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FEBS Lett. 2016 Oct;590(20):3538-3543. doi: 10.1002/1873-3468.12431. Epub 2016 Oct 4.

Three-base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core genomes.

Author information

1
Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany.
2
Clinical Research Group, 'Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics', OE 6710, Hannover Medical School, Germany. tuemmler.burkhard@mh-hannover.de.
3
Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany. tuemmler.burkhard@mh-hannover.de.

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.

KEYWORDS:

Pseudomonas aeruginosa; Staphylococcus aureus; core genome; haplotype; single nucleotide polymorphism; three-base periodicity

PMID:
27664047
DOI:
10.1002/1873-3468.12431
[Indexed for MEDLINE]
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