Comparative and functional genomics of non-photosynthetic 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。我们研究各种所谓的异养植物（俗称寄生植物）的质体基因组（质体体），目的是回答一个核心问题：质体体是否可以完全丢失，或者特定基因是否必须保留在这个基因组中？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。我们在这个建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，其质体和其他基因组在宽松的功能约束下（共同）进化。每个谱系都采用了一套独特的表达基因，因此代表了一种“解构”复杂的核-细胞器代谢途径的解决方案。考虑到在这个系统中使用反向遗传方法的困难甚至不可能，在多个天然质体“突变体”上进行复制的研究将有助于我们对光合作用、其分子成分及其相互作用的更深入的机制理解。***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，并在一个良好的历史背景下进行。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.*****