Reconstruction of Escherichia coli ancient diversification by layered phylogenomics and polymorphism fingerprinting

Abstract

The rapidly increasing availability of whole genomes provides the opportunity to reach an updated comprehensive view of bacterial evolution. The staggered diversification of evolutionary processes, based on the combined strategy of layered phylogenomics and polymorphism fingerprinting, give a new perspective in phylogenetic reconstructions. Layered phylogenomics is based on the assignation of genes according to five different evolutionary layers: minimal genome, genus-core genome, species-core genome, phylogroup-core genome and phylogroup-flexible genome. Polymorphism fingerprinting is based on the detection of conserved positions in each phylogenetic group but differing from those of their hypothetical ancestors. This approach was applied to Escherichia coli because there are unresolved evolutionary questions, although has been highly studied. Phylogenetic analysis based on 6,220 full genomes, identified three E. coli root lineages, defined as D, EB1A and FGB2. A new phylogroup, called G was detected near to phylogroup B2. The closest phylogroup to ancestral E. coli was phylogroup D, whereas E and F were the closest ones in their respective lineages; moreover, A and B2 were the most distant phylogroups in EB1A and FGB2 respectively. We suspect that EB1A and FGB2 lineages represent different adaptive strategies. In the deepest branch of EB1A lineage, the number of accumulated mutations was lower than in recent branches, whereas in FGB2 lineage the opposite occurred. The FGB2 lineage was enriched in genes related to host colonization-pathogenicity and toxin-antitoxin systems (such as hipA), whereas B1A sub-lineage acquired functions related to uptake and metabolism of carbohydrates (such as bgl, mng or xlyE). This new combined strategy shows a detailed staggered evolutionary reconstruction, which help us to understand the deepest events and the selection forces have driven E. coli diversification. This approach could add resolution in the reconstruction of the evolutionary trajectories of other microorganisms.\n\nAuthor summaryPhylogeny based on whole genome provides the opportunity to study the history of eco-adaptive diversification of any bacterial taxon. Different strategies have been proposed for knowing the evolutionary trajectories in some species, such as Escherichia coli; however, these analyses were based on a limited number of sequences, and sometimes the evolutionary reconstructions reached clashed positions, especially in the ancestral inferences. For adding resolution in evolutionary reconstructions, we propose a combination of approaches, such as layered phylogenomics based on the use of different set of genes corresponding to the successive evolutionary steps, and polymorphism fingerprinting which detects hallmarks of the ancient mutations. We propose to use E. coli because it is paradigmatic example of the evolutionary inconsistences despite being a microorganism with enough evolutionary analysis. Three ancestral lineages were established with this strategy and the staggered reconstruction about the origin and diversification of E. coli phylogroups was inferred. Moreover, in the context of this study, a new E. coli phylogroup was defined. The main lineages represent different adaptive strategies, one lineage gained genes involved in pathogenicity, and another one acquired genes allowing the obtainment of energy from different sources.