Molecular Evolution of Eukaryotes: a protistan emphasis

描述(申请人提供)：在植物、动物和真菌进化之前，真核生物仅作为微生物存在了至少500,000到10亿年。了解微生物真核生物，特别是原生生物的进化史，是了解真核生物的起源、寄生生物的出现以及这种极其多样化的组合演变为植物、动物、真菌和其他新近衍生的类群的关键。原生生物代表了一群兼收并蓄的有机体，其特点是在身体计划、生态学、生物化学和分子过程方面有许多创新。从原核生物到真核细胞结构的转变，以及多细胞真核生物的起源都植根于原生生物的世界。 这项建议描述了收集新的分子数据和构建大规模的多基因数据集，以探索不同真核生物的进化关系。我们的实验策略试图通过探索主要分支之间的关系来捕捉真核生物的多样性，并将位置不确定的分类群放在谱系上。我们将构建多达30个关键原生生物的归一化cDNA文库，并对每个文库中的10,000-20,000个cDNA克隆进行测序。使用计算机生成的比对，我们将使用高通量系统基因组学来解决以下问题：主要真核生物谱系的组成和相对分支顺序是什么？横向基因转移在多大程度上影响了真核基因组的进化？有没有对水平基因转移不起作用的基因组核心？新陈代谢进化的模式是否反映了地球历史上的环境变化？对寄生生活方式的适应是否会导致基因组结构及其转录组发生重大变化？最后，导致现代真核生物复杂性的关键超微结构和形态创新是什么？该项目产生的这些系统发育框架将成为解释基因和基因组组织模式起源和进化的基础，这些基因和基因组组织模式负责支撑生物复杂性和疾病的新表型。

DESCRIPTION (provided by applicant): Eukaryotes existed exclusively as microorganisms for a minimum of 500,000 to one billion years prior to the evolution of plants, animals and fungi. Understanding the evolutionary history of microbial eukaryotes, especially the protists, is key to understanding the origins of eukaryotes, the emergence of parasitism, and the evolution of this remarkably diverse assemblage into plants, animals, fungi and other recently derived groups. Protists represent an eclectic group of organisms marked by numerous innovations in body plans, ecology, biochemistry, and molecular processes. The transition from prokaryotic life-forms to eukaryotic cellular architecture, and the origins of multi-cellular eukaryotes are rooted in the world of protists. This proposal describes the collection of new molecular data and the construction of a large-scale, multi-gene data set for exploring evolutionary relationships for diverse eukaryotes. Our experimental strategy seeks to capture the diversity of eukaryotes by exploring relationships within major clades, and by placing taxa of uncertain position on genealogies. We will construct normalized cDNA libraries for as many as 30 key protists and sequence 10,000-20,000 cDNA clones from each library. Using computer-generated alignments we will use high-throughput phylogenomics to address the following questions: What is the composition and relative branching order of major eukaryotic lineages? To what extent has lateral gene transfer affected the evolution of eukaryotic genomes? Is there a genomic core that is refractory to horizontal gene transfer? Does the pattern of metabolic evolution mirror environmental changes in earth's history? Does adaptation to parasitic life-styles impose major changes in genome architecture and its transcriptome? And finally, what are the key ultrastructural and morphological innovations that led to modem eukaryotic complexity? These phylogenetic frameworks generated by the project will become the basis for interpreting the origin and evolution of genes and genome organization patterns that are responsible for novel phenotypes that underpin organismal complexity and disease.