Congopain genes diverged to become specific to Savannah, Forest and Kilifi subgroups of Trypanosoma congolense, and are valuable for diagnosis, genotyping and phylogenetic inferences

Rodrigues, Ana Carolina; Ortíz, Paola A.; Costa-Martins, André G.; Neves, Luís; García, Herakles A.; Alves, João M. P.; Camargo, Erney P.; Alfieri, Silvia C.; Gibson, Wendy; Teixeira, Marta Maria Geraldes

doi:10.1016/j.meegid.2014.01.012

Cited by 18 publications

(27 citation statements)

References 61 publications

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“…We are not sure which "previous authors" Tibayrenc and Ayala are referring to (see also concerns raised by Ramirez and Llewellyn (2015) and Rougeron, De Meeûs, and Banuls (2015) on the practice of self-and mis-citation by Tibayrenc and Ayala). Perhaps the authors were referring to the work of Simo et al (2013) or Rodrigues et al (2014), but these studies found evidence of clonality in Forest T. congolense while the Savannah subgroup was the main subject in our study (see also section 1). Importantly, note that the results of Rodriguez and colleagues suggested that recombination may be an important process in generating a diverse repertoire of the congopain genes in the Savannah subgroup (Rodrigues et al, 2014).…”

Section: Infrequent-recombinationmentioning

confidence: 84%

“…There is currently no evidence from the field for genetic exchange between any of the T. congolense subgroups, suggesting that the subgroups represent clades (not near‐clades). Indeed, earlier observations based on congopain gene diversity showed that the genetic distances between the T. congolense subgroups (Forest, Savannah and Kilifi) are larger than the divergence between T. simiae and T. godfreyi , suggesting that the T. congolense subgroups may represent different species (Rodrigues et al., ). Hence, the significant divergence between T. congolense Forest and Savannah supports the biological species concept (see also in Gibson, ), namely a species concept based on restricted gene flow, in which genes are exchanged by recombination within but not between species.…”

Section: Genetic Subdivision Does Not Imply Clonal Evolutionmentioning

confidence: 99%

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Mitonuclear genomics challenges the theory of clonality in Trypanosoma congolense: Reply to Tibayrenc and Ayala

et al. 2018

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We recently published the first genomic diversity study of Trypanosoma congolense, a major aetiological agent of Animal African Trypanosomiasis. We demonstrated striking levels of SNP and indel diversity in the Eastern province of Zambia as a consequence of hybridization between divergent trypanosome lineages. We concluded that these and earlier findings in T. congolense challenge the predominant clonal evolution (PCE) model. In a recent comment, Tibayrenc and Ayala claim that there are many features in T. congolense supporting their theory of clonality. While we can follow the reasoning of the authors, we also identify major limitations in their theory and interpretations that resulted in incorrect conclusions. First, we argue that each T. congolense subgroup should be analysed independently as they may represent different (sub)species rather than "near-clades". Second, the authors neglect major findings of two robust population genetic studies on Savannah T. congolense that provide clear evidence of frequent recombination. Third, we reveal additional events of introgressive hybridization in T. congolense by analysing the maxicircle coding region using next-generation sequencing analyses. At last, we pinpoint two important misinterpretations by the authors and show that there are no spatially and temporally widespread clones in T. congolense. We stand by our earlier conclusions that the clonal framework is unlikely to accurately model the population structure of T. congolense. Other theoretical frameworks such as Maynard Smith's epidemic model may better represent the complex ancestry seen in T. congolense, where clones delimited in space and time arise against a background of recombination.

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Section: Infrequent-recombinationmentioning

confidence: 84%

Section: Genetic Subdivision Does Not Imply Clonal Evolutionmentioning

confidence: 99%

Mitonuclear genomics challenges the theory of clonality in Trypanosoma congolense: Reply to Tibayrenc and Ayala

et al. 2018

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“…Novel trypanosomes from tsetse flies [7, 25, 26, 29, 30, 44–46] and African ungulates [2, 23, 24, 34] were reported in eastern and central-southern African wildlife conservation areas.…”

Section: Discussionmentioning

confidence: 99%

“…The alignment was manually adjusted, and network split decomposition was inferred using the Neighbor-Net method with Kimura 2 parameters implemented as previously described [33, 34]. Internode support was estimated with 100 bootstrap replicates, using the parameters optimised for network inferences.…”

Section: Methodsmentioning

confidence: 99%

New insights from Gorongosa National Park and Niassa National Reserve of Mozambique increasing the genetic diversity of Trypanosoma vivax and Trypanosoma vivax-like in tsetse flies, wild ungulates and livestock from East Africa

et al. 2017

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Background Trypanosoma (Duttonella) vivax is a major pathogen of livestock in Africa and South America (SA), and genetic studies limited to small sampling suggest greater diversity in East Africa (EA) compared to both West Africa (WA) and SA.MethodsMultidimensional scaling and phylogenetic analyses of 112 sequences of the glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) gene and 263 sequences of the internal transcribed spacer of rDNA (ITS rDNA) were performed to compare trypanosomes from tsetse flies from Gorongosa National Park and Niassa National Reserve of Mozambique (MZ), wild ungulates and livestock from EA, and livestock isolates from WA and SA.ResultsMultidimensional scaling (MDS) supported Tvv (T. vivax) and TvL (T. vivax-like) evolutionary lineages: 1) Tvv comprises two main groups, TvvA/B (all SA and WA isolates plus some isolates from EA) and TvvC/D (exclusively from EA). The network revealed five ITS-genotypes within Tvv: Tvv1 (WA/EA isolates), Tvv2 (SA) and Tvv3–5 (EA). EA genotypes of Tvv ranged from highly related to largely different from WA/SA genotypes. 2) TvL comprises two gGAPDH-groups formed exclusively by EA sequences, TvLA (Tanzania/Kenya) and TvLB-D (MZ). This lineage contains more than 11 ITS-genotypes, seven forming the lineage TvL-Gorongosa that diverged from T. vivax Y486 enough to be identified as another species of the subgenus Duttonella. While gGAPDH sequences were fundamental for classification at the subgenus, major evolutionary lineages and species levels, ITS rDNA sequences permitted identification of known and novel genotypes.ConclusionsOur results corroborate a remarkable diversity of Duttonella trypanosomes in EA, especially in wildlife conservation areas, compared to the moderate diversity in WA. Surveys in wilderness areas in WA may reveal greater diversity. Biogeographical and phylogenetic data point to EA as the place of origin, diversification and spread of Duttonella trypanosomes across Africa, providing relevant insights towards the understanding of T. vivax evolutionary history.Electronic supplementary materialThe online version of this article (doi:10.1186/s13071-017-2241-2) contains supplementary material, which is available to authorized users.

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“…Os tripanossomas do subgênero Nannomonas desenvolvem-se no intestino médio e na probóscide das moscas tsé-tsé, gerando patogenias severas em suínos domésticos (Adams et al, 2010;Rodrigues et al, 2014).…”

Section: O Clado T Brucei Compreende Os Tripanossomas Africanos Dos unclassified

Spliced Leader (SL) RNA: análises de genes e regiões intergênicas com aportes na filogenia, taxonomia e genotipagem de <i>Trypanosoma</i> spp. de todas as classes de vertebrados.

Alvarez¹

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Congopain genes diverged to become specific to Savannah, Forest and Kilifi subgroups of Trypanosoma congolense, and are valuable for diagnosis, genotyping and phylogenetic inferences

Cited by 18 publications

References 61 publications

Mitonuclear genomics challenges the theory of clonality in Trypanosoma congolense: Reply to Tibayrenc and Ayala

Mitonuclear genomics challenges the theory of clonality in Trypanosoma congolense: Reply to Tibayrenc and Ayala

New insights from Gorongosa National Park and Niassa National Reserve of Mozambique increasing the genetic diversity of Trypanosoma vivax and Trypanosoma vivax-like in tsetse flies, wild ungulates and livestock from East Africa

Spliced Leader (SL) RNA: análises de genes e regiões intergênicas com aportes na filogenia, taxonomia e genotipagem de <i>Trypanosoma</i> spp. de todas as classes de vertebrados.

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