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. 2017 Mar 6;11(3):e0005434. doi: 10.1371/journal.pntd.0005434

Fig 3. Unrooted tree based on the alignment of the TEND11qj_0488, TEND11qj_0548 and the remaining sequenced loci of the TEN 11q/j isolate.

Fig 3

A. An unrooted tree was constructed from a 505 bp-long sequence of the locus TP0488, shown in Fig 2A between coordinates 715–1221 corresponding to TEN Bosnia A numbering (CP007548; [16]). B. An unrooted tree constructed from a 613 bp-long sequence of the locus TP0548, shown in Fig 2B between coordinates 69 of TENDBA_0547a and coordinate 623 of TENDBA_0548 (CP007548; [16]). C. An unrooted tree was constructed from concatenated sequences of 42 genomic regions of the 11q/j isolate, except for the TP0488 and TP0548 genes, and respective sequences of TPA strains (Nichols, SS14), TPE strains (CDC-2, Gauthier, Samoa D, and Fribourg-Blanc), and the TEN strains (Bosnia A, Iraq B) using the Maximum Likelihood method and MEGA7 software [31]. Bootstrap values based on 1,000 replications are shown next to the branches. All positions containing indels in at least one genome sequence were omitted from the analysis. There was a total of 29,447 nucleotide positions aligned in the final dataset. The bar scale corresponds to a difference of 0.005 (A.), 0.005 (B.) and 0.001 (C.) nucleotides. While the 11q/j isolate cluster in the TP0488 locus with TPA strains and in the TP0548 locus with TPE strains, a tree constructed from concatenated sequences of 42 genomic regions of the 11q/j isolate cluster with TEN strains. A position within the tree where the putative recombination events, involving TP0488 and TP0548, likely occurred is shown, respectively.