Revealing the spectrum of extended-core gene variation in the Escherichia coli pan-genome.

Abstract excerpt

Standard pan-genome pipelines, such as Roary, use strict protein identity thresholds (e.g., ≥ 95%) that systematically misclassify highly conserved genes as absent. Single mutational events like large indels, nonsense mutations, or high sequence divergence can cause these false negatives, masking the true composition of the bacterial core genome. We address this by investigating 198 extended-core loci (present in...

Topics

• Escherichia coli
• Genome, Bacterial
• Genetic Variation
• Genomics
• Evolution, Molecular