Three-base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core genomes.
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.
Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany.
Patricia
P
Morán Losada
Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany.
Sebastian
S
Fischer
Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany.
Philippe
P
Chouvarine
Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany. tuemmler.burkhard@mh-hannover.de.|Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany. tuemmler.burkhard@mh-hannover.de.
Burkhard
B
Tümmler
D001482:Base Composition; D003062:Codon; D016680:Genome, Bacterial; D020641:Polymorphism, Single Nucleotide; D011550:Pseudomonas aeruginosa / Q000235:genetics*; D013211:Staphylococcus aureus / Q000235:genetics*; D026801:Synteny
D003062:Codon
Pseudomonas aeruginosa; Staphylococcus aureus; core genome; haplotype; single nucleotide polymorphism; three-base periodicity