Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.
Bottom Line: Improvements in DNA sequencing technologies have resulted in the ability to generate large numbers of high-quality draft genomes and led to a dramatic increase in the number of publically available genomes.Using Aeromonas as a test case, we compared and validated different approaches.Accurate species classification is critical not only to obviate the perpetuation of errors in public databases but also to ensure the validity of inferences made on the relationships among species within a genus and proper identification in clinical and veterinary diagnostic laboratories.
Affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.Show MeSH
Mentions: The information gained from the phylogenetic analyses provides an important depiction of the evolutionary relationships of different strains but does not translate directly into the overall similarity of the genomes, which was determined through DDH. We used two different in silico or bioinformatics approaches, isDDH and ANI, that have been proposed to overcome the challenges of conventional laboratory-based DDH to evaluate the genomic similarity of bacteria, and we evaluated the congruence of these methods (Fig. 2) (9, 16, 21, 22).
Affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.