Abstract
African trypanosomes of the sub-genus Trypanozoon) are eukaryotic parasitesthat cause disease in either humans or livestock. The development of genomic resources can be of great use to those interested in studying and controlling the spread of these trypanosomes. Here we present a large comparative analysis of Trypanozoon whole genomes, 83 in total, including human and animal infective African trypanosomes: 21 T. brucei brucei, 22 T. b. gambiense, 35 T. b. rhodesiense and 4 T. evansi strains, of which 21 were from Uganda. We constructed a maximum likelihood phylogeny based on 162,210 single nucleotide polymorphisms (SNPs.) The three Trypanosoma brucei sub-species and Trypanosoma evansi are not monophyletic, confirming earlier studies that indicated high similarity among Trypanosoma “sub-species”. We also used discriminant analysis of principal components (DAPC) on the same set of SNPs, identifying seven genetic clusters. These clusters do not correspond well with existing taxonomic classifications, in agreement with the phylogenetic analysis. Geographic origin is reflected in both the phylogeny and clustering analysis. Finally, we used sparse linear discriminant analysis to rank SNPs by their informativeness in differentiating the strains in our data set. As few as 84 SNPs can completely distinguish the strains used in our study, and discriminant analysis was still able to detect genetic structure using as few as 10 SNPs. Our results reinforce earlier results of high genetic similarity between the African Trypanozoon. Despite this, a small subset of SNPs can be used to identify genetic markers that can be used for strain identification or other epidemiological investigations.
Highlights
Trypanosomes are single-celled, eukaryotic parasites of mammalian bloodstreams that are a major health and economic burden on communities with endemic circulating strains
Comparative genomics of African trypanosomes had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
This is especially true in sub-Saharan Africa, where trypanosomes belonging to the species Trypanosoma brucei are vectored between human and animal hosts by the tsetse fly
Summary
Trypanosomes are single-celled, eukaryotic parasites of mammalian bloodstreams that are a major health and economic burden on communities with endemic circulating strains. Trypanosoma brucei brucei (Tbb) causes nagana in livestock, while Trypanosoma brucei gambiense (Tbg) causes chronic sleeping sickness and Trypanosoma brucei rhodesiense (Tbr) causes acute sleeping sickness in humans This species, along with Trypanosoma evansi (Tev) and Trypanosoma equiperdum (Teq) comprise the sub-genus Trypanozoon. Most of the African Trypanozoon taxa are morphologically indistinguishable, with the main differences between them being the host in which the trypanosome causes disease or the insect vector that enables their distribution (with the exception of Teq, which has lost its dependence on an arthropod host) Both Tev and Teq have lost all or part of their kinetoplastid DNA (analogous to mitochondrial DNA in other eukaryotes [2]). The ability for some groups to recombine [6], each group has developed divergent phenotypes that affect their range and impact on humans and livestock
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