Toward a more robust assessment of intraspecies diversity, using fewer genetic markers.

ABSTRACT: Phylogenetic sequence analysis of single or multiple genes has dominated the study and census of the genetic diversity among closely related bacteria. It remains unclear, however, how the results based on a few genes in the genome correlate with whole-genome-based relatedness and what genes (if any) best reflect whole-genome-level relatedness and hence should be preferentially used to economize on cost and to improve accuracy. We show here that phylogenies of closely related organisms based on the average nucleotide identity (ANI) of their shared genes correspond accurately to phylogenies based on state-of-the-art analysis of their whole-genome sequences. We use ANI to evaluate the phylogenetic robustness of every gene in the genome and show that almost all core genes, regardless of their

SUBMITTER: Konstantinidis KT 

PROVIDER: S-EPMC1636164 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature