Pan-genomics of model bacteria and their outcomes

Abstract Next-generation sequencing technologies have produced extensive genome sequence data for genomic analyses. Consequently, genome analyses have transformed from a single or few genomes to hundreds and thousands of genomes. The comparative studies of different strains of a species revealed that sequences of a single genome (strain) are not sufficient to describe the level of genetic diversity in a species. It is essential to perform comparative analyses of all the available sequenced strains of a species to completely understand their actual genomic contents. The concept of pan-genome was created in 2005, when six strains from five Streptococcus agalactiae serotypes were analyzed to estimate the genomic repertoire of the species. Since then, several other bacterial pan-genomes have been analyzed including model bacteria, that is, Neisseria meningitidis, Staphylococcus aureus, Escherichia coli, Streptococcus pyogenes, Haemophilus influenzae, and Streptococcus pneumoniae to explore the level of genomic diversity within species. These studies followed diverse parameters for estimations such as a number of genomes analyzed, the prediction models, and alignment algorithms and associated threshold values. This chapter explores analyses of some of these model organisms, methods adapted to accomplish these analyses, and their outcomes.