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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

Schematic of reads from T. b. brucei TREU 927/4 and T. evansi STIB805 mapped on to the procyclin loci of T. brucei.CDS are denoted by yellow arrows, with Tb927 GeneIDs above and gene names in parentheses. Reads that could be uniquely mapped to the reference are colored blue (intact paired reads), green (single forward reads) or red (single reverse reads). Reads that could be mapped to more than one position in the Tb927 reference were placed randomly and are colored yellow. Red asterisks denote mutated or absent CDS in T. evansi. Both PAG5 and PAG2* are missing in T. evansi, and mutations are present in all copies of EP2, PAG3, and GRESAG2.
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pntd-0003404-g003: Schematic of reads from T. b. brucei TREU 927/4 and T. evansi STIB805 mapped on to the procyclin loci of T. brucei.CDS are denoted by yellow arrows, with Tb927 GeneIDs above and gene names in parentheses. Reads that could be uniquely mapped to the reference are colored blue (intact paired reads), green (single forward reads) or red (single reverse reads). Reads that could be mapped to more than one position in the Tb927 reference were placed randomly and are colored yellow. Red asterisks denote mutated or absent CDS in T. evansi. Both PAG5 and PAG2* are missing in T. evansi, and mutations are present in all copies of EP2, PAG3, and GRESAG2.

Mentions: In T. evansi STIB805, the procyclin loci either lack or have disrupted versions of several CDS found in T. brucei. GPEET and EP procyclins and associated genes are encoded in loci on chromosomes 6 and 10, respectively, in various T. brucei strains [49]. Procyclin proteins are GPI-anchored coat glycoproteins that are expressed exclusively in the procyclic insect form of T. brucei, and they have been hypothesized to be involved in protection against tsetse fly midgut hydrolases [50]. Experiments in T. brucei have shown that knocking out all of the procyclin genes (Null mutants of GPEET and EP3 on chromosome 6; EP1 and EP2 on chromosome 10) causes no growth defect in vitro and permits completion of the entire life cycle, but causes a selective disadvantage during co-infection with wild type cells in the tsetse fly midgut [51]. These procyclin loci also contain procyclin-associated genes and a gene related to expression site associated gene 2 (PAG3 and GRESAG2 on chromosome 6; PAG1, 2, 2*, 4, and 5 on chromosome 10) [49]. The functions of the PAG proteins and GRESAG2 are unknown; although transcripts of PAG1–3 have been shown to increase during differentiation to procyclic forms, published experiments using cell lines with all PAG genes knocked out reported no obvious abnormal phenotypes in vitro or in vivo[49]. In multiple T. brucei strains, the chromosome 10 procyclin loci are heterozygous, with one chromosome containing EP1/EP2/PAG1/PAG5/PAG2*/PAG4 and the other chromosome containing EP1/EP2/PAG2/PAG4 (PAG2 being a fusion of the 5′ part of PAG1 and the 3′ part of PAG2*) [49], [52]–[56]. In T. evansi STIB805, chromosome 10 appears to be homozygous, with only the EP1/EP2/PAG2/PAG4 locus present, and the associated absence of the segment containing the 3′ part of PAG1, PAG5 and the 5′ part of PAG2* (Fig. 3). The full STIB805 de novo assembly contained a single 14.9 kb contig corresponding to the EP1/EP2/PAG2/PAG4 locus (S2 Fig.). Also on chromosome 10, the EP2 in T. evansi contains a stretch of 12 divergent amino acids in the domain N-terminal to the EP repeat; this region is highly conserved in T. brucei[57], [58]. Although the function of this domain is unknown, these 12 amino acids are found in all sequenced T. brucei genomes with very few variations. The chromosome 6 procyclin locus contains a triplication of three genes (EP3/PAG3/GRESAG2) in T. brucei TREU 927/4, with GPEET present only in front of the last unit (Fig. 3). Copy numbers of these genes may vary among T. brucei strains, as Southern analysis showed that these are single copy genes in the AnTat1.1 strain [49]. In TevSTIB805ra, coverage of this locus is much reduced (Fig. 3, S3 Fig.), indicating either divergence, reduced copy number, or both. The locus did not assemble into a single contig in the de novo approach and because of the repeat nature of this locus in Tb927, assigning sequence differences to particular gene copies was not possible. Nonetheless, several non-synonymous mutations in EP3 are evident, and the PAG3 and GRESAG2 genes have frameshifts and deletions. In contrast, analysis of a subset of other T. evansi orthologs to CDS shown to be upregulated in PF relative to BF T. brucei (Tb927.1.2310, Tb927.1.2350, Tb927.1.2560, Tb927.1.580, Tb927.10.10260, Tb927.10.10950, Tb927.10.4570, Tb927.11.16130, Tb927.11.8200, Tb927.4.1800, Tb927.4.1860, Tb927.4.4730, Tb927.5.1710, Tb927.5.2260, Tb927.6.510, Tb927.8.5260, Tb927.4.4730, Tb927.8.8300, Tb927.9.15110, and Tb927.9.8420) [59] detected no notable changes.


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)

Schematic of reads from T. b. brucei TREU 927/4 and T. evansi STIB805 mapped on to the procyclin loci of T. brucei.CDS are denoted by yellow arrows, with Tb927 GeneIDs above and gene names in parentheses. Reads that could be uniquely mapped to the reference are colored blue (intact paired reads), green (single forward reads) or red (single reverse reads). Reads that could be mapped to more than one position in the Tb927 reference were placed randomly and are colored yellow. Red asterisks denote mutated or absent CDS in T. evansi. Both PAG5 and PAG2* are missing in T. evansi, and mutations are present in all copies of EP2, PAG3, and GRESAG2.
© Copyright Policy
Related In: Results  -  Collection

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

pntd-0003404-g003: Schematic of reads from T. b. brucei TREU 927/4 and T. evansi STIB805 mapped on to the procyclin loci of T. brucei.CDS are denoted by yellow arrows, with Tb927 GeneIDs above and gene names in parentheses. Reads that could be uniquely mapped to the reference are colored blue (intact paired reads), green (single forward reads) or red (single reverse reads). Reads that could be mapped to more than one position in the Tb927 reference were placed randomly and are colored yellow. Red asterisks denote mutated or absent CDS in T. evansi. Both PAG5 and PAG2* are missing in T. evansi, and mutations are present in all copies of EP2, PAG3, and GRESAG2.
Mentions: In T. evansi STIB805, the procyclin loci either lack or have disrupted versions of several CDS found in T. brucei. GPEET and EP procyclins and associated genes are encoded in loci on chromosomes 6 and 10, respectively, in various T. brucei strains [49]. Procyclin proteins are GPI-anchored coat glycoproteins that are expressed exclusively in the procyclic insect form of T. brucei, and they have been hypothesized to be involved in protection against tsetse fly midgut hydrolases [50]. Experiments in T. brucei have shown that knocking out all of the procyclin genes (Null mutants of GPEET and EP3 on chromosome 6; EP1 and EP2 on chromosome 10) causes no growth defect in vitro and permits completion of the entire life cycle, but causes a selective disadvantage during co-infection with wild type cells in the tsetse fly midgut [51]. These procyclin loci also contain procyclin-associated genes and a gene related to expression site associated gene 2 (PAG3 and GRESAG2 on chromosome 6; PAG1, 2, 2*, 4, and 5 on chromosome 10) [49]. The functions of the PAG proteins and GRESAG2 are unknown; although transcripts of PAG1–3 have been shown to increase during differentiation to procyclic forms, published experiments using cell lines with all PAG genes knocked out reported no obvious abnormal phenotypes in vitro or in vivo[49]. In multiple T. brucei strains, the chromosome 10 procyclin loci are heterozygous, with one chromosome containing EP1/EP2/PAG1/PAG5/PAG2*/PAG4 and the other chromosome containing EP1/EP2/PAG2/PAG4 (PAG2 being a fusion of the 5′ part of PAG1 and the 3′ part of PAG2*) [49], [52]–[56]. In T. evansi STIB805, chromosome 10 appears to be homozygous, with only the EP1/EP2/PAG2/PAG4 locus present, and the associated absence of the segment containing the 3′ part of PAG1, PAG5 and the 5′ part of PAG2* (Fig. 3). The full STIB805 de novo assembly contained a single 14.9 kb contig corresponding to the EP1/EP2/PAG2/PAG4 locus (S2 Fig.). Also on chromosome 10, the EP2 in T. evansi contains a stretch of 12 divergent amino acids in the domain N-terminal to the EP repeat; this region is highly conserved in T. brucei[57], [58]. Although the function of this domain is unknown, these 12 amino acids are found in all sequenced T. brucei genomes with very few variations. The chromosome 6 procyclin locus contains a triplication of three genes (EP3/PAG3/GRESAG2) in T. brucei TREU 927/4, with GPEET present only in front of the last unit (Fig. 3). Copy numbers of these genes may vary among T. brucei strains, as Southern analysis showed that these are single copy genes in the AnTat1.1 strain [49]. In TevSTIB805ra, coverage of this locus is much reduced (Fig. 3, S3 Fig.), indicating either divergence, reduced copy number, or both. The locus did not assemble into a single contig in the de novo approach and because of the repeat nature of this locus in Tb927, assigning sequence differences to particular gene copies was not possible. Nonetheless, several non-synonymous mutations in EP3 are evident, and the PAG3 and GRESAG2 genes have frameshifts and deletions. In contrast, analysis of a subset of other T. evansi orthologs to CDS shown to be upregulated in PF relative to BF T. brucei (Tb927.1.2310, Tb927.1.2350, Tb927.1.2560, Tb927.1.580, Tb927.10.10260, Tb927.10.10950, Tb927.10.4570, Tb927.11.16130, Tb927.11.8200, Tb927.4.1800, Tb927.4.1860, Tb927.4.4730, Tb927.5.1710, Tb927.5.2260, Tb927.6.510, Tb927.8.5260, Tb927.4.4730, Tb927.8.8300, Tb927.9.15110, and Tb927.9.8420) [59] detected no notable changes.

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