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

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>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

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

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