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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

Frequency distribution of nucleotide identity between orthologous T. evansi vs. T. brucei coding sequences, including pseudogenes.This graph represents 8290 CDS with the highest identities out of 8421 total non-repetitive sequences analyzed.
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pntd-0003404-g002: Frequency distribution of nucleotide identity between orthologous T. evansi vs. T. brucei coding sequences, including pseudogenes.This graph represents 8290 CDS with the highest identities out of 8421 total non-repetitive sequences analyzed.

Mentions: Of the 9368 T. evansi CDS identified as T. brucei orthologs, 8421 CDS were classified as non-repetitive genes; the remaining 947 CDS were VSG, ESAG, RHS, or duplicate sequences. A comparison of the 8421 non-repetitive CDS between T. brucei and T. evansi revealed 7970 (94.6%) had a nucleotide identity of 95% or greater, 320 (3.8%) had a nucleotide identity between 70–95%, and 131 (1.6%) had a nucleotide identity less than 70% (Fig. 2; S1 Fig.). After RATT annotation transfer, a total of 503 (5.1%) Tb927 GeneIDs did not have identified orthologs in the TevSTIB805ra annotated genome (Table 1, column G; S2 Table). The majority of these (406) represent repetitive genes (e.g. VSG, ESAG, and RHS) or ‘hypothetical unlikely’ genes, which were not analyzed further. Five CDS correspond to predicted pseudogenes. T. evansi STIB805 orthologs for 49 Tb927 CDS were shown to be wholly or partially missing in TevSTIB805 reads that mapped to these gene loci (see below). T. evansi homologs for the remaining 43 Tb927 GeneIDs were ‘missed’ by RATT and AutoMagi, but were subsequently identified by manual examination of the T. evansi sequence. Thus, the majority of T. brucei CDS have extremely similar T. evansi orthologs, and very few T. brucei CDS were not found in T. evansi. This result is consistent with a very close phylogenetic relationship between these parasites.


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)

Frequency distribution of nucleotide identity between orthologous T. evansi vs. T. brucei coding sequences, including pseudogenes.This graph represents 8290 CDS with the highest identities out of 8421 total non-repetitive sequences analyzed.
© Copyright Policy
Related In: Results  -  Collection

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

pntd-0003404-g002: Frequency distribution of nucleotide identity between orthologous T. evansi vs. T. brucei coding sequences, including pseudogenes.This graph represents 8290 CDS with the highest identities out of 8421 total non-repetitive sequences analyzed.
Mentions: Of the 9368 T. evansi CDS identified as T. brucei orthologs, 8421 CDS were classified as non-repetitive genes; the remaining 947 CDS were VSG, ESAG, RHS, or duplicate sequences. A comparison of the 8421 non-repetitive CDS between T. brucei and T. evansi revealed 7970 (94.6%) had a nucleotide identity of 95% or greater, 320 (3.8%) had a nucleotide identity between 70–95%, and 131 (1.6%) had a nucleotide identity less than 70% (Fig. 2; S1 Fig.). After RATT annotation transfer, a total of 503 (5.1%) Tb927 GeneIDs did not have identified orthologs in the TevSTIB805ra annotated genome (Table 1, column G; S2 Table). The majority of these (406) represent repetitive genes (e.g. VSG, ESAG, and RHS) or ‘hypothetical unlikely’ genes, which were not analyzed further. Five CDS correspond to predicted pseudogenes. T. evansi STIB805 orthologs for 49 Tb927 CDS were shown to be wholly or partially missing in TevSTIB805 reads that mapped to these gene loci (see below). T. evansi homologs for the remaining 43 Tb927 GeneIDs were ‘missed’ by RATT and AutoMagi, but were subsequently identified by manual examination of the T. evansi sequence. Thus, the majority of T. brucei CDS have extremely similar T. evansi orthologs, and very few T. brucei CDS were not found in T. evansi. This result is consistent with a very close phylogenetic relationship between these parasites.

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