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Physical and functional organization of bacterial genomes : an evolutionary perspective ; from a physicist
Genomes are being sequenced at an exponential pace, offering us an unprecedented opportunity to study quantitatively the evolutionary processes that shape their diversity. One of the most intriguing results from recent studies is the existence of “universal laws” common to phylogenetically distant species, which suggest novel, statistical principles of evolution. In this context, I will present a statistical framework that aims at extracting conserved genomic patterns and at investigating their properties. In particular, I will show the existence of a novel law for the conservation of chromosomal proximity (synteny) between genes in bacteria. In contrast to previous laws of genome evolution, which have been explained by neutral or negative evolutionary mechanisms, this synteny law emerges from an on-going process of positive selection, whereby genes gradually aggregate into conserved clusters of co-localized genes (“syntons”). Remarkably, while the properties of syntons hold for very different genomes and genes, synton organization in a given organism corresponds to structural properties that are not conserved. Both universality and idiosyncrasy thus lie at the core of the evolution of genomes, stressing the necessity to work at the interface between physics and biology.