Location of the identified SNPs on the main chromosome (full pink bars) in comparison to the loci used for typing of Borrelia species IGS (blue), MST (pink) and MLST (green).

<p>Location of the identified SNPs on the main chromosome (full pink bars) in comparison to the loci used for typing of Borrelia species IGS (blue), MST (pink) and MLST (green).</p

BRIG representation of the shortest identified plasmid from <i>B</i>. <i>recurrentis</i> A1 pl6 in comparison to <i>B</i>. <i>miyamotoi</i>, <i>B</i>. <i>crocidurae</i>, <i>B</i>. <i>hermsii</i> and the <i>de novo</i> assembled contigs assembled with the CLC or SPAdes assembler as exemplified with A17, PMaC and PUfa isolates.

<p>BRIG representation of the shortest identified plasmid from <i>B</i>. <i>recurrentis</i> A1 pl6 in comparison to <i>B</i>. <i>miyamotoi</i>, <i>B</i>. <i>crocidurae</i>, <i>B</i>. <i>hermsii</i> and the <i>de novo</i> assembled contigs assembled with the CLC or SPAdes assembler as exemplified with A17, PMaC and PUfa isolates.</p

Isolates examined in this study.

<p>Isolates examined in this study.</p

Number of sequenced reads per sample mapped to the reference genome <i>B</i>. <i>recurrentis</i> A1.

<p>Number of sequenced reads per sample mapped to the reference genome <i>B</i>. <i>recurrentis</i> A1.</p

Statistics of <i>de novo</i> assembled contigs with SPAdes <i>de novo</i> assembler.

<p>Statistics of <i>de novo</i> assembled contigs with SPAdes <i>de novo</i> assembler.</p

Primers used for confirmation of plasmids in <i>B</i>. <i>recurrentis</i>.

<p>Primers used for confirmation of plasmids in <i>B</i>. <i>recurrentis</i>.</p

A phylogenetic tree based on 23 SNP positions identified on the main chromosome.

<p>Evolutionary analysis was performed using MEGA7. B Phylogenetic tree based on 47 SNP positions identified on the whole genome of <i>Borrelia recurrentis</i>. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model.</p

BRIG representation of the longest identified plasmid from <i>B</i>. <i>duttonii</i> pl165 in comparison to <i>B</i>. <i>crocidurae</i>, <i>B</i>. <i>recurrentis</i> A1 and the <i>de novo</i> assembled contigs assembled with the CLC assembler as exemplified by PBek, PAbJ and <i>de novo</i> assembled contigs from the 3% reads of the respective isolates not mapped to the reference strain A1 in the CLC mapping step.

<p>BRIG representation of the longest identified plasmid from <i>B</i>. <i>duttonii</i> pl165 in comparison to <i>B</i>. <i>crocidurae</i>, <i>B</i>. <i>recurrentis</i> A1 and the <i>de novo</i> assembled contigs assembled with the CLC assembler as exemplified by PBek, PAbJ and <i>de novo</i> assembled contigs from the 3% reads of the respective isolates not mapped to the reference strain A1 in the CLC mapping step.</p

Statistics of <i>de novo</i> assembled contigs with CLC <i>de novo</i> assembler.

<p>Statistics of <i>de novo</i> assembled contigs with CLC <i>de novo</i> assembler.</p

Geographic distribution of the sampling sites in Canada.

<p>A map of northern North America showing the names of the main Canadian provinces. Red dots indicate the locations of sample sites in each of the four regions where samples from animal hosts were available which are indicated by the abbreviations used in the text (MB = Manitoba, ONRv = Rainy River Ontario, QC = southern Quebec and MR = the Maritime provinces of Nova Scotia and New Brunswick).</p