Comparative genomic and functional approaches for investigating biology and evolution of heterotrophic plants

一些植物从普通的绿色植物那里偷取营养和/或水，结果减少或完全失去了光合作用的能力。我们研究了各种所谓的异养植物（通常称为寄生植物）的质体基因组以及它们与其他植物基因组的相互作用。对整个营养谱上的质体进行比较分析，从自养到混合养再到完全异养，将使我们能够评估在光合作用完全丧失之前基因组变化的程度，并剖析质体代谢功能对质体施加的进化压力。许多异养植物群是从它们各自的光合亲戚中分离出来的。我们在这个提议中利用的基本思想是，每一个异养生物谱系都代表了一个独立的自然遗传实验，其质体和基因在宽松的功能约束下进化，因此，每一个都代表了研究基因组功能和进化的独特机会。鉴于逆向遗传方法在这一系统中的困难甚至不可能，对多种天然质体“突变体”的研究将有助于我们更深入地了解光合作用及其分子组成及其相互作用。我们将对异养植物及其自养近亲的细胞器基因组内容、序列和表达模式进行广泛的研究，以便最终能够整合基因组、功能和进化数据。这将通过对大量异养植物的转录组和/或全基因组进行测序，比较在进化上不同的群体中发现的结果，并在一个确定的历史背景下进行。这些新的下一代测序数据将使我们能够测试一些预测，即一些基因组变化先于完全异源性的进化，质体的减少方式是有限的，以及确定质体进化的模式是渐进的还是逐步的（间断的）。这项研究将补充正在密切相关领域进行的其他研究，并将影响基因组学、分子进化、基因工程、生理学和分类学等领域。

Some plants steal nutrients and/or water from regular green plants and consequently have reduced or completely lost their ability to photosynthesize. We study plastid genomes in a variety of these so-called heterotrophic plants (commonly known as parasitic plants) as well as their interaction with other plant genomes. Comparative analyses of the plastomes along the full trophic spectrum, from autotrophy to mixotrophy to full heterotrophy, will allow us to assess the degree to which genomic changes take place prior to complete loss of photosynthesis, and to dissect the evolutionary pressures on plastomes exerted by other plastid metabolic functions. Many groups of heterotrophic plants arose separately from their respective photosynthetic relatives. The basic idea we take advantage of in this proposal is that each of those lineages of heterotrophs represents an independent natural genetic experiment whose plastids and genes have evolved under relaxed functional constraints and therefore, each represents a unique opportunity to study genome function and evolution. Given the difficulties or even the impossibility of reverse genetic approach in this system, study of multiple natural plastid "mutants" will contribute to our deeper understanding of photosynthesis, its molecular components, and their interaction.       We will conduct an extensive study of organellar genome content, sequence, and expression patterns in heterotrophic plants and their closest autotrophic relatives in order to ultimately be able to integrate genomic, functional, and evolutionary data. This will be achieved by sequencing transcriptomes and/or whole genomes in a large number of heterotrophic plants, comparison of results found in evolutionarily distinct groups, and doing so in a well-established historical context. These new next-generation sequencing data will allow us to test the predictions that some genomic changes precede the evolution of full-blown heterotrophy, that there are limits to how reduced plastomes can be, as well as to ascertain whether the patterns of plastome evolution are gradual or stepwise (punctuated). This investigation will complement other studies being performed in closely related areas and will impact the fields of genomics, molecular evolution, genetic engineering, physiology, and systematics.