Median-Joining network of 9 and 15 haplotypes observed in <i>T</i>. <i>parva</i> population in South Sudan based on the polymorphic sites of (A) Tp1 and (B) Tp2 genes, respectively.

<p>The sizes of the circles are proportional to the haplotype frequencies. The origin of each haplotype is colour coded as follows: Bor = Yellow; Juba = Red; Yei = Blue; Kajo keji = Green; Median vector = Brown; <i>T</i>. <i>parva</i> Muguga = Black. The numbers in red in (A) represent the mutations that differentiate the haplotypes.</p

Multiple amino acid sequence alignment of Tp1 and Tp2 antigen variants present in cattle from South Sudan.

<p>(A) Multiple sequence alignment of the four Tp1 antigen variants. Antigen variants Var-1, -3 and -9 were first described by Pelle et al. (2011) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171426#pone.0171426.ref017" target="_blank">17</a>]. (B) Multiple sequence alignment of 14 Tp2 antigen variants. The naming of the antigen variants follows the nomenclature by Pelle et al. (2011) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171426#pone.0171426.ref017" target="_blank">17</a>]. Antigen variants Var-1, -2 and -5 were first described by Pelle et al. (2011) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0171426#pone.0171426.ref017" target="_blank">17</a>]. The CD8⁺ T-cell target epitopes are boxed and the polymorphic residues in the epitopes are shown in red. The frequency of each variant amongst the samples tested is indicated in square brackets. Residues conserved in all sequences are identified below the alignment (*). The shaded flanking regions are equivalent to the positions of the secondary (nested) PCR primers, and are not included in estimations of the percentage of the residues that are conserved.</p

Map of South Sudan showing the sampling sites.

<p>The four areas where cattle samples were collected are colour coded as follows: Bor = Blue; Juba = Orange; Yei = Green; Kajo keji = Red. Numbers in brackets indicate the number of cattle sampled at each site.</p

Neighbour-joining trees of Tp1 and Tp2 gene sequences indicating phylogeographic relationships among cattle derived <i>T</i>. <i>parva</i> isolates.

<p>The isolates are color-coded based on their geographic origin in South Sudan and alleles which are represented by these samples are shown in brackets. The colour codes are as follows: Bor = Blue; Juba = Orange; Yei = Green; Kajo keji = Red. Bootstrap values >50% are shown above the nodes. (A) Tree showing relationships between Tp1 gene sequences from 79 cattle isolates of <i>T</i>. <i>parva</i>. The TP03_0849 gene from the <i>T</i>. <i>parva</i> (Muguga) genome sequence was also included in the analysis (Tp1-F100-TpM). The sequence of <i>T</i>. <i>annulata</i> Tp1 homologue (TA17450) was used to root the tree. (B) Tree showing relationships among Tp2 gene sequences from 65 cattle-derived <i>T</i>. <i>parva</i> isolates. The TP01_0056 gene from <i>T</i>. <i>parva</i> (Muguga) genome sequence was also included in the analysis (Tp2-F100-TpM). The Tp2 homologous sequence from <i>T</i>. <i>annulata</i> (TA19865) was used to root the tree.</p

Principal component analysis (PCA) of Tp1 (A) and Tp2 (B).

<p>This diagram illustrates the relationship between the geographic origin of the samples and the Muguga strain. The proportion of variation in the dataset explained by the 1^st and 2^nd principal components is indicated in parentheses.</p