THE BACTEROIDES FORSYTHUS GENOME PROJECT

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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.