TRYPANASOMA CRUZI GENOME-SBRI

克鲁兹锥虫基因组

• 批准号: 6510958
• 负责人: KENNETH D STUART
• 金额: $ 85.15万
• 依托单位: SEATTLE BIOMEDICAL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-03-15 至 2005-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6510958
• 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

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.

作为互动研究项目的一部分，我们建议对克氏锥虫（一种具有全球重要性的人类病原体）进行基因组测序。 该项目以及互动项目的其他组成部分旨在利用正在进行的三种相关病原体的基因组测序项目；西雅图生物医学研究所 (SBRI) 的利什曼原虫、基因组研究所 (TIGR) 的布氏锥虫和乌普萨拉大学 (UU) 的克氏锥虫。 该项目还将与世界卫生组织组织的基因组网络协调进行，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对来自 CL-Brener 参考菌株的 BAC 克隆进行末端测序，以生成覆盖该实验室约 16% 基因组的序列（占三个实验室基因组总和的 55%）。这一阶段将在第一年完成，将生成用于核型和重叠群作图的数据和材料，补充现有克氏锥虫 EST 数据库中的数据，并鉴定克氏锥虫中的许多基因。 选定染色体的序列主干将通过使用“即用图谱”策略对 BAC 克隆的最小平铺路径进行鸟枪法 (4x) 测序来生成，以生成每条染色体约 96% 的序列覆盖率。染色体将根据兴趣分配到互动实验室，这将在很大程度上反映 SBRI 在 L. Major 测序和 TIGR 的 T. brucei 测序方面的活动。 将这些序列与来自 L. Major 或 T. brucei 的相应完整染色体的序列进行比较将扩展我们对同线性程度的了解，并将为确定哪些区域将被连续测序提供基础。 BAC 克隆将被测序至大约 8 倍覆盖度，其中含有具有高生物学意义的基因的克隆将获得最高优先级，这些基因是 T. cruzi 特有的，或在其他相关物种中未表征的。 如果没有令人信服的生物学基础，具有大量重复序列的克隆将不会被测序到高覆盖率。通过这种方式，生物相关性最高的基因组区域将被连续测序，从而为每个实验室提供大约 10-15 Mb 的高度准确的序列。每个实验室还将获得另外约 2-5 Mb 的中等准确度的非连续序列。 该序列将被分析和注释，这些数据将提供给研究界。 该项目将加速获得这三种生物的完整基因组序列，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、基因库和序列保守性。 这些信息将有助于诊断、治疗和预防措施的发展，并进一步加深我们对基本分子现象的理解。