THE BACTEROIDES FORSYTHUS GENOME PROJECT

拟杆菌基因组计划

• 批准号: 6226289
• 负责人: STEVEN R. GILL
• 金额: $ 20.35万
• 依托单位: INSTITUTE FOR GENOMIC RESEARCH
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-09-01 至 2003-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6226289
• 关键词: Bacteroides; DNA; RNA; bacteria infection mechanism; computer assisted sequence analysis; cooperative study; genetic library; genetic mapping; genome; high throughput technology; molecular biology information system; nucleic acid sequence; open reading frames; oral bacteria; periodontium disorder; polymerase chain reaction; transfer RNA

The gram negative anaerobe Bacteroide forsythus is consistently associated with chronic and severe adult periodontitis. Periodontal disease is routinely treated with surgery and tooth scaling. Determining the complete DNA sequence of the 2.2 Mbp genome of B. forsythus will identify all the open reading frames and other features associated with the genome. The DNA sequence and its annotation provide the information for functional genomic studies leading to the identification of targets for therapeutics and candidates for vaccine development. We will determine the complete genome sequence of the 2.2 Mbp genome of B. forsythus using a whole genome shotgun strategy. Small and large insert plasmid libraries will-be prepared from B. forsythus randomly sheared genomic DNA. A sufficient number of random sequences (approximately 35,000 for 8-fold coverage) will be produced in TIGR's state of the art high throughput DNA sequencing facility. The sequence and physical gaps remaining following assembly and editing with TIGR's assembly and editing software (TIGR_Assembler ver 2.0, TIGR_Editor) are closed using a variety of sequencing and PCR strategies. Difficult repeat regions such as IS elements and rRNAs will be specifically PCR'd to insure the fidelity of the final genome structure and sequence. The DNA sequence data will be made available in compliance with the NIAID/NIDCR guidelines for large-scale genome sequencing projects. The complete genome sequence will be annotated using a variety of computer techniques. Open reading frames are identified with GLIMMER and searches of the predicted coding reading regions are done with BLASTP searched against a non-redundant bacterial protein database. Gene identification is enhanced by utilizing tools for multiple sequence alignment allowing us to build both orthologous and paralogous gene families. Additional structural features such as membrane spanning domains in proteins, untranslated RNAs, tRNAs, insertion sequences, and repeats will also be identified. The complete genome sequence and its analysis will be made available through the world wide web as part of the Comprehensive Microbial Resource (CMR) database developed at TIGR. We will also work closely with those investigators developing a specific Oral Pathogens database to make our data and analysis available.

革兰氏阴性厌氧菌类杆菌始终与慢性和严重的成人牙周炎有关。牙周病通常通过手术和洁牙治疗。确定B的2.2 Mbp基因组的完整DNA序列。因此，该方法将识别所有开放阅读框和与基因组相关的其他特征。DNA序列及其注释为功能基因组研究提供信息，从而鉴定治疗靶点和疫苗开发候选物。我们将确定B的2.2 Mbp基因组的全基因组序列。使用全基因组鸟枪策略。将从B制备小和大插入质粒文库。因此随机剪切基因组DNA。将在TIGR最先进的高通量DNA测序设施中产生足够数量的随机序列（8倍覆盖率约35，000个）。使用多种测序和PCR策略闭合在用TIGR的组装和编辑软件（TIGR_Assembler ver 2.0，TIGR_Editor）组装和编辑后剩余的序列和物理缺口。困难的重复区域如IS元件和rRNA将被特异性PCR以确保最终基因组结构和序列的保真度。DNA序列数据将按照NIAID/NIDCR关于大规模基因组测序项目的准则提供。完整的基因组序列将使用各种计算机技术进行注释。用GLIMMER鉴定开放阅读框，并用BLASTP对非冗余细菌蛋白质数据库进行搜索，以完成预测的编码阅读区的搜索。利用多序列比对工具，使我们能够建立直系同源和旁系同源基因家族，从而增强基因鉴定。还将鉴定其他结构特征，如蛋白质中的跨膜结构域、非翻译RNA、tRNA、插入序列和重复序列。完整的基因组序列及其分析将通过万维网提供，作为TIGR开发的综合微生物资源（CMR）数据库的一部分。我们还将与那些开发特定口腔病原体数据库的研究人员密切合作，以提供我们的数据和分析。