A coarse-graining, ultrametric approach to resolve the phylogeny of prokaryotic strains with frequent homologous recombination.

ABSTRACT: BACKGROUND:A frequent event in the evolution of prokaryotic genomes is homologous recombination, where a foreign DNA stretch replaces a genomic region similar in sequence. Recombination can affect the relative position of two genomes in a phylogenetic reconstruction in two different ways: (i) one genome can recombine with a DNA stretch that is similar to the other genome, thereby reducing their pairwise sequence divergence; (ii) one genome can recombine with a DNA stretch from an outgroup genome, increasing the pairwise divergence. While several recombination-aware phylogenetic algorithms exist, many of these cannot account for both types of recombination; some algorithms can, but do so inefficiently. Moreover, many of them reconstruct the ancestral recombination graph (ARG) to help infer

SUBMITTER: Pang TY 

PROVIDER: S-EPMC7204016 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature