TRYPANASOMA CRUZI GENOME-SBRI

克鲁兹锥虫基因组

基本信息

批准号：
6710117
负责人：
KENNETH D STUART
金额：
$ 96.33万
依托单位：
SEATTLE BIOMEDICAL RESEARCH INSTITUTE
依托单位国家：
美国
项目类别：
财政年份：
2000
资助国家：
美国
起止时间：
2000-03-15 至 2006-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/6710117
关键词：
Leishmania major Trypanosoma brucei rhodesiense Trypanosoma cruzi artificial chromosomes autoradiography gene expression genetic library genetic mapping genome linkage mapping nucleic acid sequence polymerase chain reaction

项目摘要

We propose to sequence the genome of Trypanosoma cruzi, a human pathogen of global importance, as part of an interactive research project. This project, and the other components of the interactive project, are designed to exploit ongoing genome sequencing projects on three related pathogens; Leishmania major at the Seattle Biomedical Research Institute (SBRI), Trypanosoma brucei at the Institute for Genome Research (TIGR), and T. cruzi at Uppsala University (UU). The project will also be conducted in coordination with the genome networks that were organized by the World Health Organization to sequence the genomes of these three pathogens. The first phase of the project entails end-sequencing of BAC clones from the CL-Brener reference strain to generate sequence covering about 16 percent of the genome in this lab (55 percent of the genome in the three labs combined). This phase, which will be completed in the first year, will generate data and materials for karyotype and contig mapping, complement data in the existing T. cruzi EST database, and identify many of the genes in T. cruzi. A sequence backbone for selected chromosomes will be generated from shotgun (4x) sequencing of a minimum tile path of BAC clones using a "map-as-you-go" strategy to generate approximately 96 percent sequence coverage of each chromosome. Chromosomes will be assigned to the interactive labs on the basis of interest, which will largely reflect SBRI's activity in L. major sequencing and TIGR's T. brucei sequencing. Comparison of these sequences with those of the corresponding completed chromosomes from L. major or T. brucei will extend our knowledge of the degree of synteny and will provide a basis for determining which regions will be sequenced to contiguity. BAC clones will be sequenced to approximately 8x coverage with highest priority given to those containing genes with high biological significance, that are unique to T. cruzi, or uncharacterized in the other related species. Clones with substantial repetitive sequence will not be sequenced to high coverage without a compelling biological basis. In this way, the genomic regions of the highest biological relevance will be sequenced to contiguity, resulting in approximately 10-15 Mb of highly accurate sequence for each lab. An additional approximately 2-5 Mb of moderately accurate non- contiguous sequence will also be obtained from each lab. The sequence will be analyzed and annotated and these data will be made available to the research community. This project will accelerate the acquisition of the complete genomic sequence of these three organisms and reduce the cost of each project. It will determine relative genomic organizations, gene repertoire and sequence conservation among three important pathogens. This information will aid the development on diagnostic, therapeutic, and preventative measures, as well as further our understanding of fundamental molecular phenomena.

我们建议作为互动研究项目的一部分，对克鲁兹锥虫的基因组进行测序，这是一种全球重要性的人类病原体。该项目以及交互式项目的其他组成部分旨在利用三种相关病原体的正在进行的基因组测序项目；西雅图生物医学研究所（SBRI），基因组研究所（TIGR）和乌普萨拉大学（UU）的T. Cruzi的Leishmania专业。该项目还将与世界卫生组织组织的基因组网络进行协调，以对这三种病原体的基因组进行测序。该项目的第一阶段需要从Cl-Brener参考菌株中进行BAC克隆的最终测序，以产生该实验室中约16％的基因组的序列（三个实验室中的55％的基因组的55％）。此阶段将在第一年完成，将生成核型和重叠式映射的数据和材料，补充现有的T. Cruzi EST数据库中的数据，并确定Cruzi T. Cruzi中的许多基因。使用“ map-as as you-go”策略对BAC克隆的最小瓷砖路径进行shot弹枪（4倍）测序，将生成用于选定染色体的序列主链，以产生每个染色体的大约96％的序列覆盖率。染色体将根据感兴趣的染色体分配给交互式实验室，这将在很大程度上反映了SBRI在L.主要测序和Tigr的Tigr t. brucei测序中的活性。将这些序列与来自L. Brucei的相应完成的染色体的序列进行比较，将扩展我们对同步程度的了解，并将为确定将哪些区域测序的基础。 BAC克隆将被测序约8倍覆盖范围，优先级最高，含有含有高生物学意义的基因，这些基因是克鲁齐独有的，或在其他相关物种中未表征。没有引人注目的生物学基础，具有实质重复序列的克隆将不会在高覆盖范围内测序。这样，最高生物学相关性的基因组区域将被测序与连续性，每种实验室的高度精确序列约为10-15 mb。还将从每个实验室获得大约2-5 MB中等准确的非连续序列。该序列将进行分析和注释，并将这些数据提供给研究社区。该项目将加速这三种生物的完整基因组序列的获取，并降低每个项目的成本。它将确定三种重要病原体之间的相对基因组组织，基因库和序列保守。这些信息将有助于开发诊断，治疗和预防措施，并进一步了解我们对基本分子现象的理解。