16S rRNA gene SNP-based phylogeny of <i>C</i>. <i>burnetii</i>.

<p>This rooted phylogenetic tree was created from pairwise distances observed from 16S rRNA gene SNP sites. The five SNPs and one insertion identified among the 55 16S rRNA gene sequences gave rise to six groups (color coded). Based on sequence alignment to the 16S rRNA gene of <i>C</i>. <i>burnetii</i> Nine Mile (bold), SNPs at positions 64, 164, 622, 830, and 1022 and an insertion at positon 213 (in parentheses) gave rise to the six distinct SNP signatures, which are displayed on their respective branches.</p

55 <i>Coxiella burnetii</i> strains used in this study and SNPs within their respective 16S rRNA genes.

<p>55 <i>Coxiella burnetii</i> strains used in this study and SNPs within their respective 16S rRNA genes.</p

Comparison of typing methods.

<p>Comparison of typing methods.</p

Insertion polymorphism identified in the 16S rRNA gene of <i>C</i>. <i>burnetii</i> Mauriet.

<p>(A) DNA sequences obtained using primers E8F and E341R designate an adenine insertion at nucleotide position 213 which is confirmed in the electropherograms generated by Sequencher™ analysis software. (B) Sequence alignment shows 16S rRNA genes of <i>C</i>. <i>burnetii</i> Z3055 (GenBank accession number NZ_LK937696) and 3262 (GenBank accession number CP013667) also possess this insertion which is absent in the Nine Mile reference (Ref) strain sequence.</p

MST loci SNP-based phylogeny of <i>C</i>. <i>burnetii</i>.

<p>This rooted phylogenetic tree was created from pairwise distances observed from 14 SNP sites within MST loci. SNP positions in <i>C</i>. <i>burnetii</i> Nine Mile (bold) are outlined in Hornstra <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0189910#pone.0189910.ref019" target="_blank">19</a>]. The predicted genomic groups from this phylogenetic analysis are circled in blue and the 16S rRNA gene-based groups are color coded for comparison.</p

SupportingInformationS3

S3. Rooted maximum parsimony tree of C. burnetii MST genotypes (1-34 and Dugway) after Hornstra et al. (Hornstra, Priestley, et al. 2011). Whole genome sequences are mapped onto the tree and the major genomic groups of C. burnetii are identified

Supplementary Information S1

S1. SNP matrix of 11,286 orthologous SNPs discovered among ten C. burnetii genomes