Newly identified genomic regions showing intrastrain heterogeneity in the TPA SS14-RS genome.

<p>Underlined variants were used in the improved whole genome sequence of the TPA SS14 strain (CP004011.1). Corresponding amino acid variants are shown in brackets.</p>a<p>variant nucleotides are part of the same codon (therefore cause the same amino acid change).</p

Effects of error correction on the improved TPA Nichols-RS genome with respect to comparisons with other TPA strains.

<p>The left part of the table shows former number of differences between the original TPA Nichols genome (AE000520.1) and other TPA genomes, the right part of the table shows verified number of differences between the improved TPA Nichols genome (CP004010.2) and other TPA genomes. Numbers in brackets show the percentage of verified differences between the improved TPA Nichols genome and other genomes compared to numbers observed during the comparison of the original Nichols genome and other TPA genomes. Because of high sequence diversities, <i>tprD</i> and <i>tprK</i> were excluded from the analyses.</p><p>sub, substitution; in, insertion; del, deletion.</p

Distribution of identified errors in the original TPA Nichols and TPA SS14 genome sequences.

<p>Note that the chromosomal positions of identified errors are highly similar in both genomes as a result of the CGS sequencing approach used for sequencing the SS14 genome <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074319#pone.0074319-Matjkov1" target="_blank">[9]</a>.</p

Unrooted trees constructed from whole genome sequences of TPA strains.

<p>Trees were constructed using the Neighbor-Joining method using the Tamura-Nei genetic distance model and 1,000 bootstrap replicates. The numbers above the branches show bootstrap support and the bar scale represents 0.0001 substitutions per target site. A. A tree constructed from the alignment of genomes from TPA strains Chicago (CP001752.1), DAL-1 (CP003115.1) and Mexico A (CP003064.1) with original versions of whole genome sequences of TPA Nichols (AE000520.1) and SS14 (CP000805.1). B. A tree constructed from alignment of genomes from TPA strains Chicago (CP001752.1), DAL-1 (CP003115.1) and Mexico A (CP003064.1) with the improved whole genome sequences of TPA Nichols-RS (CP004010.2) and SS14-RS (CP004011.1).</p

Calculated nucleotide diversities (π ± standard deviation) between individual TPA strains and the original and resequenced versions of the Nichols and SS14 strains.

<p>Calculated nucleotide diversities (π ± standard deviation) between individual TPA strains and the original and resequenced versions of the Nichols and SS14 strains.</p

A schematic representation of errors identified in the original TPA Nichols and TPA SS14 genomes.

<p>The corresponding effects of error corrections are shown. AF stands for authentic frameshift. The group denoted “Other changes” includes in-frame errors; indels in the RNA region and indels in genes with annotated authentic frameshifts (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074319#pone.0074319.s004" target="_blank">Table S4</a>). A. Effects of error corrections on the TPA Nichols genome. B. Effects of error corrections on the TPA SS14 genome. The numbers close to arrows indicate the number of nucleotide changes leading to changes in the proteome.</p

Effects of error correction on the improved TPA SS14-RS genome with respect to other TPA strains.

<p>The left part of the table shows former number of differences between the original TPA SS14 genome (CP000805.1) and other TPA genomes, the right part of the table shows verified number of differences between the improved TPA SS14 genome (CP004011.1) and other TPA genomes. Numbers in brackets show the percentage of verified differences between the improved TPA SS14 genome and other genomes compared to numbers observed during the comparison of the original SS14 genome and other TPA genomes. Because of high sequence diversities, <i>tprD</i> and <i>tprK</i> were excluded from the analyses. Please note that the number of sequence differences between TPA SS14 and Nichols genomes increased after error correction.</p><p>sub, substitution; in, insertion; del, deletion.</p

G+C content variation in selected <i>Treponema</i> strains.

<p>TPA Mexico A, TPA SS14, TPE Samoa D and <i>Treponema paraluiscuniculi</i> strain Cuniculi A were analyzed. Colored vertical lines represent 501 bp-long windows with G+C content above the 63% or below the 41% threshold. Black vertical lines represent genome locations of <i>tpr</i> genes. Stars denote 5 kb-long DNA regions with 40 or more nucleotide positions differentiating TPA and TPE strains <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Cejkova1" target="_blank">[7]</a>. Please note that there is no clear association of DNA regions with different G+C content and regions differentiating TPA and TPE strains <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Cejkova1" target="_blank">[7]</a> or locations of <i>tpr</i> genes.</p

A list of changes found in the TPAMA_0326 locus.

<p>Three TPA (Nichols, SS14, and Chicago) and three TPE (CDC-2, Gauthier, and Samoa D) strains were analyzed. The numbers in square brackets correspond to amino acid position in the TPAMA_0326 protein. The amino acid sequence of the encoded protein is shown in brackets.</p>1)<p>Domain prediction according to Desrosiers <i>et al.</i><a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001832#pntd.0001832-Desrosiers1" target="_blank">[41]</a>.</p>2)<p>G (R) was found in TPE CDC-2 strain, G (E) in TPE Gauthier, while T (N) was found in TPE Samoa D strain.</p>3)<p>15 bp (GTAGAACCACCAGCT) encode SRTTS in TPA Nichols and Chicago strain and 15 bp (GTAGCACCACCAGCT) encode SSTTS in TPA SS14 strain.</p

Two possible molecular mechanisms resulting in formation of the mosaic structure of the TPAMA_0326 locus.

<p>Green lines are nucleotide sequences specific for TPA strains (Nichols, SS14, Chicago), red ones for TPE strains (CDC-2, Gauthier, Samoa D). Vertical black lines denote corresponding positions of the TPAMA_0326 loci. A) Homologous recombination. 1. Homologous recombination between TPA and TPE loci with suggested possible recombination sites (x); arrow indicates direction of branch migration. 2. The resulting heteroduplex contains both TPA and TPE sequences; green loop denotes a 15 bp insertion present in all investigated TPA strains. 3. Recognition of mismatched DNA by MutS-MutL complex and subsequent cleavage of DNA strands by endonucleases (marked by arrows). 4. Unwinding of cleaved strands by DNA helicase (open elipse) and DNA polymerase-mediated (grey) gap filling. 5. Reparation of DNA breaks with DNA ligase. Alternatively, there is a possibility of an active DNA uptake across the cell membrane. Although no gene orthologs involved in natural competence have been identified in the TPA genomes, one cannot exclude this activity in one or several genes with unknown function. B) Gene conversion. Successive half crossing-over model. 1. First half crossing-over with suggested recombination site (x). 2. Successive second half crossing-over and the second recombination site (x). 3. Duplex recovery and degradation of both displaced ends. Please note that model B) requires the presence of two TPA-like nucleotide sequences in the donor TPE sequence.</p