Figure 1.
Distribution of identified errors in the original TPA Nichols and TPA SS14 genome sequences.
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 [9].
Figure 2.
A schematic representation of errors identified in the original TPA Nichols and TPA SS14 genomes.
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 Table S4). 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.
Figure 3.
Nucleotide (amino acid) sequence alignments of TPA Nichols tprK (TprK) variable regions.
Only sequence variants obtained by sequencing at least two independent clones are shown. Numbers in brackets correspond to number of clones with the same sequence variant. Because one could expect higher variability with more clones sequenced, Ns (Xs) were placed along the entire length of variable area. A) Nucleotide alignment of TPA Nichols tprK variable regions. B) Amino acid alignment of TPA Nichols TprK variable regions.
Table 1.
Newly identified genomic regions showing intrastrain heterogeneity in the TPA SS14-RS genome.
Figure 4.
Unrooted trees constructed from whole genome sequences of TPA strains.
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).
Table 2.
Effects of error correction on the improved TPA Nichols-RS genome with respect to comparisons with other TPA strains.
Table 3.
Effects of error correction on the improved TPA SS14-RS genome with respect to other TPA strains.
Table 4.
Calculated nucleotide diversities (π ± standard deviation) between individual TPA strains and the original and resequenced versions of the Nichols and SS14 strains.