许多这些反应，而对基因剂量的选择可能会推动基因家族和网络的进化。然而，令人惊讶的是，人们对基因组复制如何影响单个基因表达或整个转录组(给定组织中基因组中所有基因的组合表达)知之甚少。该项目将使用一套新的方法来估计整个转录组的大小，并分析整个基因组对WGD的响应基因的表达变化。为了确定基因组复制对基因表达的直接和长期影响，我们将研究几种合成的和最近形成的天然多倍体及其二倍体祖先。该项目具有广泛的意义和影响，因为在基因组水平上量化剂量反应将澄清我们对基因剂量选择如何塑造植物进化的理解，从而导致具有农业重要性的物种的重要性状，如大豆，其近亲是该项目的目标。此外，该项目为本科生参与研究的机会提供资金，并促进主要研究型大学(康奈尔大学)和仅限本科生的机构(里德学院)之间的科学合作。

The genomes (total cellular DNA) of flowering plants, including all crop species, have undergone multiple rounds of whole genome duplication (WGD, polyploidy). The availability of duplicated genes, combined with extensive genome remodeling that follows WGD events, gives rise to a wide range of novel traits. It is clear that gene expression mediates many of these responses, and selection on gene dosage may drive gene family and network evolution. Yet surprisingly little is known about how genome duplication affects individual gene expression or the entire transcriptome (the combined expression of all genes in the genome in a given tissue). This project will use a suite of novel approaches to estimate whole transcriptome size and to assay expression changes of genes across the genome in response to WGD. Several synthetic and recently formed natural polyploids and their diploid progenitors will be studied in order to determine both the immediate and longer-term effects of genome duplication on gene expression. This project is of broad significance and impact because quantifying dosage responses on a genomic scale will clarify our understanding of how selection on gene dosage has shaped plant evolution, leading to important traits in species of agricultural importance, such as soybean, whose close relatives are the targets of this project. In addition, the project funds opportunities for undergraduates to participate in the research, and facilitates scientific collaboration between a major research university (Cornell) and an undergraduate-only institution (Reed College).