Genome Sequencing and Annotation

The availability of complete microbial genome sequences enormously facilitates experimental molecular investigations of the respective organisms by providing complete lists of genes, their genetic contexts, and their predicted functions. This can be used in a number of ways to focus studies on bacterial pathogenesis and also vaccine development (1 ,2 ). The complete genome sequences from two unrelated strains of Neisseria meningitidis , a derivative of isolate MC58 which originally expressed serogroup B capsule and strain Z2491, which is serogroup A, are now available (3 ,4 ). The genome sequences of both these strains were determined using the whole genome shotgun approach (5 ). In this approach, randomly sheared chromosomal DNA is cloned to make a small insert library (1.5–2.0 kb for MC58, 0.5–0.8 kb and 1.0–1.5 kb for Z2491), then each insert is sequenced from both ends using plasmidspecific primers. For the MC58 genome sequence, a large insert lambda library (8–24 kb) was also used. In the initial sequencing phase, 6-8 times coverage of the estimated size of the genome is generally achieved. The DNA sequences are linked together (assembled) into large contigs (a derivative of the word contiguous). Polymerase chain reaction (PCR) and sequencing of large insert libraries are then used to join the contigs, close gaps, and resolve ambiguities (see ref. 6 for a review).