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.
