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Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J - MBio (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.

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ANI and isDDH values. The lower triangle displays ANI values, and the upper triangle shows the isDDH values. ANI values are colored according to three historical species cutoff values: 94% (yellow), 95% (orange), and 96%+ (red). The isDDH values displayed are the upper limits of the 95% confidence intervals and are colored red if the met the laboratory DDH species cutoff of 70% hybridization. ANI of 96% correlates well with 70% isDDH values, with only the A. allosaccharophila isolates failing to match (68.7%).
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fig2: ANI and isDDH values. The lower triangle displays ANI values, and the upper triangle shows the isDDH values. ANI values are colored according to three historical species cutoff values: 94% (yellow), 95% (orange), and 96%+ (red). The isDDH values displayed are the upper limits of the 95% confidence intervals and are colored red if the met the laboratory DDH species cutoff of 70% hybridization. ANI of 96% correlates well with 70% isDDH values, with only the A. allosaccharophila isolates failing to match (68.7%).

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).


Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case.

Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP, Graf J - MBio (2014)

ANI and isDDH values. The lower triangle displays ANI values, and the upper triangle shows the isDDH values. ANI values are colored according to three historical species cutoff values: 94% (yellow), 95% (orange), and 96%+ (red). The isDDH values displayed are the upper limits of the 95% confidence intervals and are colored red if the met the laboratory DDH species cutoff of 70% hybridization. ANI of 96% correlates well with 70% isDDH values, with only the A. allosaccharophila isolates failing to match (68.7%).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4251997&req=5

fig2: ANI and isDDH values. The lower triangle displays ANI values, and the upper triangle shows the isDDH values. ANI values are colored according to three historical species cutoff values: 94% (yellow), 95% (orange), and 96%+ (red). The isDDH values displayed are the upper limits of the 95% confidence intervals and are colored red if the met the laboratory DDH species cutoff of 70% hybridization. ANI of 96% correlates well with 70% isDDH values, with only the A. allosaccharophila isolates failing to match (68.7%).
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).

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.

Show MeSH