Microbial Genome Sequencing: Genome Sequence of Streptococcus pneumoniae Strain D39

本项目的目标是确定带有完整注释的肺炎链球菌(肺炎球菌)菌株D39的完整基因组序列。由于几个原因，这个基因组序列在历史和科学上都具有重要意义。菌株D39是奥斯瓦尔德·艾弗里和他的同事用来确定DNA是遗传物质的2型肺炎球菌菌株。从那时起，D39菌株已经成为研究肺炎球菌生理学、遗传学、细胞生物学和致病机理的标准模型之一，但其基因组序列尚不清楚。D39菌株的基因组序列将与实验室菌株R6和TIGR4菌株进行比较，R6菌株来自D39菌株，TIGR4菌株是4型肺炎球菌。这一比较将深入了解长期在实验室保持的菌株的遗传漂移，以及这些不同类型肺炎球菌毒力特性的差异。D39菌株的基因组序列还将加快对这种重要的革兰氏阳性细菌的生理学的了解，并为其未来的研究提供同基因菌株和遗传工具，包括一套可供科学界使用的有序PCR引物。基于几个方面的考虑，菌株D39富含T的基因组序列将通过使用有序聚合酶链式反应引物的策略来确定。除了其历史和科学意义外，该项目还将对本科生的培养产生广泛的影响。该项目将作为至少六名本科生的强化基因组学培训项目进行，他们将获得分子生物学、DNA测序、基因组注释和生物信息学方面的基本经验。

The goal of this project is to determine the complete genome sequence with full annotation of Streptococcus pneumoniae (pneumococcus) strain D39. This genome sequence is historically and scientifically important for several reasons. Strain D39 was the Type 2 strain of pneumococcus used by Oswald Avery and coworkers to determine that DNA is the genetic material. Since then, strain D39 has become one of the standard models for the study of pneumococcal physiology, genetics, cell biology, and pathogenesis; yet, its genome sequence is not known. The genome sequence of strain D39 will be compared with those of laboratory strain R6, which was derived from strain D39, and strain TIGR4, which is a Type 4 pneumococcus. This comparison will give insights into the genetic drift of strains maintained for long periods in laboratories and the differences in virulence properties of these different types of pneumococcus. The genome sequence of strain D39 will also accelerate the understanding of the physiology of this important gram positive bacterium and contribute isogenic strains and genetic tools for its future study, including a set of ordered PCR primers that will be available to the scientific community. Based on several considerations, the A+T-rich genome sequence of strain D39 will be determined by a strategy using ordered PCR primers. Besides its historical and scientific importance, this project will have broad impact on training undergraduate students. The project will be conducted as an intensive genomics training project for at least six undergraduate students, who will gain fundamental experience in molecular biology, DNA sequencing, genome annotation, and bioinformatics.