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Barnabé C, Mobarec HI, Jurado MR, Cortez JA, Brenière SF. Reconsideration of the seven discrete typing units within the species Trypanosoma cruzi , a new proposal of three reliable mitochondrial clades. INFECTION GENETICS AND EVOLUTION 2016; 39:176-186. [DOI: 10.1016/j.meegid.2016.01.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022]
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Tibayrenc M, Ayala FJ. The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model. Acta Trop 2015; 151:156-65. [PMID: 26188332 PMCID: PMC7117470 DOI: 10.1016/j.actatropica.2015.05.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 01/18/2023]
Abstract
Comparing the population structure of Trypanosoma cruzi with that of other pathogens, including parasitic protozoa, fungi, bacteria and viruses, shows that the agent of Chagas disease shares typical traits with many other species, related to a predominant clonal evolution (PCE) pattern: statistically significant linkage disequilibrium, overrepresented multilocus genotypes, near-clades (genetic subdivisions somewhat blurred by occasional genetic exchange/hybridization) and "Russian doll" patterns (PCE is observed, not only at the level of the whole species, but also, within the near-clades). Moreover, T. cruzi population structure exhibits linkage with the diversity of several strongly selected genes, with gene expression profiles, and with some major phenotypic traits. We discuss the evolutionary significance of these results, and their implications in terms of applied research (molecular epidemiology/strain typing, analysis of genes of interest, vaccine and drug design, immunological diagnosis) and of experimental evolution. Lastly, we revisit the long-term debate of describing new species within the T. cruzi taxon.
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Phylogenetic character mapping of RADES Probing, a new marker for exploring the clonal evolution of expressed coding sequences in Trypanosoma cruzi, the agent of Chagas disease. INFECTION GENETICS AND EVOLUTION 2013; 19:287-91. [DOI: 10.1016/j.meegid.2013.03.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/19/2013] [Accepted: 03/18/2013] [Indexed: 11/21/2022]
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Restrepo CM, De La Guardia C, Sousa OE, Calzada JE, Fernández PL, Lleonart R. AFLP polymorphisms allow high resolution genetic analysis of American Tegumentary Leishmaniasis agents circulating in Panama and other members of the Leishmania genus. PLoS One 2013; 8:e73177. [PMID: 24039881 PMCID: PMC3767818 DOI: 10.1371/journal.pone.0073177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/18/2013] [Indexed: 11/18/2022] Open
Abstract
American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP), a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at both intra and inter-specific levels.
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Affiliation(s)
- Carlos M Restrepo
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad de Panamá, Panamá ; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
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Aquilino C, Gonzalez Rubio ML, Seco EM, Escudero L, Corvo L, Soto M, Fresno M, Malpartida F, Bonay P. Differential trypanocidal activity of novel macrolide antibiotics; correlation to genetic lineage. PLoS One 2012; 7:e40901. [PMID: 22859958 PMCID: PMC3409201 DOI: 10.1371/journal.pone.0040901] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 06/14/2012] [Indexed: 12/18/2022] Open
Abstract
Here we report the systematic study of the anti-trypanocidal activity of some new products derived from S. diastatus on 14 different T. cruzi strains spanning the six genetic lineages of T. cruzi. As the traditional growth inhibition curves giving similar IC(50) showed great differences on antibiotic and lineage tested, we decided to preserve the wealth of information derived from each inhibition curve and used an algorithm related to potency of the drugs, combined in a matrix data set used to generate a cluster tree. The cluster thus generated based just on drug susceptibility data closely resembles the phylogenies of the lineages derived from genetic data and provides a novel approach to correlate genetic data with phenotypes related to pathogenesis of Chagas disease. Furthermore we provide clues on the drugs mechanism of action.
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Affiliation(s)
- Carolina Aquilino
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Maria Luisa Gonzalez Rubio
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Elena Maria Seco
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Madrid, Spain
| | - Leticia Escudero
- Centro Nacional de Biotecnología, Campus de Cantoblanco, Madrid, Spain
| | - Laura Corvo
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Manuel Soto
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | - Manuel Fresno
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
| | | | - Pedro Bonay
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- * E-mail:
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The Trypanosoma cruzi genome; conserved core genes and extremely variable surface molecule families. Res Microbiol 2011; 162:619-25. [PMID: 21624458 DOI: 10.1016/j.resmic.2011.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Accepted: 04/14/2011] [Indexed: 11/21/2022]
Abstract
The protozoan parasite Trypanosoma cruzi is an important but neglected pathogen that causes chagas disease, which affects millions of people, mainly in latin America. The population structure and epidemiology of the parasite are complex, with much variability among strains. The genome sequence of a reference strain, CL Brener, was published in 2005, and the availability of this sequence has both revealed the complexity of the parasite genome and greatly facilitated research into parasite biology and pathogenesis, by making the sequences of more than 8000 core genes available. The T. cruzi genome is highly repetitive, which has resulted in inaccuracies in the genome sequence, and attempts have been made to provide a deeper analysis of repeated genes as a complement to the genome sequence. The genome was found to be organized in stable core regions containing housekeeping and other genes, surrounded by highly repetitive, often sub-telomeric highly variable regions containing multiple members of large families of surface molecule genes. Comparative sequencing of T. cruzi strains has been initiated and the results show that the core gene content of the parasite is highly conserved, but that much sequence variability, 3-4% difference at the DNA level on average between strains in coding regions, is present. The additional genomes will improve the understanding of parasite biology and epidemiology.
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Franzén O, Ochaya S, Sherwood E, Lewis MD, Llewellyn MS, Miles MA, Andersson B. Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener. PLoS Negl Trop Dis 2011; 5:e984. [PMID: 21408126 PMCID: PMC3050914 DOI: 10.1371/journal.pntd.0000984] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 02/09/2011] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite. Chagas disease is a major health problem in Latin America and it is caused by the protozoan parasite Trypanosoma cruzi. The genome sequence of the T. cruzi strain CL Brener (TcVI) has revealed a genome with large repertoires of genes for surface antigens, among other features. In the present study, we sequenced the genome of a representative member of TcI, the predominant agent of Chagas disease North of the Amazon and performed comparative analyses with CL Brener. Genetic variation between strains can potentially explain differences in disease pathogenesis, host preferences and aid the identification of drug targets. Our analysis showed that the two genomes have very similar sets of genes, but contain large differences in the relative size of several important gene families. Moreover, an abundance of allelic sequence variation was found in a large fraction of genes, and an evolutionary analysis indicated that many genes have evolved at different rates.
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Affiliation(s)
- Oscar Franzén
- Science for Life Laboratory, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi. Proc Natl Acad Sci U S A 2010; 107:20411-6. [PMID: 21059959 DOI: 10.1073/pnas.1015496107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We performed a phylogenetic character mapping on 26 stocks of Trypanosoma cruzi, the parasite responsible for Chagas disease, and 2 stocks of the sister taxon T. cruzi marinkellei to test for possible associations between T. cruzi-subspecific phylogenetic diversity and levels of protein expression, as examined by proteomic analysis and mass spectrometry. We observed a high level of correlation (P < 10(-4)) between genetic distance, as established by multilocus enzyme electrophoresis, and proteomic dissimilarities estimated by proteomic Euclidian distances. Several proteins were found to be specifically associated to T. cruzi phylogenetic subdivisions (discrete typing units). This study explores the previously uncharacterized links between infraspecific phylogenetic diversity and gene expression in a human pathogen. It opens the way to searching for new vaccine and drug targets and for identification of specific biomarkers at the subspecific level of pathogens.
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Pérez-Escobar M, Cevallos AM, Espinoza B, Espinosa N, Martínez I, Hernández R. Trypanosoma cruzi ribosomal protein S4: characterization of its coding locus, analysis of transcripts, and antigenicity of the protein. Mem Inst Oswaldo Cruz 2007; 102:473-9. [PMID: 17612768 DOI: 10.1590/s0074-02762007005000031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 03/07/2007] [Indexed: 01/23/2023] Open
Abstract
Two allelic genomic fragments containing ribosomal protein S4 encoding genes (rpS4) from Trypanosoma cruzi (CL-Brener strain) were isolated and characterized. One allele comprises two complete tandem repeats of a sequence encoding an rpS4 gene. In the other, only one rpS4 gene is found. Sequence comparison to the accessed data in the genome project database reveals that our two-copy allele corresponds to a variant haplotype. However, the deduced aminoacid sequence of all the gene copies is identical. The rpS4 transcripts processing sites were determined by comparison of genomic sequences with published cDNA data. The obtained sequence data demonstrates that rpS4 genes are expressed in epimastigotes, amastigotes, and trypomastigotes. A recombinant version of rpS4 was found to be an antigenic: it was recognized by 62.5% of the individuals with positive serology for T. cruzi and by 93.3% of patients with proven chronic chagasic disease.
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Affiliation(s)
- Mariana Pérez-Escobar
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D. F., 04510, México
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Zemanová E, Jirků M, Mauricio IL, Horák A, Miles MA, Lukes J. The Leishmania donovani complex: Genotypes of five metabolic enzymes (ICD, ME, MPI, G6PDH, and FH), new targets for multilocus sequence typing. Int J Parasitol 2007; 37:149-60. [PMID: 17027989 DOI: 10.1016/j.ijpara.2006.08.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 08/15/2006] [Indexed: 10/24/2022]
Abstract
Flagellates of the Leishmania donovani complex are causative agents of human cutaneous and visceral leishmaniasis. The complex is comprised of L. donovani, Leishmania infantum and Leishmania archibaldi, although the latter is not now considered to be a valid species. Morphological distinction of Leishmania species is impractical, so biochemical, immunological and DNA-based criteria were introduced. Multilocus enzyme electrophoresis (MLEE) is the present gold standard. We have sequenced the genes encoding five metabolic enzymes used for MLEE, both to resolve the DNA diversity underlying isoenzyme mobility differences and to explore the potential of these targets for higher resolution PCR-based multilocus sequence typing. The genes sequenced were isocitrate dehydrogenase, malic enzyme, mannose phosphate isomerase, glucose-6-phosphate dehydrogenase, and fumarate hydratase, for 17 strains of L. infantum, seven strains of L. donovani, and three strains of L. archibaldi. Protein mobilities predicted from amino acid sequences did not always accord precisely with reported MLEE profiles. A high number of heterozygous sites was detected. Heterozygosity was particularly frequent in some strains and indirectly supported the presence of genetic exchange in Leishmania. Phylogenetic analysis of a concatenated alignment based on a total of 263 kb protein-coding sequences showed strong correlation of genotype with geographical origin. Europe and Africa appear to represent independent evolutionary centres.
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Affiliation(s)
- Eva Zemanová
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences and Faculty of Biology, University of South Bohemia, Ceské Budejovice, (Budweis), Czech Republic
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Telleria J, Lafay B, Virreira M, Barnabé C, Tibayrenc M, Svoboda M. Trypanosoma cruzi: sequence analysis of the variable region of kinetoplast minicircles. Exp Parasitol 2006; 114:279-88. [PMID: 16730709 DOI: 10.1016/j.exppara.2006.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 04/11/2006] [Accepted: 04/11/2006] [Indexed: 11/16/2022]
Abstract
The comparisons of 170 sequences of kinetoplast DNA minicircle hypervariable region obtained from 19 stocks of Trypanosoma cruzi and 2 stocks of Trypanosoma cruzi marenkellei showed that only 56% exhibited a significant homology one with other sequences. These sequences could be grouped into homology classes showing no significant sequence similarity with any other homology group. The 44% remaining sequences thus corresponded to unique sequences in our data set. In the DTU I ("Discrete Typing Units") 51% of the sequences were unique. In contrast, in the DTU IId, 87.5% of sequences were distributed into three classes. The results obtained for T. cruzi marinkellei, showed that all sequences were unique, without any similarity between them and T. cruzi sequences. Analysis of palindromes in all sequence sets show high frequency of the EcoRI site. Analysis of repetitive sequences suggested a common ancestral origin of the kDNA. The editing mechanism that occurs in kinetoplastidae is discussed.
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Affiliation(s)
- Jenny Telleria
- Laboratoire de Génétique et Evolution des Maladies Infectieuses, UMR CNRS-IRD 2724 and UR IRD 165, Centre IRD, 911 avenue Agropolis, BP 64501, 34394 Montpellier Cedex 5, France.
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Branche C, Ochaya S, Aslund L, Andersson B. Comparative karyotyping as a tool for genome structure analysis of Trypanosoma cruzi. Mol Biochem Parasitol 2006; 147:30-8. [PMID: 16481054 DOI: 10.1016/j.molbiopara.2006.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 01/06/2006] [Accepted: 01/09/2006] [Indexed: 01/22/2023]
Abstract
As a part of the Trypanosoma cruzi genome project, 239 genetic markers were hybridised to PFGE separated DNA from T. cruzi, in order to determine the number and size of chromosomes and to aid the assembly of the genome sequence. We used three strains, T. cruzi IIe CL Brener (the genome project reference strain) and two T. cruzi I strains, Sylvio X10/7 and CAI/72, to perform a comparative study of their karyotypes and to determine marker linkage. A densitometry analysis of the separations estimated the total chromosome numbers to be 55 in CL Brener and 57 in the two other strains. In all, 45 markers hybridised to single chromosomal bands and 103 markers to two bands in CL Brener, while the number of markers in Sylvio X10/7 and CAI/72 were 102/68 and 61/105, respectively. Size differences between homologous chromosomes were often large, up to 1900 kb (173%). The average difference was 36% for CL Brener and 23.5% for the T. cruzi I strains. Larger differences in CL Brener are consistent with a recent hybrid origin. Forty markers distributed into 15 linkage groups were found to identify specific chromosomes or chromosomes pairs. While the same markers are generally linked in all three strains, the sizes of the chromosomes vary extensively, indicating large chromosomal rearrangements. These data provide valuable information for the finishing of the CL Brener genome sequence.
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Affiliation(s)
- Carole Branche
- Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, SE-171 77 Stockholm, Sweden
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Abstract
The population structure of Plasmodial parasites, especially Plasmodium falciparum, has received much attention in the recent years. Like many other micropathogens, the debate has focused on the clonality/sexuality question. Considered a panmictic species for very long, P. falciparum actually exhibits strong departures from panmictic expectations in many of its populations, which corroborates the proposal that it is able to undergo uniparental propagation.(1) The currently accepted idea to account for this surprising result is kind of "mechanical" self-fertilization due to the lack of availability of gametes with different genetic make-ups in low transmission areas. However, it could be misleading to make this simple working hypothesis a dogma, for many other explanations are possible (unknown cycles, sibling species, mating types) that deserve to be explored as well. The consequences of this combination of uniparental(1) and sexual propagation on the circulation of genes of interest (drug resistance, antigenic variability, pathogenicity) are discussed, together with the need to use more sophisticated technologies, analysing much broader samples and considering better the host and vector factors in P. falciparum population dynamics.
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Affiliation(s)
- C Gauthier
- Unit of Research 165 "Genetics and Evolution of Infectious Diseases", UMR CNRS/IRD 2724, IRD, BP 64501, 34394 Montpellier Cedex 5, France
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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