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Abstract
Trypanosomes (genus Trypanosoma) are parasites of humans, and wild and domestic mammals, in which they cause several economically and socially important diseases, including sleeping sickness in Africa and Chagas disease in the Americas. Despite the development of numerous molecular diagnostics and increasing awareness of the importance of these neglected parasites, there is currently no universal genetic barcoding marker available for trypanosomes. In this review we provide an overview of the methods used for trypanosome detection and identification, discuss the potential application of different barcoding techniques and examine the requirements of the 'ideal' trypanosome genetic barcode. In addition, we explore potential alternative genetic markers for barcoding Trypanosoma species, including an analysis of phylogenetically informative nucleotide changes along the length of the 18S rRNA gene.
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Leonard G, Soanes DM, Stevens JR. Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling. INFECTION GENETICS AND EVOLUTION 2011; 11:955-9. [PMID: 21419879 DOI: 10.1016/j.meegid.2011.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/10/2011] [Accepted: 03/11/2011] [Indexed: 11/16/2022]
Abstract
Since the first attempts to classify the evolutionary history of trypanosomes, there have been conflicting reports regarding their true phylogenetic relationships and, in particular, their relationships with other vertebrate trypanosomatids, e.g. Leishmania sp., as well as with the many insect parasitising trypanosomatids. Perhaps the issue that has provided most debate is that concerning the monophyly (or otherwise) of genus Trypanosoma and, even with the advent of molecular methods, the findings of numerous studies have varied significantly depending on the gene sequences analysed, number of taxa included, choice of outgroup and phylogenetic methodology. While of arguably limited applied importance, resolution of the question as to whether or not trypanosomes are monophyletic is critical to accurate evaluation of competing, mutually exclusive evolutionary scenarios for these parasites, namely the 'vertebrate-first' or 'insect-first' hypotheses. Therefore, a new approach, which could overcome previous limitations was needed. At its most simple, the problem can be defined within the framework of a trifurcated tree with three hypothetical positions at which the root can be placed. Using BLASTp and whole-genome gene-by-gene phylogenetic analyses of Trypanosoma brucei, Trypanosoma cruzi, Leishmania major and Naegleria gruberi, we have identified 599 gene markers--putative homologues--that were shared between the genomes of these four taxa. Of these, 75 homologous gene families that demonstrate monophyly of the kinetoplastids were identified. We then used these data sets in combination with an additional outgroup, Euglena gracilis, coupled with large-scale gene concatenation and diverse phylogenetic techniques to investigate the relative branching order of T. brucei, T. cruzi and L. major. Our findings confirm the monophyly of genus Trypanosoma and demonstrate that <1% of the analysed gene markers shared between the genomes of T. brucei, T. cruzi and L. major reject the hypothesis that the trypanosomes form a monophyletic group.
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Affiliation(s)
- Guy Leonard
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
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Molecular phylogeny: reconstructing the forest. C R Biol 2008; 332:171-82. [PMID: 19281950 DOI: 10.1016/j.crvi.2008.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 07/09/2008] [Indexed: 11/22/2022]
Abstract
Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come.
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Akamine RN, Winter CE. Oscheius tipulae as an example of eEF1A gene diversity in nematodes. J Mol Evol 2008; 67:278-90. [PMID: 18696027 DOI: 10.1007/s00239-008-9147-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 04/15/2008] [Accepted: 07/14/2008] [Indexed: 10/21/2022]
Abstract
We characterized four eEF1A genes in the alternative rhabditid nematode model organism Oscheius tipulae. This is twice the copy number of eEF1A genes in C. elegans, C. briggsae, and, probably, many other free-living and parasitic nematodes. The introns show features remarkably different from those of other metazoan eEF1A genes. Most of the introns in the eEF1A genes are specific to O. tipulae and are not shared with any of the other genes described in metazoans. Most of the introns are phase 0 (inserted between two codons), and few are inserted in protosplice sites (introns inserted between the nucleotide sequence A/CAG and G/A). Two of these phase 0 introns are conserved in sequence in two or more of the four eEF1A gene copies, and are inserted in the same position in the genes. Neither of these characteristics has been detected in any of the nematode eEF1A genes characterized to date. The coding sequences were also compared with other eEF1A cDNAs from 11 different nematodes to determine the variability of these genes within the phylum Nematoda. Parsimony and distance trees yielded similar topologies, which were similar to those created using other molecular markers. The presence of more than one copy of the eEF1A gene with nearly identical coding regions makes it difficult to define the orthologous cDNAs. As shown by our data on O. tipulae, careful and extensive examination of intron positions in the eEF1A gene across the phylum is necessary to define their potential for use as valid phylogenetic markers.
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Affiliation(s)
- Rubens N Akamine
- Departmento de Parasitologia, Instituto de Ciências Biomédicas/Universidade de São Paulo, Av. Prof. Lineu Prestes 1374, 05508-900, Sao Paulo, SP, Brazil
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Khuchareontaworn S, Singhaphan P, Viseshakul N, Chansiri K. Genetic diversity of Trypanosoma evansi in buffalo based on internal transcribed spacer (ITS) regions. J Vet Med Sci 2008; 69:487-93. [PMID: 17551221 DOI: 10.1292/jvms.69.487] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The nucleotide sequences of 18S rDNA and internal transcribed spacer (ITS) regions were used for studying the relationships of Trypanosoma evansi isolate from a buffalo. The sequences were analyzed and compared to 18S rDNA and the ITS regions of the other Trypanosoma spp. Maximum likelihood phylogenetic trees were constructed using Leishmania major as the outgroup. The tree of 18S rDNA indicated that T. evansi (buffalo B18) isolate was closely related to those of Taiwan and T. brucei stock. The ITS tree showed the genetic diversity among 32 clones of T. evansi (B18) within a single host. This data will be useful for epidemiological and dynamic studies for designing the rational control programs of the disease.
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Affiliation(s)
- Sintawee Khuchareontaworn
- Department of Biochemistry, Faculty of Medicine, Srinakharinwirot University, Sukhumvit, Bangkok, Thailand
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Simpson AGB, Stevens JR, Lukes J. The evolution and diversity of kinetoplastid flagellates. Trends Parasitol 2006; 22:168-74. [PMID: 16504583 DOI: 10.1016/j.pt.2006.02.006] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 01/09/2006] [Accepted: 02/09/2006] [Indexed: 11/15/2022]
Abstract
Five years ago, little was known about kinetoplastid evolution. Recent improvements in the taxon sampling for nuclear rRNA genes and several protein markers have transformed this understanding. Parasitism evolved at least four times in kinetoplastids. Obligate parasitic trypanosomatids are a relatively 'derived' group within kinetoplastids; their closest relative is likely to be the free-living Bodo saltans, and the ancestral trypanosomatids were probably parasites of insects. Although subject to recent controversy, trypanosomes (genus Trypanosoma) probably constitute a monophyletic group. Several unusual features of trypanosomatid genomes (e.g. trans-splicing, mitochondrial RNA editing and intron poverty) are common in kinetoplastids and pre-date the adoption of parasitism. The framework of relationships is becoming robust enough for real comparative approaches to be used to understand kinetoplastid biology.
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Affiliation(s)
- Alastair G B Simpson
- Canadian Institute for Advanced Research and Department of Biology, Dalhousie University, Halifax, Canada, B3H 4J1
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Overath P, Haag J, Lischke A, O'hUigin C. The surface structure of trypanosomes in relation to their molecular phylogeny. Int J Parasitol 2001; 31:468-71. [PMID: 11334931 DOI: 10.1016/s0020-7519(01)00152-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Molecular phylogenetic analysis using genes coding for ribosomal RNA and proteins suggests that trypanosomes are monophyletic. Salivarian trypanosomes showing antigenic variation of the variant surface glycoprotein (VSG) diverged from non-Salivarian trypanosomes some 200-300 million years ago. Representatives of the non-Salivarian group, the mammalian parasite, Trypanosoma cruzi, and the fresh-water fish trypanosome, T. carassii, are characterised by surfaces dominated by carbohydrate-rich mucin-like glycoproteins, which are not subject to antigenetic variation. It is suggested that this latter surface structure is typical for non-Salivarian trypanosomes as well as members of the other Kinetoplastid suborder, the Bodonina. This would imply that at some point in time in the evolution of the Salivaria the highly abundant and comparatively poorly immunogenetic mucin-like molecules must have been replaced for equally abundant but highly immunogenic VSG-like molecules. While the selective advantage for such a unique transition is difficult to imagine, the subsequent diversification of VSG genes/molecules may have been comparatively straightforward because even the most limited form of antigenic variation would have extended the duration of infection in the vertebrate and thus would have increased the chance for transfer to the vector.
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Affiliation(s)
- P Overath
- Max-Planck-Institut für Biologie, Abteilung Membranbiochemie, Correnstrasse 38, D-72076, Tübingen, Germany.
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Abstract
Trypanosoma cruzi and the majority of its insect vectors (Hemiptera, Reduviidae, Triatominae) are confined to the Americas. But while recent molecular studies indicate a relatively ancient origin for the parasite ( approximately 65 million years ago) there is increasing evidence that the blood-sucking triatomine vectors have evolved comparatively recently (<5 mya). This review examines the evidence for these ideas, and attempts to reconcile the apparent paradox by suggesting that marsupial opossums (Didelphidae) may have played a role, not just as original reservoir hosts, but also as original vectors of the parasite.
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Affiliation(s)
- C Schofield
- London School of Hygiene and Tropical Medicine, UK.
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Abstract
The absence of a fossil record has meant that the evolution of protozoa has remained largely a matter for speculation. Recent advances in molecular biology and phylogenetic analysis, however, are allowing the 'history written in the genes' to be interpreted. Here, Jamie Stevens and Wendy Gibson review progress in reconstruction of trypanosome phylogeny based on molecular data from rRNA and protein-coding genes.
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Affiliation(s)
- J R Stevens
- School of Biological Sciences, University of Exeter, Exeter, UK EX4 4PS
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Abstract
In the absence of a fossil record, the evolution of protozoa has until recently largely remained a matter for speculation. However, advances in molecular methods and phylogenetic analysis are now allowing interpretation of the "history written in the genes". This review focuses on recent progress in reconstruction of trypanosome phylogeny based on molecular data from ribosomal RNA, the miniexon and protein-coding genes. Sufficient data have now been gathered to demonstrate unequivocally that trypanosomes are monophyletic; the phylogenetic trees derived can serve as a framework to reinterpret the biology, taxonomy and present day distribution of trypanosome species, providing insights into the coevolution of trypanosomes with their vertebrate hosts and vectors. Different methods of dating the divergence of trypanosome lineages give rise to radically different evolutionary scenarios and these are reviewed. In particular, the use of one such biogeographically based approach provides new insights into the coevolution of the pathogens, Trypanosoma brucei and Trypanosoma cruzi, with their human hosts and the history of the diseases with which they are associated.
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Affiliation(s)
- J R Stevens
- School of Biological Sciences, University of Exeter, Exeter EX4 4PS, UK.
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Unkles SE, Logsdon JM, Robison K, Kinghorn JR, Duncan JM. The tigA gene is a transcriptional fusion of glycolytic genes encoding triose-phosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase in oomycota. J Bacteriol 1997; 179:6816-23. [PMID: 9352934 PMCID: PMC179613 DOI: 10.1128/jb.179.21.6816-6823.1997] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Genes encoding triose-phosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are fused and form a single transcriptional unit (tigA) in Phytophthora species, members of the order Pythiales in the phylum Oomycota. This is the first demonstration of glycolytic gene fusion in eukaryotes and the first case of a TPI-GAPDH fusion in any organism. The tigA gene from Phytophthora infestans has a typical Oomycota transcriptional start point consensus sequence and, in common with most Phytophthora genes, has no introns. Furthermore, Southern and PCR analyses suggest that the same organization exists in other closely related genera, such as Pythium, from the same order (Oomycota), as well as more distantly related genera, Saprolegnia and Achlya, in the order Saprolegniales. Evidence is provided that in P. infestans, there is at least one other discrete copy of a GAPDH-encoding gene but not of a TPI-encoding gene. Finally, a phylogenetic analysis of TPI does not place Phytophthora within the assemblage of crown eukaryotes and suggests TPI may not be particularly useful for resolving relationships among major eukaryotic groups.
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Affiliation(s)
- S E Unkles
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom.
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Early evolution of eukaryotes inferred from protein phylogenies of translation elongation factors 1α and 2. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0003-9365(97)80009-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yamamoto A, Hashimoto T, Asaga E, Hasegawa M, Goto N. Phylogenetic position of the mitochondrion-lacking protozoan Trichomonas tenax, based on amino acid sequences of elongation factors 1alpha and 2. J Mol Evol 1997; 44:98-105. [PMID: 9010141 DOI: 10.1007/pl00006127] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Major parts of amino-acid-coding regions of elongation factor (EF)-1alpha and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones from each of the products of the EF-1alpha and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1alpha coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long, and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1alpha and EF-2 gene per chromosome were estimated as four and two, respectively. The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1alpha and 761 and 762 residues from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1alphas and EF-2s, respectively. The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1alpha and EF-2 data sets. The EF-1alpha analysis suggested that three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the divergence of T. tenax to be immediately next to G. lamblia.
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Affiliation(s)
- A Yamamoto
- Department of Oral Microbiology, Showa University School of Dentistry, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142, Japan.
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Nakamura Y, Hashimoto T, Yoshikawa H, Kamaishi T, Nakamura F, Okamoto K, Hasegawa M. Phylogenetic position of Blastocystis hominis that contains cytochrome-free mitochondria, inferred from the protein phylogeny of elongation factor 1 alpha. Mol Biochem Parasitol 1996; 77:241-5. [PMID: 8813670 DOI: 10.1016/0166-6851(96)02600-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Y Nakamura
- Laboratory of Gene Manipulation, School of Medicine, Showa University, Tokyo, Japan
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Fukura K, Yamamoto A, Hashimoto T, Goto N. Nucleotide sequence of the SrRNA gene and phylogenetic analysis of Trichomonas tenax. Microbiol Immunol 1996; 40:183-8. [PMID: 8934671 DOI: 10.1111/j.1348-0421.1996.tb03331.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The small subunit ribosomal RNA (SrRNA) gene of Trichomonas tenax ATCC30207 was amplified by PCR and the 1.55-kb product was cloned into plasmid vector pUC18. Four clones were isolated and sequenced. The insert DNAs were 1,552 bp long and their G+C contents were 48.1%; three of them had exactly the same DNA sequences and one had only one nucleotide change. A representative SrRNA sequence was analyzed and a phylogenetic tree was estimated by the neighbor-joining (NJ) method. Among the protists examined, T. tenax was placed as the closest relative of Tritrichomonas foetus, as expected from the traditional taxonomy. The total homology between the two SrRNA sequences was 89.2%.
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Affiliation(s)
- K Fukura
- Department of Oral Microbiology, Showa University School of Dentistry, Tokyo, Japan
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Kamaishi T, Hashimoto T, Nakamura Y, Nakamura F, Murata S, Okada N, Okamoto K, Shimizu M, Hasegawa M. Protein phylogeny of translation elongation factor EF-1 alpha suggests microsporidians are extremely ancient eukaryotes. J Mol Evol 1996; 42:257-63. [PMID: 8919877 DOI: 10.1007/bf02198852] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Partial regions of the mRNA encoding a major part of translation elongation factor 1 alpha (EF-1 alpha) from a mitochondrion-lacking protozoan, Glugea plecoglossi, that belongs to microsporidians, were amplified by polymerase chain reaction (PCR) and their primary structures were analyzed. The deduced amino acid sequence was highly divergent from typical EF-1 alpha's of eukaryotes, although it clearly showed a eukaryotic feature when aligned with homologs of the three primary kingdoms. Maximum likelihood (ML) analyses on the basis of six different stochastic models of amino acid substitutions and a maximum parsimony (MP) analysis consistently suggest that among eukaryotic species being analyzed, G. plecoglossi is likely to represent the earliest offshoot of eukaryotes. Microsporidians might be the extremely ancient eukaryotes which have diverged before an occurrence of mitochondrial symbiosis.
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Affiliation(s)
- T Kamaishi
- Department of Medical Biology, Showa University, Tokyo, Japan
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