Genome Diversity: A Grammar of Microbial Genomes

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Abstract
The metaphor of the genetic program is ubiquitously used. Does it bring about a deeper insight into what cells are? In brief, computers do not make computers, but cells make cells. Pursuing the analogy in its deepest consequences we explore bacterial genome diversity as organized around core programs meant to couple the expression of the program with the architecture of the cell. At first sight genomes appear to evolve fast and exhibit no rule of organization. However, when the huge number of generations separating various organisms is taken into account, diversity appears only as a trivial observation. In contrast, rules of gene organization are observed, for example in the separation between Archaea and Bacteria, in the composition of the leading and lagging strand of the chromosomes, in the distribution of genes along the DNA strands, or in the formation (and conservation) of operons and pathogenicity islands.