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

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

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

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

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

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

Variability and genovar distribution based on the 16S rRNA gene (<i>rrs</i>) sequences of <i>B. persica</i> in Israel and Iran.

<p>The accession numbers of all <i>rrs</i> sequences of Israeli isolates, complete and partial, are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014105#s2" target="_blank">materials and methods</a>. Accession numbers of the Iranian strains are U42297 (complete sequence) and EU914141 (partial sequence).</p>1<p>The number in parenthesis indicates the number of isolates in each genovar for which the complete <i>rrs</i> sequences are available.</p>2<p>Numbering of the nucleotide positions is according to the complete <i>rrs</i> sequence of the R1 strain H1039 (HM161645). Bold letters indicate the nucleotide changes that define the genovars.</p

Variable nucleotide positions and genovar definition based on the sequences of the <i>glp</i>Q gene of 18 human and tick-borne isolates of <i>B. persica</i> in Israel and the West Bank.

1<p>List of isolates for 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 <i>glp</i>Q sequence of isolate H1015 (HM161654) (this work). Where relevant, the resulting amino acid modification is shown in parenthesis.</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