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Chapter 25 : Genomics
Category: Environmental Microbiology; Applied and Industrial Microbiology
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The availability of the complete genome sequence of the free-living bacterium Haemophilus influenzae in 1995 opened the field of microbial genomics. Although a variety of sequencing technologies have been used for genome sequencing projects, the random shotgun sequencing strategy has demonstrated itself to be the most successful and efficient and has become the preferred method for whole-genome sequencing. Following on the closure and assembly of the DNA replicons, a complete analysis of the genome necessitates the identification of all DNA-encoded open reading frames (ORFs) or candidate genes in the DNA sequence and the assignment of gene names and associated function to these ORFs. Following the completion of the annotation phase of the sequencing project, the sequence allows for detailed comparative and functional genomics. Available tools of functional genomics include expression profiling, identification and analysis of protein-protein interactions, deletion phenotype analysis, and proteomics. In addition to the listed features that can be identified through bioinformatics analysis, insights can also be gained into previously unidentified biochemical pathways and transporter systems. The magnitude of the possible diversity that exists is evident when we consider that more than 99% of microbial species remain to be identified. Further details on the methodology of genome hybridization (CGH) are discussed. In the postgenomic era, the discipline of functional genomics is facing the challenge of associating function to the thousands of genes of unknown function that remain at the end of each genome project.