List of the primers used in this work.

1<p>An s in a primer's name indicates that it was used for sequencing only. Primers marked with n were used in nested PCR reactions.</p

Coefficient of similarity between genetic loci of local <i>B. persica</i> and other TBRF <i>Borrelia</i> species.

<p>na: not available.</p><p>All local strains were included in the assessment of similarity range among <i>B. persica</i> isolates studied in this work. We used the sequences of <i>B. persica</i> strain HL2610 (relevant accession numbers are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#s2" target="_blank">materials and methods</a>) for comparison with other TBRF <i>Borrelia</i> available homologous genes: <i>B. persica</i> Iran <i>rrs</i> (U42297), <i>glp</i>Q of <i>B. persica</i> Iran (EU914143), <i>B. hispanica rrs</i> (U42294), <i>B. hispanica rrs-ileT</i> IGS (FJ827590), <i>B. recurrentis</i> complete genome (CP000993), <i>B. duttonii</i> complete genome (CP000976), <i>B. hermsii</i> complete genome (CP000048) and <i>B. turicatae</i> complete genome (CP000049). Vector NTI advance 11 software was used for sequence alignments.</p

Phylogenetic tree based on <i>pur</i>A nucleotide sequences.

<p>The complete <i>pur</i>A sequences of <i>B. persica</i> isolates in Israel and the West Bank were compared to <i>pur</i>A sequences from other <i>Borrelia</i> species (accession number are given in parentheses). The Phylogenic tree was inferred using the UPGMA method. Parameters were as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-g002" target="_blank">Figure 2</a>. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). There were a total of 1284 positions in the final dataset.</p

Phylogenic tree based on <i>glp</i>Q nucleotide sequences.

<p><i>glp</i>Q sequences of 18 independent isolates from Israel and the West Bank belonging to genovars G1 to G4 were compared to <i>glp</i>Q sequences from other <i>Borrelia</i> species (accession numbers are given in parentheses). The isolates in each genovar are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-t001" target="_blank">Table 1</a>. The phylogenic tree was inferred using the UPGMA method as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-g002" target="_blank">Figure 2</a>. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). There were a total of 637 positions in the final dataset.</p

Phylogenic tree based on <i>rrs-ile</i>T spacer (IGS) sequences.

<p>The <i>rrs-ile</i>T spacer (IGS) sequences for 16 independent isolates from Israel and the West Bank belonging to genovars a to c were compared to IGS sequences from other <i>Borrelia</i> species (accession numbers are given in parentheses). The isolates in each genovar are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-t001" target="_blank">Table 1</a>. The phylogenic tree was inferred using the UPGMA method as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-g002" target="_blank">Figure 2</a>. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). There were a total of 349 positions in the final dataset.</p

Variable nucleotide positions and genovar definition based on the <i>pur</i>A gene of 8 human and tickborne isolates of <i>B. persica</i> in Israel and the West Bank.

<p>nd: not done.</p>1<p>List of isolates in each genovar is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-t001" target="_blank">Table 1</a>.</p>2<p>Positions of nucleotide changes are numbered according to the 7231 contig (HM131216) (this work). Where relevant, the resulting amino acid modification is shown in parenthesis.</p

Characterization of the isolates investigated in this work.

1<p>Typing and genovar determination were performed for the genes encoding Flagellin (<i>fla</i>B), Glycerophosphodiester phosphodiesterase (<i>glp</i>Q), 16S rRNA (rrs), Adenylosuccinate synthetase (<i>pur</i>A), and the intergenic spacer (IGS) between <i>rrs</i> and the ile tRNA (<i>ile</i>T) and between <i>rrs</i> and the 23S rRNA (<i>rrlA</i>).</p>2<p>nd: not done.</p

Phylogenic tree based on <i>rrs</i> sequences.

<p>The complete <i>rrs</i> sequences of <i>B. persica</i> isolates in Israel were compared to <i>rrs</i> sequences from <i>B. persica</i> (Iran) and other <i>Borrelia</i> species (accession numbers are given in parentheses). The phylogenic tree was inferred using the UPGMA method. Parameters were as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#pone-0014105-g002" target="_blank">Figure 2</a>. All positions containing gaps and missing data were eliminated from the dataset (Complete deletion option). There were a total of 1522 positions in the final dataset.</p

Phylogenetic tree based on the concatenated alignments of <i>pur</i>A, <i>glp</i>Q, <i>fla</i>B and <i>rrs-ile</i>T IGS nucleotide sequences.

<p>The tree was inferred using the PHYML program. The percentage of trees in which the associated taxa clustered together in the bootstrap test (100 replicates) is shown next to the branches if higher than 80%. The tree was arbitrarily rooted at midpoint.</p

Physical map of the <i>rrs</i>-<i>rrl</i>A genomic region (7231 contig) of <i>Borrelia persica</i>.

<p>The genes and their orientation are indicated by empty arrows. The position of each locus on the 7231 contig is given in parentheses. Positions of nucleotides polymorphism are indicated by black arrows. Nucleotide changes resulting in amino acid modifications are marked with an asterisk.</p