DOI: 10.1101/486399Dec 3, 2018Paper

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

BioRxiv : the Preprint Server for Biology
Jose M González-AlbaJuan Carlos Galán

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 respect...Continue Reading

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Antitoxins
Conserved Sequence
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