Variables Historically Proposed to Explain GC Variation in Prokaryotes.

<p>Variables Historically Proposed to Explain GC Variation in Prokaryotes.</p

The GC composition of genomes is strongly correlated with second codon (GC₂) and 4-fold degenerate positions (GC₄) [<b>2</b>].

<p>Second codon positions show low variability due to purifying selection on non-synonymous changes. 4-fold degenerate positions vary between 5% and 97% GC among published genomes. In the classical neutral scenario (red), 4-fold degenerate positions are nearly neutral and their composition results essentially from mutational patterns. These patterns are modified in bacteria that lose repair genes, such as mutators, which show additional AT pressure (grey area) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001104#pgen.1001104-Lind1" target="_blank">[19]</a>. In the selectionist view (blue), the composition of 4-fold degenerate positions results from selection for GC content, the mutational patterns are AT-rich relative to genome composition, and there are no neutral positions. Naturally, this is an idealized view of genomes that code for many additional overlapping signals that are under selection, e.g., codon usage bias, regulatory signals, etc.</p

Allelic profiles and sequence types (ST) obtained for the 16 <i>B. quintana</i> isolates and the HROEH DNA extract.

<p>Allelic profiles and sequence types (ST) obtained for the 16 <i>B. quintana</i> isolates and the HROEH DNA extract.</p

Localization of the 9 genetic loci used in the <i>B. quintana</i> MLST scheme on the chromosome of <i>B. quintana</i>.

<p>The genomic map was adapted from <a href="http://wishart.biology.ualberta.ca/BacMap/graphs_cgview.html" target="_blank">http://wishart.biology.ualberta.ca/BacMap/graphs_cgview.html</a><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009765#pone.0009765-Stothard1" target="_blank">[32]</a>. The position of the loci has been marked by arrows.</p

Characteristics of the nine loci evaluated for the <i>B. quintana</i> MLST scheme.

<p>Characteristics of the nine loci evaluated for the <i>B. quintana</i> MLST scheme.</p

Phylogenetic relationship between different <i>B. quintana</i> STs as determined by eBURST.

<p>A clonal complex contains STs that have 8 out of 9 alleles in common. ST5 is assigned as a singleton since it differed in 3–7 alleles from all other STs. The size of the circles relates to the frequency of the corresponding ST, and illustrates that the assigned primary founder of the major clonal complex (ST2) is a common clone.</p

Primers used for the amplification and sequencing of the nine genetic loci evaluated for the <i>B. quintana</i> MLST scheme.

1<p>Corresponding to the complete genome sequence of <i>B. quintana</i> strain Toulouse/copy Uppsala, GenBank accession number BX897700.1.</p

Characteristics of the 16 <i>B. quintana</i> isolates studied.

<p>HROEH was a DNA extract from the cardiac valve tissue of a patient with culture-negative endocarditis by <i>B. quintana</i>.</p>1<p>BA, bacillary angiomatosis.</p

Frequency of feline and human <i>B. henselae</i> isolates within each ST in correlation with the geographic origin of the isolates.

<p>Frequency of feline and human <i>B. henselae</i> isolates within each ST in correlation with the geographic origin of the isolates.</p

Correlation between ST and host species in 182 <i>B. henselae</i> isolates analysed.

a<p>Frequency of each ST among feline isolates</p>b<p>Frequency of each ST among human isolates</p>c<p>Frequency of an individual ST among all isolates</p>d<p>As determined by Fisher's exact test</p