Comparative and functional genomics of non-photosynthetic plants

一些植物从普通绿色植物中窃取养分和/或水分，因此降低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)中的叶绿体基因组，目的是回答核心问题：叶绿体基因组是否会完全消失，或者特定的基因是否必须保留在这个基因组中？对从自养到混合营养再到完全异养的全营养范围内的质体进行比较分析，将使我们能够评估在光合作用完全丧失之前基因组发生变化的程度，并剖析其他叶绿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作用亲缘植物中分离出来的。我们在这一提议中利用的基本思想是，每一种异养细胞都代表着一个独立的自然遗传实验，其质体和其他基因组是在放松的功能约束下(共同)进化的。每一种谱系都采用了一套独特的表达基因，因此代表了“解构”复杂的核-细胞器代谢途径的一种解决方案。鉴于反向遗传方法在这个系统中的困难甚至是不可能的，复制多个天然叶绿体突变体的研究将有助于我们从更深的机制上理解光合作用、其分子组成及其相互作用。*我们将对异养植物及其最近的自养亲缘植物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中的转录本和/或整个基因组进行测序，比较在进化上不同的类群中发现的结果，并在良好的历史背景下进行来实现。这些新的下一代测序数据将使我们能够检验这样的预测，即一些基因组变化在完全异养的进化之前，质体的减少程度是有限的，以及质体进化的模式是渐进的还是逐步的(点缀)。这项研究将补充在密切相关领域进行的其他研究，并将影响生物技术、基因组学、分子进化、生理学、合成生物学和系统学等领域。

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 (plastomes) in a variety of these so-called heterotrophic plants (commonly known as parasitic plants), with the goal of answering the central question: can the plastome be lost entirely or is it essential that particular genes be retained in this genome? 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 plastomes and other genomes have (co)evolved under relaxed functional constraints. Each lineage has adopted a unique suite of expressed genes and therefore represents one solution to*"deconstructing" complex nuclear-organellar metabolic pathways. Given the difficulties or even the impossibility of reverse genetic approach in this system, a study that replicates over multiple natural plastid “mutants” will contribute to our deeper mechanistic 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 biotechnology, genomics, molecular evolution, physiology, synthetic biology, and systematics.*****