Starter Grant: Cis-acting signals and genome-wide effects of extensive genome processing in diverse ciliates

微生物真核生物基因组的多样性使研究成为发现基本生物现象的关键，包括自我剪接RNA，端粒添加和RNA编辑。 发育调控的基因组重排发生在许多不同的类群，但在这些过程中的多样性的演变仍然在很大程度上未被探索。纤毛虫是一种在发育过程中经历了广泛而多样的基因组重排的微生物，是研究基因组加工进化的有用系统。纤毛虫基因组的研究将：（1）允许更好地了解真核生物发育基因组加工的进化，（2）有助于确定基因组结构对全基因组分子进化模式的影响。 纤毛虫在每个细胞中含有两个基因组：微核中的生殖细胞基因组和大核中的体细胞基因组。 在从合子核发育大核的过程中，基因组通过染色体片段化和扩增以及消除内部序列来加工。 一些纤毛虫经历如此广泛的基因组加工，所得到的大核基因组包含染色体，这些染色体通常包含单个基因和短的非编码区。本研究将描述和比较的顺式作用序列参与染色体片段化和切除的内部序列在这一广泛的基因组加工在一类研究不足的纤毛虫。 此外，通过对编码区和非编码区进行测序，它将允许比较具有广泛加工的纤毛虫、其他纤毛虫和其他真核生物之间的分子进化速率和模式。这些研究将揭示驱动基因组加工多样化的进化机制，并评估加工对纤毛虫分子进化模式的影响。 基因组的结构在整个生命树中是高度可变的，然而这种变异的起源及其对进化模式的影响仍然不清楚。 通过关注一组具有不同和不寻常的基因组结构的微生物（纤毛虫），这项研究将表征基因组结构的多样性，并评估其对蛋白质进化和基因调控的影响。 这些数据将增强我们对决定分子和基因组进化速率和模式的重要生物因素的理解。 此外，该项目将对社会产生更广泛的影响。对一名初出茅庐的女调查员的这种支持将有助于增加妇女在生物学教授中的代表性。 至少有一名研究生和两名本科生将直接参与研究。这两名本科生都来自传统上代表性不足的群体。此外，这项研究将有助于开发原生生物多样性和基因组进化的研究生课程，该课程将于2007年春季学期在休斯顿大学教授。

n The diversity of microbial eukaryotic genomes has allowed studies pivotal to the discovery of basic biological phenomena, including self-splicing RNA, telomere addition, and RNA editing. Developmentally regulated genome rearrangements occur in many disparate taxa, but evolution of the diversity in these processes remains largely unexplored. Ciliates are microbial eukaryotes that undergo diverse and extensive genome rearrangements during development, thus serve as a useful system to study the evolution of genome processing. Studies of ciliate genomes will: (1) allow a better understanding of the evolution of developmental genome processing in eukaryotes, and (2) help to determine the effects of genome architecture on genome-wide patterns of molecular evolution. Ciliates contain two genomes in each cell: a germline genome in the micronucleus and a somatic genome in the macronucleus. During development of the macronucleus from a zygotic nucleus, the genome is processed by chromosomal fragmentation and amplification, and elimination of internal sequences. Some ciliates undergo such extensive genome processing that the resultant macronuclear genomes contain chromosomes that often contain a single gene and short non-coding regions. This research will characterize and compare the cis-acting sequences involved in chromosome fragmentation and excision of internal sequences during this extensive genome processing in a class of understudied ciliates. In addition, by sequencing coding and non-coding regions, it will allow for comparisons of rates and patterns of molecular evolution among ciliates with extensive processing, other ciliates, and other eukaryotes. These studies will both shed light on the evolutionary mechanisms driving the diversification of genome processing and assess the effects of processing on patterns of molecular evolution in ciliates. The structure of genomes is highly variable across the tree of life, however the origins of this variation and its impact on patterns of evolution remain unclear. By focusing on a group of microbial organisms with diverse and unusual genomic structure (ciliates), this research will characterize the diversification of genome structures and assess its effect on the evolution of proteins and gene regulation. These data will enhance our understanding of the biological factors that are important in determining the rates and patterns of molecular and genome evolution. Furthermore, this project will have broader impacts for society. This support for a beginning female investigator will help increase the representation of women in the biological professoriate. At least one graduate student and two undergraduates will be directly integrated into the research. Both undergraduates are from traditionally underrepresented groups. In addition, this research will be instrumental in the development of a graduate course in protist diversity and genome evolution, which will be taught during the spring 2007 semester at the University of Houston.