Microbial Genome Sequencing: Genome Sequence of Streptococcus pneumoniae Strain D39

本项目的目的是确定肺炎链球菌（肺炎球菌）菌株D39的全基因组序列并进行全注释。这个基因组序列在历史上和科学上都很重要，原因有几个。菌株D39是Oswald Avery及其同事用来确定DNA是遗传物质的2型肺炎球菌菌株。自此，菌株D39成为肺炎球菌生理学、遗传学、细胞生物学和发病机制研究的标准模型之一；然而，它的基因组序列尚不清楚。将菌株D39的基因组序列与实验室菌株R6（源自菌株D39）和菌株TIGR4（4型肺炎球菌）的基因组序列进行比较。这种比较将深入了解在实验室中长期维持的菌株的遗传漂变以及这些不同类型的肺炎球菌的毒力特性的差异。菌株D39的基因组序列也将加速对这种重要的革兰氏阳性细菌的生理学的理解，并为其未来的研究提供等基因菌株和遗传工具，包括一套有序的PCR引物，将可供科学界使用。基于多种考虑，菌株D39的富A+ t基因组序列将采用有序PCR引物策略确定。除了具有重要的历史和科学意义外，该项目还将对本科生的培养产生广泛的影响。该项目将作为一个密集的基因组学培训项目进行，至少有6名本科生，他们将获得分子生物学，DNA测序，基因组注释和生物信息学的基础经验。

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.