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Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

Carnes J, Anupama A, Balmer O, Jackson A, Lewis M, Brown R, Cestari I, Desquesnes M, Gendrin C, Hertz-Fowler C, Imamura H, Ivens A, Kořený L, Lai DH, MacLeod A, McDermott SM, Merritt C, Monnerat S, Moon W, Myler P, Phan I, Ramasamy G, Sivam D, Lun ZR, Lukeš J, Stuart K, Schnaufer A - PLoS Negl Trop Dis (2015)

Bottom Line: Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality.Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA.Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

View Article: PubMed Central - PubMed

Affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.

ABSTRACT
Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

No MeSH data available.


Related in: MedlinePlus

Evaluation of the genetic differentiation between isolates of T. evansi and T. equiperdum and subspecies of T. brucei using principal component analysis (PCA) of microsatellite data.PCA was performed in R using the package adegenet. Within subspecies of T. brucei, the differentiation between temporally and geographically cohesive subgroups was estimated using DEST and calculated with the program smogd. Points representing individual genotypes are connected by a line to the centroid of an ellipse, which circumscribes a region encompassing 95% of the variance observed within six trypanosome subgroups identified: major T. evansi and T. equiperdum group (grey and pink), T. b. rhodesiense (red), T. b. brucei Kiboko (dark blue), T. b. brucei non-Kiboko (light blue), T. b. gambiense group 1 (dark green), T. b. gambiense group 2 (light green). T. evansi and T. equiperdum isolates that fell outside the major group are shown as black data points. The wide distribution of T. evansi and T. equiperdum isolates among distinct subgroups strongly supports multiple independent origins for these dyskinetoplastic strains. The first two principal components (PC1 and PC2) explain 29.2% and 8.4% of the total variance in the data, respectively. Data for isolates other than T. evansi and T. equiperdum had been published previously [40].
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pntd-0003404-g007: Evaluation of the genetic differentiation between isolates of T. evansi and T. equiperdum and subspecies of T. brucei using principal component analysis (PCA) of microsatellite data.PCA was performed in R using the package adegenet. Within subspecies of T. brucei, the differentiation between temporally and geographically cohesive subgroups was estimated using DEST and calculated with the program smogd. Points representing individual genotypes are connected by a line to the centroid of an ellipse, which circumscribes a region encompassing 95% of the variance observed within six trypanosome subgroups identified: major T. evansi and T. equiperdum group (grey and pink), T. b. rhodesiense (red), T. b. brucei Kiboko (dark blue), T. b. brucei non-Kiboko (light blue), T. b. gambiense group 1 (dark green), T. b. gambiense group 2 (light green). T. evansi and T. equiperdum isolates that fell outside the major group are shown as black data points. The wide distribution of T. evansi and T. equiperdum isolates among distinct subgroups strongly supports multiple independent origins for these dyskinetoplastic strains. The first two principal components (PC1 and PC2) explain 29.2% and 8.4% of the total variance in the data, respectively. Data for isolates other than T. evansi and T. equiperdum had been published previously [40].

Mentions: Incorporation of microsatellite data for a subset of T. evansi/T. equiperdum isolates into an established PCA network [40] also gave results that are inconsistent with monophyly of either species (Fig. 7). Most T. evansi isolates, together with Teq24 (STIB818), formed a cluster (grey circle) related to, but somewhat distinct from, non-Kiboko T. b. brucei (light blue circle) and T. b. rhodesiense (red circle). The single exception among T. evansi was again Tev42 (KETRI2479), which localized near the centre of the non-Kiboko cluster. Teq21 (BoTat1.1) was also more related to non-Kiboko T. b. brucei, but relatively distant from Tev42. The PCA analysis, consistent with the COX1 and LipDH data, suggested a relatively close evolutionary relationship of T. equiperdum STIB841/OVI (Teq23) with the Kiboko group of T. b. brucei (dark blue circle).


Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty.

Carnes J, Anupama A, Balmer O, Jackson A, Lewis M, Brown R, Cestari I, Desquesnes M, Gendrin C, Hertz-Fowler C, Imamura H, Ivens A, Kořený L, Lai DH, MacLeod A, McDermott SM, Merritt C, Monnerat S, Moon W, Myler P, Phan I, Ramasamy G, Sivam D, Lun ZR, Lukeš J, Stuart K, Schnaufer A - PLoS Negl Trop Dis (2015)

Evaluation of the genetic differentiation between isolates of T. evansi and T. equiperdum and subspecies of T. brucei using principal component analysis (PCA) of microsatellite data.PCA was performed in R using the package adegenet. Within subspecies of T. brucei, the differentiation between temporally and geographically cohesive subgroups was estimated using DEST and calculated with the program smogd. Points representing individual genotypes are connected by a line to the centroid of an ellipse, which circumscribes a region encompassing 95% of the variance observed within six trypanosome subgroups identified: major T. evansi and T. equiperdum group (grey and pink), T. b. rhodesiense (red), T. b. brucei Kiboko (dark blue), T. b. brucei non-Kiboko (light blue), T. b. gambiense group 1 (dark green), T. b. gambiense group 2 (light green). T. evansi and T. equiperdum isolates that fell outside the major group are shown as black data points. The wide distribution of T. evansi and T. equiperdum isolates among distinct subgroups strongly supports multiple independent origins for these dyskinetoplastic strains. The first two principal components (PC1 and PC2) explain 29.2% and 8.4% of the total variance in the data, respectively. Data for isolates other than T. evansi and T. equiperdum had been published previously [40].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4288722&req=5

pntd-0003404-g007: Evaluation of the genetic differentiation between isolates of T. evansi and T. equiperdum and subspecies of T. brucei using principal component analysis (PCA) of microsatellite data.PCA was performed in R using the package adegenet. Within subspecies of T. brucei, the differentiation between temporally and geographically cohesive subgroups was estimated using DEST and calculated with the program smogd. Points representing individual genotypes are connected by a line to the centroid of an ellipse, which circumscribes a region encompassing 95% of the variance observed within six trypanosome subgroups identified: major T. evansi and T. equiperdum group (grey and pink), T. b. rhodesiense (red), T. b. brucei Kiboko (dark blue), T. b. brucei non-Kiboko (light blue), T. b. gambiense group 1 (dark green), T. b. gambiense group 2 (light green). T. evansi and T. equiperdum isolates that fell outside the major group are shown as black data points. The wide distribution of T. evansi and T. equiperdum isolates among distinct subgroups strongly supports multiple independent origins for these dyskinetoplastic strains. The first two principal components (PC1 and PC2) explain 29.2% and 8.4% of the total variance in the data, respectively. Data for isolates other than T. evansi and T. equiperdum had been published previously [40].
Mentions: Incorporation of microsatellite data for a subset of T. evansi/T. equiperdum isolates into an established PCA network [40] also gave results that are inconsistent with monophyly of either species (Fig. 7). Most T. evansi isolates, together with Teq24 (STIB818), formed a cluster (grey circle) related to, but somewhat distinct from, non-Kiboko T. b. brucei (light blue circle) and T. b. rhodesiense (red circle). The single exception among T. evansi was again Tev42 (KETRI2479), which localized near the centre of the non-Kiboko cluster. Teq21 (BoTat1.1) was also more related to non-Kiboko T. b. brucei, but relatively distant from Tev42. The PCA analysis, consistent with the COX1 and LipDH data, suggested a relatively close evolutionary relationship of T. equiperdum STIB841/OVI (Teq23) with the Kiboko group of T. b. brucei (dark blue circle).

Bottom Line: Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality.Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA.Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

View Article: PubMed Central - PubMed

Affiliation: Seattle Biomedical Research Institute, Seattle, United States of America.

ABSTRACT
Two key biological features distinguish Trypanosoma evansi from the T. brucei group: independence from the tsetse fly as obligatory vector, and independence from the need for functional mitochondrial DNA (kinetoplast or kDNA). In an effort to better understand the molecular causes and consequences of these differences, we sequenced the genome of an akinetoplastic T. evansi strain from China and compared it to the T. b. brucei reference strain. The annotated T. evansi genome shows extensive similarity to the reference, with 94.9% of the predicted T. b. brucei coding sequences (CDS) having an ortholog in T. evansi, and 94.6% of the non-repetitive orthologs having a nucleotide identity of 95% or greater. Interestingly, several procyclin-associated genes (PAGs) were disrupted or not found in this T. evansi strain, suggesting a selective loss of function in the absence of the insect life-cycle stage. Surprisingly, orthologous sequences were found in T. evansi for all 978 nuclear CDS predicted to represent the mitochondrial proteome in T. brucei, although a small number of these may have lost functionality. Consistent with previous results, the F1FO-ATP synthase γ subunit was found to have an A281 deletion, which is involved in generation of a mitochondrial membrane potential in the absence of kDNA. Candidates for CDS that are absent from the reference genome were identified in supplementary de novo assemblies of T. evansi reads. Phylogenetic analyses show that the sequenced strain belongs to a dominant group of clonal T. evansi strains with worldwide distribution that also includes isolates classified as T. equiperdum. At least three other types of T. evansi or T. equiperdum have emerged independently. Overall, the elucidation of the T. evansi genome sequence reveals extensive similarity of T. brucei and supports the contention that T. evansi should be classified as a subspecies of T. brucei.

No MeSH data available.


Related in: MedlinePlus