Comparative Genomics of the Chlamydiaceae

描述(由申请人提供)： 我们打算将基因组学从描述单个细菌基因组的特征扩展到描述引起传染病的细菌的进化。衣原体是一种革兰氏阴性的细胞内专性病原体，非常适合这种方法。这一目的成员会引起一系列疾病，但对传统的基因分析仍然难以奏效。 我们的新的，多方面的方法，我们被称为“分类基因组学”，是首先对以前或现在的项目没有解决的衣冠菌科物种的模式菌株进行测序-猪衣原体，胸衣原体和鹦鹉热衣原体(一种潜在的生物战剂)。此外，我们将对考拉株肺炎衣原体和衣原体中进化最远的成员Waddlia chondroPhila和Simkania Negevens进行测序。为了鉴定那些可能已被实验室适应的模式菌株丢失或被“野生”菌株获得的基因，我们将应用消减杂交方法，从每个物种中汇集多个菌株，并减去模式菌株共享的那些基因。用来自所有基因组代表的序列和来自分类基因组减去的序列，然后我们将创建一个来自这个进化上分离的家族的所有已知ORF的基因数据库。我们将利用这个数据库来设计一个非冗余的衣原体基因变异微阵列(这里称为“TaxoChip”)。在这项研究中，我们将使用TaxoChip进行一系列比较基因组杂交(CGH)实验，使用我们从全球各地汇编的一组独特的不同衣原体分离物。 我们希望使用这些基因组数据来研究衣原体的进化，并识别那些可能区分观察到的宿主/组织生态位的多样性和导致的疾病结果的基因。我们还将评估水平基因转移在创造新的致病表型方面的潜在重要作用，以及动物和人类衣原体菌株之间可能的重要关系。此外，TaxoChip的设计和衣原体基因数据库将为所有衣原体学家和分子进化学家带来长期利益，他们越来越多地将衣原体作为研究还原进化过程的标准模型。 这项研究旨在解决广泛的问题，涉及衣原体细胞内寄生和致病性发展的遗传和进化基础。在科学界的广泛和国际支持下，我们认为这是一个开创性的建议，并预计它将成为比较微生物基因组学的基准研究。

DESCRIPTION (provided by applicant): We intend to extend genomics from the characterization of individual bacterial genomes to characterizing the evolution of infectious disease-causing bacteria. The Chlamydiales, an order of Gram-negative obligate intracellular pathogens, are ideally suited to this approach. Members of this order cause a range of diseases but continue to be refractory to conventional genetic analyses. Our novel, multifaceted approach, which we have named "Taxogenomics," is to first sequence the type strains of the Chlamydiaceae species not addressed by previous or current projects - C. suis, C. pecorum, and C. psittaci (a potential biological warfare agent). Additionally, we will sequence the koala strain of C. pneumoniae and the most evolutionarily distant members of the Chlamydiales, Waddlia chondrophila and Simkania negevensis. To identify those genes which may have been lost by the laboratory adapted type strains or been acquired by "wild" isolates, we will apply subtractive hybridization by pooling multiple isolates from each species and subtracting those genes shared by the type strain. With sequences from representatives of all genomes and with sequences derived from the taxonomic genomic subtractions, we will then create a gene database of all known ORFs from this evolutionarily isolated family. We will use this database to design a non-redundant microarray of Chlamydiales gene variation (called here the "Taxochip"). In this study, we will use the Taxochip in a suite of comparative genomic hybridization (CGH) experiments using a unique set of diverse Chlamydiales isolates that we have compiled from around the globe. We expect to use this genome data to investigate the evolution of the Chlamydiales and identify those genes that may differentiate the variety of observed host/tissue niches and resulting disease outcomes. We also will assess the potentially important role of horizontal gene transfer in creating novel pathogenicity phenotypes and the likely important relationship between animal and human chlamydial strains. Additionally, the Taxochip design and the Chlamydiales gene database will be of long-term benefit to all chlamydiologists and molecular evolutionists who are increasingly using the Chlamydiales as a standard model for studying reductive evolutionary processes. This study is designed to address broad questions that deal with the genetic and evolutionary basis of the development of intracellular parasitism and pathogenicity in the Chlamydiales. With broad and international support from the scientific community, we consider this a groundbreaking proposal and anticipate it will be a benchmark study in comparative microbial genomics.