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Updated: Mar 14, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
Three-base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core
Patricia Morán Losada1, Sebastian Fischer1, Philippe Chouvarine1
1Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany.
Abstract:
The three-base periodicity property is characteristic of protein-coding sequences. Here, we report on three-base periodicity of sequence variation in the core genome of bacteria. Single nucleotide polymorphism (SNP) syntenies were extracted from pairwise genome alignments of 41 Staphylococcus aureus or 20 Pseudomonas aeruginosa strains. The length of fragment pairs with identical nucleotides at all SNP positions showed a length-dependent overrepresentation of multiples of three nucleotides at corresponding codon positions of the AT-rich S. aureus and the GC-rich P. aeruginosa. Three-base SNP periodicity seems to be a characteristic feature of the tightly arranged bacterial core genome.
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