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Boscaro V, James ER, Fiorito R, Del Campo J, Scheffrahn RH, Keeling PJ. Updated classification of the phylum Parabasalia. J Eukaryot Microbiol 2024; 71:e13035. [PMID: 38825738 DOI: 10.1111/jeu.13035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/04/2024]
Abstract
The phylum Parabasalia includes very diverse single-cell organisms that nevertheless share a distinctive set of morphological traits. Most are harmless or beneficial gut symbionts of animals, but some have turned into parasites in other body compartments, the most notorious example being Trichomonas vaginalis in humans. Parabasalians have garnered attention for their nutritional symbioses with termites, their modified anaerobic mitochondria (hydrogenosomes), their character evolution, and the wholly unique features of some species. The molecular revolution confirmed the monophyly of Parabasalia, but considerably changed our view of their internal relationships, prompting a comprehensive reclassification 14 years ago. This classification has remained authoritative for many subgroups despite a greatly expanded pool of available data, but the large number of species and sequences that have since come out allow for taxonomic refinements in certain lineages, which we undertake here. We aimed to introduce as little disruption as possible but at the same time ensure that most taxa are truly monophyletic, and that the larger clades are subdivided into meaningful units. In doing so, we also highlighted correlations between the phylogeny of parabasalians and that of their hosts.
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Affiliation(s)
- Vittorio Boscaro
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erick R James
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca Fiorito
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Javier Del Campo
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Céza V, Kotyk M, Kubánková A, Yubuki N, Šťáhlavský F, Silberman JD, Čepička I. Free-living Trichomonads are Unexpectedly Diverse. Protist 2022; 173:125883. [DOI: 10.1016/j.protis.2022.125883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
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Abstract
Tritrichomonas foetus is a venereal trichomonad parasite which causes reproductive issues in cattle. No other trichomonads are known to be urogenital pathogens in cattle, but there are several reports of Tetratrichomonas and Pentatrichomonas isolates of unclear origin from the cattle urogenital tract (UGT) in the Americas. This study reports the first case of a non-T. foetus cattle urogenital trichomonad isolate in Europe. Molecular analysis of the internal transcribed spacer (ITS) 1-5.8S ribosomal RNA-ITS 2 and 18S ribosomal RNA loci suggest that the isolate is a Tetratrichomonas species from a lineage containing other previously described bull preputial isolates. We identified close sequence similarity between published urogenital and gastrointestinal Tetratrichomonas spp., and this is reviewed alongside further evidence regarding the gastrointestinal origin of non-T. foetus isolates. Routine screening for T. foetus is based on culture and identification by microscopy, and so considering other trichomonad parasites of the bovine UGT is important to avoid misdiagnosis.
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Taerum SJ, De Martini F, Liebig J, Gile GH. Incomplete Co-cladogenesis Between Zootermopsis Termites and Their Associated Protists. ENVIRONMENTAL ENTOMOLOGY 2018; 47:184-195. [PMID: 29325010 DOI: 10.1093/ee/nvx193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Coevolution is a major driver of speciation in many host-associated symbionts. In the termite-protist digestive symbiosis, the protists are vertically inherited by anal feeding among nest mates. Lower termites (all termite families except Termitidae) and their symbionts have broadly co-diversified over ~170 million yr. However, this inference is based mainly on the restricted distribution of certain protist genera to certain termite families. With the exception of one study, which demonstrated congruent phylogenies for the protist Pseudotrichonympha and its Rhinotermitidae hosts, coevolution in this symbiosis has not been investigated with molecular methods. Here we have characterized the hindgut symbiotic protists (Phylum Parabasalia) across the genus Zootermopsis (Archotermopsidae) using single cell isolation, molecular phylogenetics, and high-throughput amplicon sequencing. We report that the deepest divergence in the Zootermopsis phylogeny (Zootermopsis laticeps [Banks; Isoptera: Termopsidae]) corresponds with a divergence in three of the hindgut protist species. However, the crown Zootermopsis taxa (Zootermopsis angusticollis [Hagen; Isoptera: Termopsidae], Z. nevadensis nevadensis [Hagen; Isoptera: Termopsidae], and Z. nevadensis nuttingi [Haverty & Thorne; Isoptera: Termopsidae]) share the same protist species, with no evidence of co-speciation under our methods. We interpret this pattern as incomplete co-cladogenesis, though the possibility of symbiont exchange cannot be entirely ruled out. This is the first molecular evidence that identical communities of termite-associated protist species can inhabit multiple distinct host species.
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Affiliation(s)
| | | | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Tempe, AZ
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Radek R, Meuser K, Strassert JFH, Arslan O, Teßmer A, Šobotník J, Sillam-Dussès D, Nink RA, Brune A. Exclusive Gut Flagellates of Serritermitidae Suggest a Major Transfaunation Event in Lower Termites: Description of Heliconympha glossotermitis
gen. nov. spec. nov. J Eukaryot Microbiol 2017; 65:77-92. [DOI: 10.1111/jeu.12441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Renate Radek
- Evolutionary Biology, Institute for Biology/Zoology; Freie Universität Berlin; Berlin 14195 Germany
| | - Katja Meuser
- Insect Gut Microbiology and Symbiosis Group; Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Jürgen F. H. Strassert
- Insect Gut Microbiology and Symbiosis Group; Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
- Department of Organismal Biology; Uppsala University; Uppsala 75236 Sweden
| | - Oguzhan Arslan
- Evolutionary Biology, Institute for Biology/Zoology; Freie Universität Berlin; Berlin 14195 Germany
| | - Anika Teßmer
- Evolutionary Biology, Institute for Biology/Zoology; Freie Universität Berlin; Berlin 14195 Germany
| | - Jan Šobotník
- Faculty of Forestry and Wood Sciences; Czech University of Life Sciences Prague; Prague 6 - Suchdol 16500 Czech Republic
| | - David Sillam-Dussès
- Laboratory of Experimental and Comparative Ethology EA 4443; Université Paris 13; Sorbonne Paris Cité Villetaneuse 93430 France
- Institute of Research for Development U 242; Sorbonne Universités, Institute of Ecology and Environmental Sciences of Paris; Bondy 93143 France
| | - Ricardo A. Nink
- Insect Gut Microbiology and Symbiosis Group; Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
| | - Andreas Brune
- Insect Gut Microbiology and Symbiosis Group; Max Planck Institute for Terrestrial Microbiology; Marburg 35043 Germany
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Céza V, Pánek T, Smejkalová P, Čepička I. Molecular and morphological diversity of the genus Hypotrichomonas (Parabasalia: Hypotrichomonadida), with descriptions of six new species. Eur J Protistol 2015; 51:158-72. [PMID: 25855142 DOI: 10.1016/j.ejop.2015.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/30/2022]
Abstract
The genus HypotrichomonasLee, 1960 belongs to the small parabasalian class Hypotrichomonadea. Although five Hypotrichomonas species have been described from intestines of lizards and birds, some descriptions were brief and incomplete. Only the type species H. acosta has been observed repeatedly. We have established 23 strains of the genus Hypotrichomonas in culture. Phylogenetic and morphological analyses showed that these isolates represent eight distinct species, six of which are novel. Three of the species showed unusual morphology, such as a reduced undulating membrane, absence of the free part of the recurrent flagellum or a costa-like fiber. Our strains were isolated from a wide range of hosts including cockroaches, frogs, tortoises, lizards, snakes, marsupials, pigs, rodents, and primates. The genus Hypotrichomonas thus contains a relatively large number of species that differ in morphology, phylogenetic position and host range. It is remarkable that such diversity of hypotrichomonads was previously undetected, although a number of studies dealt with intestinal trichomonads of vertebrates and invertebrates. Our results indicate that the diversity of the genus Hypotrichomonas as well as of the whole Parabasalia is still only poorly understood, and the lineages described so far likely represent only a small fraction of the true diversity of parabasalids.
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Affiliation(s)
- Vít Céza
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Pavla Smejkalová
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic; Department of Parasitology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, Prague 2, Czech Republic.
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Kamaruddin M, Tokoro M, Rahman MM, Arayama S, Hidayati APN, Syafruddin D, Asih PBS, Yoshikawa H, Kawahara E. Molecular characterization of various trichomonad species isolated from humans and related mammals in Indonesia. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:471-8. [PMID: 25352694 PMCID: PMC4210728 DOI: 10.3347/kjp.2014.52.5.471] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/05/2014] [Accepted: 08/13/2014] [Indexed: 11/23/2022]
Abstract
Trichomonad species inhabit a variety of vertebrate hosts; however, their potential zoonotic transmission has not been clearly addressed, especially with regard to human infection. Twenty-one strains of trichomonads isolated from humans (5 isolates), pigs (6 isolates), rodents (6 isolates), a water buffalo (1 isolate), a cow (1 isolate), a goat (1 isolate), and a dog (1 isolate) were collected in Indonesia and molecularly characterized. The DNA sequences of the partial 18S small subunit ribosomal RNA (rRNA) gene or 5.8S rRNA gene locus with its flanking regions (internal transcribed spacer region, ITS1 and ITS2) were identified in various trichomonads; Simplicimonas sp., Hexamastix mitis, and Hypotrichomonas sp. from rodents, and Tetratrichomonas sp. and Trichomonas sp. from pigs. All of these species were not detected in humans, whereas Pentatrichomonas hominis was identified in humans, pigs, the dog, the water buffalo, the cow, and the goat. Even when using the high-resolution gene locus of the ITS regions, all P. hominis strains were genetically identical; thus zoonotic transmission between humans and these closely related mammals may be occurring in the area investigated. The detection of Simplicimonas sp. in rodents (Rattus exulans) and P. hominis in water buffalo in this study revealed newly recognized host adaptations and suggested the existence of remaining unrevealed ranges of hosts in the trichomonad species.
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Affiliation(s)
- Mudyawati Kamaruddin
- Department of Parasitology, School of Health Sciences, Faculty of Medicine, Kanazawa University, Kanazawa, Japan. ; Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Kanazawa University, Kanazawa, Japan
| | - Masaharu Tokoro
- Department of Parasitology, School of Health Sciences, Faculty of Medicine, Kanazawa University, Kanazawa, Japan
| | - Md Moshiur Rahman
- Department of Parasitology, School of Health Sciences, Faculty of Medicine, Kanazawa University, Kanazawa, Japan
| | - Shunsuke Arayama
- Department of Parasitology, School of Health Sciences, Faculty of Medicine, Kanazawa University, Kanazawa, Japan
| | | | - Din Syafruddin
- Eijkman Institute of Molecular Biology, Jakarta, Indonesia
| | - Puji B S Asih
- Eijkman Institute of Molecular Biology, Jakarta, Indonesia
| | - Hisao Yoshikawa
- Department of Biological Sciences, Graduate School of Humanities and Sciences, Nara Women's University, Nara, Japan
| | - Ei Kawahara
- Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Kanazawa University, Kanazawa, Japan
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Tai V, Gile GH, Pan J, James ER, Carpenter KJ, Scheffrahn RH, Keeling PJ. The phylogenetic position of Kofoidia loriculata (Parabasalia) and its implications for the evolution of the Cristamonadea. J Eukaryot Microbiol 2014; 62:255-9. [PMID: 25155455 DOI: 10.1111/jeu.12163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 11/29/2022]
Abstract
Kofoidia loriculata is a parabasalid symbiont inhabiting the hindgut of the lower termite Paraneotermes simplicicornis. It was initially described as a lophomonad due to its apical tuft of multiple flagella that disintegrate during cell division, but its phylogenetic relationships have not been investigated using molecular evidence. From single cell isolations, we sequenced the small subunit rRNA gene and determined that K. loriculata falls within the Cristamonadea, but is unrelated to other lophomonads. This analysis further demonstrates the polyphyly of the lophomonads and the necessity to re-assess the morphological and cellular evolution of the Cristamonadea.
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Affiliation(s)
- Vera Tai
- Department of Botany, Canadian Institute for Advanced Research Program in Integrated Microbial Biodiversity, University of British Columbia, 3529-6270 University Blvd., Vancouver, British Columbia, Canada
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Martinez-Girón R, Cornelis van Woerden H. Lophomonas blattarum and bronchopulmonary disease. J Med Microbiol 2013; 62:1641-1648. [PMID: 23946475 DOI: 10.1099/jmm.0.059311-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The natural habitat of the multiflagellate protozoon Lophomonas blattarum is as an endocommensal in the hindgut of insects such as cockroaches. However, it also causes bronchopulmonary disease in humans. The aim of this paper was to review the literature on this organism in the context of respiratory disease. The biology epidemiology, route of transmission, pathogenic mechanisms and diagnosis methods are also described. A total of 61 cases were identified in the literature. The majority of these reports were from China, with some cases from Peru and Spain. Most cases were adult males, although paediatric cases were reported in Peru. Clinical presentation was non-specific, including symptoms such as fever, cough and breathless. Antiprotozoal therapy was generally effective.
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Affiliation(s)
- Rafael Martinez-Girón
- Protozoal Respiratory Pathology Research Unit. Fundación INCLÍNICA, Calvo Sotelo, 16-3 dcha, 33007-Oviedo, Spain
| | - Hugo Cornelis van Woerden
- Institute of Primary Care & Public Health, Cardiff University School of Medicine, Neuadd Meirionnydd, Heath Park, Cardiff CF14 4YS, UK
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Noda S, Mantini C, Meloni D, Inoue JI, Kitade O, Viscogliosi E, Ohkuma M. Molecular phylogeny and evolution of parabasalia with improved taxon sampling and new protein markers of actin and elongation factor-1α. PLoS One 2012; 7:e29938. [PMID: 22253832 PMCID: PMC3253790 DOI: 10.1371/journal.pone.0029938] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/08/2011] [Indexed: 11/27/2022] Open
Abstract
Background Inferring the evolutionary history of phylogenetically isolated, deep-branching groups of taxa—in particular determining the root—is often extraordinarily difficult because their close relatives are unavailable as suitable outgroups. One of these taxonomic groups is the phylum Parabasalia, which comprises morphologically diverse species of flagellated protists of ecological, medical, and evolutionary significance. Indeed, previous molecular phylogenetic analyses of members of this phylum have yielded conflicting and possibly erroneous inferences. Furthermore, many species of Parabasalia are symbionts in the gut of termites and cockroaches or parasites and therefore formidably difficult to cultivate, rendering available data insufficient. Increasing the numbers of examined taxa and informative characters (e.g., genes) is likely to produce more reliable inferences. Principal Findings Actin and elongation factor-1α genes were identified newly from 22 species of termite-gut symbionts through careful manipulations and seven cultured species, which covered major lineages of Parabasalia. Their protein sequences were concatenated and analyzed with sequences of previously and newly identified glyceraldehyde-3-phosphate dehydrogenase and the small-subunit rRNA gene. This concatenated dataset provided more robust phylogenetic relationships among major groups of Parabasalia and a more plausible new root position than those previously reported. Conclusions/Significance We conclude that increasing the number of sampled taxa as well as the addition of new sequences greatly improves the accuracy and robustness of the phylogenetic inference. A morphologically simple cell is likely the ancient form in Parabasalia as opposed to a cell with elaborate flagellar and cytoskeletal structures, which was defined as most basal in previous inferences. Nevertheless, the evolution of Parabasalia is complex owing to several independent multiplication and simplification events in these structures. Therefore, systematics based solely on morphology does not reflect the evolutionary history of parabasalids.
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Affiliation(s)
- Satoko Noda
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Yamanashi, Japan
- * E-mail: (SN); (MO)
| | - Cléa Mantini
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France, and Inserm U1019, CNRS UMR 8204, and University Lille – Nord de France, Lille, France
| | - Dionigia Meloni
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France, and Inserm U1019, CNRS UMR 8204, and University Lille – Nord de France, Lille, France
- Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, Sassari, Italy
| | - Jun-Ichi Inoue
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan
| | - Osamu Kitade
- Natural History Laboratory, College of Science, Ibaraki University, Mito, Ibaraki, Japan
| | - Eric Viscogliosi
- Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France, and Inserm U1019, CNRS UMR 8204, and University Lille – Nord de France, Lille, France
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama, Japan
- * E-mail: (SN); (MO)
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Husník F, Chrudimský T, Hypša V. Multiple origins of endosymbiosis within the Enterobacteriaceae (γ-Proteobacteria): convergence of complex phylogenetic approaches. BMC Biol 2011; 9:87. [PMID: 22201529 PMCID: PMC3271043 DOI: 10.1186/1741-7007-9-87] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 12/28/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The bacterial family Enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (S) symbionts, to obligate mutualists, called primary (P) symbionts. Determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic reconstructions within this group of bacteria. The main reasons have been the absence of sufficient data, the highly derived nature of the symbiont genomes and lack of appropriate phylogenetic methods. Due to the extremely aberrant nature of their DNA, the symbiotic lineages within Enterobacteriaceae form long branches and tend to cluster as a monophyletic group. This state of phylogenetic uncertainty is now improving with an increasing number of complete bacterial genomes and development of new methods. In this study, we address the monophyly versus polyphyly of enterobacterial symbionts by exploring a multigene matrix within a complex phylogenetic framework. RESULTS We assembled the richest taxon sampling of Enterobacteriaceae to date (50 taxa, 69 orthologous genes with no missing data) and analyzed both nucleic and amino acid data sets using several probabilistic methods. We particularly focused on the long-branch attraction-reducing methods, such as a nucleotide and amino acid data recoding and exclusion (including our new approach and slow-fast analysis), taxa exclusion and usage of complex evolutionary models, such as nonhomogeneous model and models accounting for site-specific features of protein evolution (CAT and CAT+GTR). Our data strongly suggest independent origins of four symbiotic clusters; the first is formed by Hamiltonella and Regiella (S-symbionts) placed as a sister clade to Yersinia, the second comprises Arsenophonus and Riesia (S- and P-symbionts) as a sister clade to Proteus, the third Sodalis, Baumannia, Blochmannia and Wigglesworthia (S- and P-symbionts) as a sister or paraphyletic clade to the Pectobacterium and Dickeya clade and, finally, Buchnera species and Ishikawaella (P-symbionts) clustering with the Erwinia and Pantoea clade. CONCLUSIONS The results of this study confirm the efficiency of several artifact-reducing methods and strongly point towards the polyphyly of P-symbionts within Enterobacteriaceae. Interestingly, the model species of symbiotic bacteria research, Buchnera and Wigglesworthia, originated from closely related, but different, ancestors. The possible origins of intracellular symbiotic bacteria from gut-associated or pathogenic bacteria are suggested, as well as the role of facultative secondary symbionts as a source of bacteria that can gradually become obligate maternally transferred symbionts.
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Affiliation(s)
- Filip Husník
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Tomáš Chrudimský
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice 37005, Czech Republic
| | - Václav Hypša
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice 37005, Czech Republic
- Institute of Parasitology, Biology Centre of ASCR, Branišovská 31, České Budějovice 37005, Czech Republic
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Phylogenetic position of Lophomonas striata Bütschli (Parabasalia) from the hindgut of the cockroach Periplaneta americana. Protist 2011; 163:274-83. [PMID: 21840257 DOI: 10.1016/j.protis.2011.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 06/26/2011] [Indexed: 11/22/2022]
Abstract
Lophomonas striata is a multiflagellate parabasalid commensal in the hindgut of the omnivorous cockroaches Blatta orientalis and Periplaneta americana. Its closest relatives were traditionally thought to include similar multiflagellate parabasalids with a single flagellar area that degenerates during mitosis, such as Joenia and Kofoidia. However, molecular phylogenetic analyses have shown that "lophomonads" are not monophyletic. We have determined the SSU rRNA sequence of L. striata and we find that it branches sister to the Trichonymphida with strong support. This is surprising because all other lophomonads sampled to date branch within the Cristamonadida, and the order Trichonymphida (e.g. Trichonympha, Pseudotrichonympha, and Hoplonympha) is both morphologically coherent and monophyletic in SSU rRNA phylogenies. Trichonymphida, unlike the lophomonads, share a bilateral symmetry, in which their multiple flagella occur in two (or sometimes four) regions, and instead of degenerating upon mitosis, half of the flagella are passed to each daughter cell. The single apical flagellar region characteristic of lophomonads is therefore either plesiomorphic or it has arisen multiple times in parabasalids; our phylogenetic analyses and available ultrastructural evidence suggest the latter. Our results also suggest that parabasalid gut symbionts may have been vertically transmitted in cockroaches before the common ancestor of Cryptocercus and termites.
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Malik SB, Brochu CD, Bilic I, Yuan J, Hess M, Logsdon JM, Carlton JM. Phylogeny of parasitic parabasalia and free-living relatives inferred from conventional markers vs. Rpb1, a single-copy gene. PLoS One 2011; 6:e20774. [PMID: 21695260 PMCID: PMC3111441 DOI: 10.1371/journal.pone.0020774] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 05/09/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms. PRINCIPAL FINDINGS Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas. CONCLUSIONS/SIGNIFICANCE The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia.
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Affiliation(s)
- Shehre-Banoo Malik
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- Department of Biology, Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Cynthia D. Brochu
- Department of Biology, Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Ivana Bilic
- Department for Farm Animals and Veterinary Public Health, Clinic for Avian, Reptile and Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - Jing Yuan
- Department of Biology, Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Michael Hess
- Department for Farm Animals and Veterinary Public Health, Clinic for Avian, Reptile and Fish Medicine, University of Veterinary Medicine, Vienna, Austria
| | - John M. Logsdon
- Department of Biology, Roy J. Carver Center for Comparative Genomics, University of Iowa, Iowa City, Iowa, United States of America
| | - Jane M. Carlton
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
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YUBUKI NAOJI, CÉZA VÍT, CEPICKA IVAN, YABUKI AKINORI, INAGAKI YUJI, NAKAYAMA TAKESHI, INOUYE ISAO, LEANDER BRIANS. Cryptic Diversity of Free-Living Parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as Inferred from Small Subunit rDNA Sequences. J Eukaryot Microbiol 2010; 57:554-61. [DOI: 10.1111/j.1550-7408.2010.00509.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Critical Taxonomic Revision of Parabasalids with Description of one New Genus and three New Species. Protist 2010; 161:400-33. [DOI: 10.1016/j.protis.2009.11.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 11/21/2009] [Indexed: 11/17/2022]
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16
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Histomonas meleagridis possesses three α-actinins immunogenic to its hosts. Mol Biochem Parasitol 2010; 169:101-7. [DOI: 10.1016/j.molbiopara.2009.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/02/2009] [Accepted: 10/26/2009] [Indexed: 11/18/2022]
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17
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Pereira-Neves A, Benchimol M. Tritrichomonas foetus: Budding from Multinucleated Pseudocysts. Protist 2009; 160:536-51. [DOI: 10.1016/j.protis.2009.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 05/16/2009] [Indexed: 11/16/2022]
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18
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Molecular identification and phylogenetic relationships of trichomonad isolates of galliform birds inferred from nuclear small subunit rRNA gene sequences. Parasitol Res 2009; 106:163-70. [DOI: 10.1007/s00436-009-1643-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Accepted: 09/18/2009] [Indexed: 10/20/2022]
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19
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Noda S, Hongoh Y, Sato T, Ohkuma M. Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites. BMC Evol Biol 2009; 9:158. [PMID: 19586555 PMCID: PMC2717939 DOI: 10.1186/1471-2148-9-158] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 07/09/2009] [Indexed: 12/03/2022] Open
Abstract
Background The microbial community in the gut of termites is responsible for the efficient decomposition of recalcitrant lignocellulose. Prominent features of this community are its complexity and the associations of prokaryotes with the cells of cellulolytic flagellated protists. Bacteria in the order Bacteroidales are involved in associations with a wide variety of gut protist species as either intracellular endosymbionts or surface-attached ectosymbionts. In particular, ectosymbionts exhibit distinct morphological patterns of the associations. Therefore, these Bacteroidales symbionts provide an opportunity to investigate not only the coevolutionary relationships with the host protists and their morphological evolution but also how symbiotic associations between prokaryotes and eukaryotes occur and evolve within a complex symbiotic community. Results Molecular phylogeny of 31 taxa of Bacteroidales symbionts from 17 protist genera in 10 families was examined based on 16S rRNA gene sequences. Their localization, morphology, and specificity were also examined by fluorescent in situ hybridizations. Although a monophyletic grouping of the ectosymbionts occurred in three related protist families, the symbionts of different protist genera were usually dispersed among several phylogenetic clusters unique to termite-gut bacteria. Similar morphologies of the associations occurred in multiple lineages of the symbionts. Nevertheless, the symbionts of congeneric protist species were closely related to one another, and in most cases, each host species harbored a unique Bacteroidales species. The endosymbionts were distantly related to the ectosymbionts examined so far. Conclusion The coevolutionary history of gut protists and their associated Bacteroidales symbionts is complex. We suggest multiple independent acquisitions of the Bacteroidales symbionts by different protist genera from a pool of diverse bacteria in the gut community. In this sense, the gut could serve as a reservoir of diverse bacteria for associations with the protist cells. The similar morphologies are considered a result of evolutionary convergence. Despite the complicated evolutionary history, the host-symbiont relationships are mutually specific, suggesting their cospeciations at the protist genus level with only occasional replacements.
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Affiliation(s)
- Satoko Noda
- Ecomolecular Biorecycling Science Research Team, RIKEN Advanced Science Institute, Wako, Saitama 351-0198, Japan.
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20
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Noda S, Mantini C, Bordereau C, Kitade O, Dolan MF, Viscogliosi E, Ohkuma M. Molecular phylogeny of parabasalids with emphasis on the order Cristamonadida and its complex morphological evolution. Mol Phylogenet Evol 2009; 52:217-24. [PMID: 19306937 DOI: 10.1016/j.ympev.2009.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 02/14/2009] [Accepted: 03/16/2009] [Indexed: 11/15/2022]
Abstract
Parabasalia represents a complex assemblage of species, which recently received extensive reorganization. The newly created order Cristamonadida unites complex hypermastigids belonging to the Lophomonadida like the joeniids, the multinucleate polymonad Calonymphidae, and well-developed trichomonads in the Devescovinidae. All these protists exclusively occur in the guts of termites and related insects. In this study, small subunit rRNA and glyceraldehyde-3-phosphate dehydrogenase genes were identified without cultivation from 14 species in Cristamonadida including previously unstudied genera such as Joenina, Joenia, Joenoides, Macrotrichomonas, Gigantomonas, and Foaina. Despite the great morphological diversity of Cristamonadida, our phylogenetic analyses supported the monophyly of this order. However, almost all the families and subfamilies composing this order are polyphyletic suggesting a complicated morphological evolution. Our analyses also showed that Cristamonadida descends from one lineage of rudimentary trichomonads and that joeniids was basal in this order. Several successive and independent morphological transitions such as the development and reduction of flagellar apparatus and associated cytoskeleton and transition to multinucleated status have likely led to the diversity and complexity of cristamonad lineages.
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Affiliation(s)
- Satoko Noda
- Ecomolecular Biorecycling Science Research Team, RIKEN Advanced Science Institute, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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21
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Ohkuma M, Noda S, Hongoh Y, Nalepa CA, Inoue T. Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and the cockroach Cryptocercus. Proc Biol Sci 2009; 276:239-45. [PMID: 18812290 DOI: 10.1098/rspb.2008.1094] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cryptocercus cockroaches and lower termites harbour obligate, diverse and unique symbiotic cellulolytic flagellates in their hindgut that are considered critical in the development of social behaviour in their hosts. However, there has been controversy concerning the origin of these symbiotic flagellates. Here, molecular sequences encoding small subunit rRNA and glyceraldehyde-3-phosphate dehydrogenase were identified in the symbiotic flagellates of the order Trichonymphida (phylum Parabasalia) in the gut of Cryptocercus punctulatus and compared phylogenetically to the corresponding species in termites. In each of the monophyletic lineages that represent family-level groups in Trichonymphida, the symbionts of Cryptocercus were robustly sister to those of termites. Together with the recent evidence for the sister-group relationship of the host insects, this first comprehensive study comparing symbiont molecular phylogeny strongly suggests that a set of symbiotic flagellates representative of extant diversity was already established in an ancestor common to Cryptocercus and termites, was vertically transmitted to their offspring, and subsequently became diversified to distinct levels, depending on both the host and the symbiont lineages.
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Affiliation(s)
- Moriya Ohkuma
- Ecomolecular Biorecycling Science Research Team, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan.
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22
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Kostka M, Uzlikova M, Cepicka I, Flegr J. SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis. BMC Bioinformatics 2008; 9:341. [PMID: 18702831 PMCID: PMC2529323 DOI: 10.1186/1471-2105-9-341] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 08/15/2008] [Indexed: 11/15/2022] Open
Abstract
Background Slow-fast analysis is a simple and effective method to reduce the influence of substitution saturation, one of the causes of phylogenetic noise and long branch attraction (LBA) artifacts. In several steps of increasing stringency, the slow-fast analysis omits the fastest substituting alignment positions from the analysed dataset and thus increases its signal/noise ratio. Results Our program SlowFaster automates the process of assessing the substitution rate of the alignment positions and the process of producing new alignments by deleting the saturated positions. Its use is very simple. It goes through the whole process in several steps: data input – necessary choices – production of new alignments. Conclusion SlowFaster is a user-friendly tool providing new alignments prepared with slow-fast analysis. These data can be used for further phylogenetic analyses with lower risk of long branch attraction artifacts.
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Affiliation(s)
- Martin Kostka
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic.
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23
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Ohkuma M. Symbioses of flagellates and prokaryotes in the gut of lower termites. Trends Microbiol 2008; 16:345-52. [PMID: 18513972 DOI: 10.1016/j.tim.2008.04.004] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 04/15/2008] [Accepted: 04/15/2008] [Indexed: 11/30/2022]
Abstract
The microbial community in the gut of phylogenetically lower termites, comprising both flagellated protists and prokaryotes, has fascinated many scientists because of the symbiotic relationships that are responsible for the efficient degradation of lignocellulose. However, the complex nature of this microbial community and the formidable unculturability of most members have hampered detailed microbial studies. Comprehensive phylogenetic descriptions of the community members in the past decade still provide little information about their functions because the community contains diverse novel microbial species. Recent advances in molecular approaches have shed new light on species-specific spatial distributions, particularly the cellular associations of flagellated protists and prokaryotes, their functional interactions and coevolutionary relationships. These advances have gradually unveiled how this symbiotic complex functions to efficiently utilize lignocellulose.
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Affiliation(s)
- Moriya Ohkuma
- Ecomolecular Biorecycling Science Research Team, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan.
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24
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Detection of Cryptosporidium spp., Entamoeba spp. and Monocercomonas spp. in the gastrointestinal tract of snakes by in-situ hybridization. J Comp Pathol 2008; 138:63-71. [PMID: 18295780 DOI: 10.1016/j.jcpa.2007.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 11/05/2007] [Indexed: 11/22/2022]
Abstract
This report describes the development of a diagnostic method for protozoal infections of the gastrointestinal tract of captive snakes, based on chromogenic in-situ hybridization with probes designed for the detection of 18S rRNA genes from Cryptosporidium spp., Entamoeba spp., Entamoeba invadens and Monocercomonas spp. The specificity of the probes was confirmed with the help of parasitic cultures and gene sequence analysis. The probes gave clear positive signals. Of 182 snakes examined, seven were positive with the Cryptosporidium probe, 13 with the Entamoeba probe (of which nine were also positive with the E. invadens probe), and 34 with the Monocercomonas probe.
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25
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Dacks JB, Walker G, Field MC. Implications of the new eukaryotic systematics for parasitologists. Parasitol Int 2007; 57:97-104. [PMID: 18180199 DOI: 10.1016/j.parint.2007.11.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 11/15/2007] [Accepted: 11/16/2007] [Indexed: 11/24/2022]
Abstract
An accurate understanding of evolutionary relationships is central in biology. For parasitologists, understanding the relationships among eukaryotic organisms allows the prediction of virulence mechanisms, reconstruction of metabolic pathways, identification of potential drug targets, elucidation of parasite-specific cellular processes and understanding of interactions with the host or vector. Here we consider the impact of major recent revisions of eukaryotic systematics and taxonomy on parasitology. The previous, ladder-like model placed some protists as early diverging, with the remaining eukaryotes "progressing" towards a "crown radiation" of animals, plants, Fungi and some additional protistan lineages. This model has been robustly disproven. The new model is based on vastly increased amounts of molecular sequence data, integration with morphological information and the rigorous application of phylogenetic methods to those data. It now divides eukaryotes into six major supergroups; the relationships between those groups and the order of branching remain unknown. This new eukaryotic phylogeny emphasizes that organisms including Giardia, Trypanosoma and Trichomonas are not primitive, but instead highly evolved and specialised for their specific environments. The wealth of newly available comparative genomic data has also allowed the reconstruction of ancient suites of characteristics and mapping of character evolution in diverse parasites. For example, the last common eukaryotic ancestor was apparently complex, suggesting that lineage-specific adaptations and secondary losses have been important in the evolution of protistan parasites. Referring to the best evidence-based models for eukaryotic evolution will allow parasitologists to make more accurate and reliable inferences about pathogens that cause significant morbidity and mortality.
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Affiliation(s)
- Joel B Dacks
- The Molteno Building, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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26
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Noël C, Noda S, Mantini C, Dolan MF, Moriya S, Delgado-Viscogliosi P, Kudo T, Capron M, Pierce RJ, Ohkuma M, Viscogliosi E. Molecular phylogenetic position of the genera Stephanonympha and Caduceia (Parabasalia) inferred from nuclear small subunit rRNA gene sequences. J Eukaryot Microbiol 2007; 54:93-9. [PMID: 17300526 DOI: 10.1111/j.1550-7408.2006.00234.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nuclear small subunit (SSU) rRNA gene sequences were obtained by polymerase chain reaction from trichomonad symbionts of termites that belong to the Devescovinidae (Caduceia versatilis) and polymastigont Calonymphidae (Stephanonympha nelumbium). The unidentified SSU rRNA sequence Nk3, previously obtained from the termite Neotermes koshunensis, has also been shown to derive from a Stephanonympha sp. by in situ hybridization. These sequences were analysed in a broad phylogeny including nearly all identified parabasalid sequences available in the databases, and some as yet unidentified sequences likely deriving from the new order Cristamonadida (Devescovinidae, Calonymphidae, and hypermastigids Lophomonadida). A global phylogeny of parabasalids reveals a partial agreement between the clades identified in this work and the last classification of this phylum into four orders. However, this classification is still incongruent with our data and new taxonomic considerations are proposed. The analysis confirms the monophyly of the Cristamonadida and separates this order into two groups: the first unites nearly all the Devescovinidae including Caduceia and the Calonymphidae Coronympha and Metacoronympha, whereas the second group is composed of a few Devescovinidae, Lophomonadida, and Calonymphidae such as Stephanonympha. Caduceia is closely related to Devescovina, corroborating the marked morphological similarity between these two genera whereas Stephanonympha groups together with the Calonymphidae Snyderella and Calonympha. These data also confirm the polyphyly of the families Devescovinidae and Calonymphidae and support the arrangement of the axostyle-pelta complexes as a valuable character for taxonomic considerations within the Calonymphidae.
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Affiliation(s)
- Christophe Noël
- Inserm, U547, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59019 Lille cedex, France
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27
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Dufernez F, Walker RL, Noël C, Caby S, Mantini C, Delgado-Viscogliosi P, Ohkuma M, Kudo T, Capron M, Pierce RJ, Villanueva MR, Viscogliosi E. Morphological and molecular identification of non-Tritrichomonas foetus trichomonad protozoa from the bovine preputial cavity. J Eukaryot Microbiol 2007; 54:161-8. [PMID: 17403157 DOI: 10.1111/j.1550-7408.2007.00247.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tritrichomonas foetus is the causative agent of bovine trichomonosis. This protozoan is found in the preputial cavity of bulls and is transmitted to cows during coitus. Currently, the diagnosis of this parasite is based on microscopic examination of preputial washings or scrapings, but it was recently recognized that other trichomonads similar in size, shape, and motility to T. foetus can be present in preputial samples. Despite the serious consequences of an incorrect diagnosis for bovine trichomonosis, the precise speciation of these other trichomonads has remained uncertain. Here, a total of 12 non-T. foetus isolates were microscopically examined. On the basis of morphological criteria, seven of these isolates were identified as Tetratrichomonas sp., whereas four other isolates coincided with the description of Pentatrichomonas hominis. In the last isolate, a third non-T. foetus species was identified as belonging to the genera Pseudotrichomonas or Monocercomonas: the first time that species of either of these genera have been reported in preputial samples. To confirm these data, small subunit rRNA gene sequences were obtained by PCR from the 12 trichomonad isolates. These new sequences were analysed in a broad phylogeny including 72 other parabasalid sequences. From our phylogenetic trees, we confirmed the taxonomic status of non-T. foetus organisms isolated from preputial samples (Tetratrichomonas, Pentatrichomonas, and Pseudotrichomonas) and suggested the existence of two Tetratrichomonas species, despite their morphological similarity. The route of transmission of the non-T. foetus organisms identified in the bovine preputial cavity is discussed and we confirm that the PCR assay using the previously described T. foetus-specific primers TFR3 and TFR4 could be a useful alternative method for the diagnosis of bovine trichomonosis.
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Affiliation(s)
- Fabienne Dufernez
- Inserm, U547, Institut Pasteur de Lille, 1 Rue du Professeur Calmette, BP 245, 59019 Lille Cedex, France
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28
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Inoue JI, Saita K, Kudo T, Ui S, Ohkuma M. Hydrogen production by termite gut protists: characterization of iron hydrogenases of Parabasalian symbionts of the termite Coptotermes formosanus. EUKARYOTIC CELL 2007; 6:1925-32. [PMID: 17766465 PMCID: PMC2043399 DOI: 10.1128/ec.00251-07] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cellulolytic flagellated protists in the guts of termites produce molecular hydrogen (H(2)) that is emitted by the termites; however, little is known about the physiology and biochemistry of H(2) production from cellulose in the gut symbiotic protists due to their formidable unculturability. In order to understand the molecular basis for H(2) production, we here identified two genes encoding proteins homologous to iron-only hydrogenases (Fe hydrogenases) in Pseudotrichonympha grassii, a large cellulolytic symbiont in the phylum Parabasalia, in the gut of the termite Coptotermes formosanus. The two Fe hydrogenases were phylogenetically distinct and had different N-terminal accessory domains. The long-form protein represented a phylogenetic lineage unique among eukaryotic Fe hydrogenases, whereas the short form was monophyletic with those of other parabasalids. Active recombinant enzyme forms of these two Fe hydrogenases were successfully obtained without the specific auxiliary maturases. Although they differed in their extent of specific activity and optimal pH, both enzymes preferentially catalyzed H(2) evolution rather than H(2) uptake. H(2) evolution, at least that associated with the short-form enzyme, was still active even under high hydrogen partial pressure. H(2) evolution activity was detected in the hydrogenosomal fraction of P. grassii cells; however, the vigorous H(2) uptake activity of the endosymbiotic bacteria compensated for the strong H(2) evolution activity of the host protists. The results suggest that termite gut symbionts are a rich reservoir of novel Fe hydrogenases whose properties are adapted to the gut environment and that the potential of H(2) production in termite guts has been largely underestimated.
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Affiliation(s)
- Jun-Ichi Inoue
- Environmental Molecular Biology Laboratory, RIKEN, Hirosawa 2-1, Wako, Saitama, Japan
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29
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Borges FP, Gottardi B, Stuepp C, Larré AB, de Brum Vieira P, Tasca T, De Carli GA. Morphological aspects of Monocercomonas sp. and investigation on probable pseudocysts occurrence. Parasitol Res 2007; 101:1503-9. [PMID: 17687569 DOI: 10.1007/s00436-007-0667-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 07/05/2007] [Accepted: 07/09/2007] [Indexed: 12/01/2022]
Abstract
Monocercomonas sp. is a flagellate protozoan found in the large intestine of snakes and in insects. Light microscopy revealed the measurements of morphological features of the trophozoites. Scanning electron microscopy showed in detail the emergence of the three anterior flagella, the recurrent flagellum, the axostyle, and the absence of undulating membrane. In addition, we described spherical forms which are probably pseudocysts. The investigation on the occurrence of this process was carried out through the incubation of Monocercomonas sp. trophozoites in several stressful conditions, such as pH change, nutrient depletion and different temperatures. Results revealed high pseudocyst formation at acidic pH values (4.0, 5.0, and 6.0), in absence of serum and in incubation at 37 degrees C. The occurrence of these pseudocystic forms in trichomonads life cycle is under investigation. This study describes the external structure of Monocercomonas sp., as demonstrated by light and scanning electron microscopy. Moreover, to our knowledge, this is the first time that formation of probable pseudocysts is shown in Monocercomonas sp., contributing to the research field on termite protozoa biology.
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Affiliation(s)
- Fernanda Pires Borges
- Laboratório de Parasitologia Clínica, Faculdade de Farmácia, Pontifícia Universidade Católica do Rio Grande do Sul, Avenida Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil
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30
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An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. PLoS One 2007; 3:e2879. [PMID: 18663385 PMCID: PMC2488364 DOI: 10.1371/journal.pone.0002879] [Citation(s) in RCA: 192] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Accepted: 06/08/2008] [Indexed: 12/23/2022] Open
Abstract
Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)-which represent the majority of eukaryotic 'supergroups'. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful "meiosis detection toolkit". Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.
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31
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Hampl V, Cepicka I, Flegr J, Tachezy J, Kulda J. Morphological and molecular diversity of the monocercomonadid genera Monocercomonas, Hexamastix, and Honigbergiella gen. nov. Protist 2007; 158:365-83. [PMID: 17499022 DOI: 10.1016/j.protis.2007.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 02/24/2007] [Indexed: 10/23/2022]
Abstract
The family Monocercomonadidae (Parabasala, Trichomonadida) is characterized by the absence of a costa and in most species also of an undulating membrane; both of which are typical structures of trichomonadids. We have examined 25 isolates of Monocercomonadidae species by sequencing of the SSU rDNA and the ITS region and by light and transmission electron microscopy. The isolates formed three distinct phylogenetically unrelated clades: (1) Monocercomonas colubrorum, (2) Monocercomonas ruminantium together with a strain ATCC 50321 designated as Pseudotrichomonas keilini, and (3) Hexamastix. Twenty isolates of Monocercomonas colubrorum split into three clades with no host-specificity. The morphological differences among clades were insufficient to classify them as a separate species. Non-monophyly of the cattle commensal Monocercomonas ruminantium with the type species Monocercomonas colubrorum and absence of Pseudotrichomonas characters in the free-living strain ATCC 50321 led to their reclassification into a new genus (Honigbergiella gen. nov.). The close relationship of these strains indicates a recent switch between a free-living habit and endobiosis. Two strains of Hexamastix represented different species -Hexamastix kirbyi Honigberg 1955 and Hexamastix mitis sp. nov. Polyphyly of the Monocercomonadidae confirmed that the absence of a costa and an undulating membrane are not taxonomically significant characters and were probably secondarily lost in some or all clades. Our observations, however, indicated that other characters - infrakinetosomal body, comb-like structure, marginal lamella, and the type of axostyle - are fully consistent with the position of Monocercomonadidae species in the parabasalian tree and are, therefore, reasonable taxonomic characters.
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MESH Headings
- Animals
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Organelles/ultrastructure
- Phylogeny
- RNA, Protozoan/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Trichomonadida/classification
- Trichomonadida/cytology
- Trichomonadida/genetics
- Trichomonadida/ultrastructure
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Affiliation(s)
- Vladimír Hampl
- Department of Parasitology, Charles University in Prague, Prague, Czech Republic.
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Brady SG, Schultz TR, Fisher BL, Ward PS. Evaluating alternative hypotheses for the early evolution and diversification of ants. Proc Natl Acad Sci U S A 2006; 103:18172-7. [PMID: 17079492 PMCID: PMC1838725 DOI: 10.1073/pnas.0605858103] [Citation(s) in RCA: 258] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Indexed: 11/18/2022] Open
Abstract
Ants are the world's most diverse and ecologically dominant eusocial organisms. Resolving the phylogeny and timescale for major ant lineages is vital to understanding how they achieved this success. Morphological, molecular, and paleontological studies, however, have presented conflicting views on early ant evolution. To address these issues, we generated the largest ant molecular phylogenetic data set published to date, containing approximately 6 kb of DNA sequence from 162 species representing all 20 ant subfamilies and 10 aculeate outgroup families. When these data were analyzed with and without outgroups, which are all distantly related to ants and hence long-branched, we obtained conflicting ingroup topologies for some early ant lineages. This result casts strong doubt on the existence of a poneroid clade as currently defined. We compare alternate attachments of the outgroups to the ingroup tree by using likelihood tests, and find that several alternative rootings cannot be rejected by the data. These alternatives imply fundamentally different scenarios for the early evolution of ant morphology and behavior. Our data strongly support several notable relationships within the more derived formicoid ants, including placement of the enigmatic subfamily Aenictogitoninae as sister to Dorylus army ants. We use the molecular data to estimate divergence times, employing a strategy distinct from previous work by incorporating the extensive fossil record of other aculeate Hymenoptera as well as that of ants. Our age estimates for the most recent common ancestor of extant ants range from approximately 115 to 135 million years ago, indicating that a Jurassic origin is highly unlikely.
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Affiliation(s)
- Seán G. Brady
- *Department of Entomology and
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | | | - Brian L. Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, CA 94103; and
| | - Philip S. Ward
- Department of Entomology and Center for Population Biology, University of California, Davis, CA 95616
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Ohkuma M, Saita K, Inoue T, Kudo T. Comparison of four protein phylogeny of parabasalian symbionts in termite guts. Mol Phylogenet Evol 2006; 42:847-53. [PMID: 17098447 DOI: 10.1016/j.ympev.2006.09.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 09/22/2006] [Accepted: 09/22/2006] [Indexed: 11/27/2022]
Affiliation(s)
- Moriya Ohkuma
- Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan.
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Cepicka I, Hampl V, Kulda J, Flegr J. New evolutionary lineages, unexpected diversity, and host specificity in the parabasalid genus Tetratrichomonas. Mol Phylogenet Evol 2006; 39:542-51. [PMID: 16473027 DOI: 10.1016/j.ympev.2006.01.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 12/12/2005] [Accepted: 01/05/2006] [Indexed: 11/27/2022]
Abstract
We studied morphological and molecular polymorphism of 53 Tetratrichomonas isolates obtained from amphibian, reptilian, mammalian hosts, and from a slug with the aid of protargol staining and analyses of ITS1-5.8S rRNA-ITS2, SSU rRNA, and alpha-tubulin gene sequences. The phylogenetic tree based on the concatenate of all sequences showed the monophyly of the genus Tetratrichomonas with respect to the genus Trichomonas. Our data suggest that two parabasalid genera, Pentatrichomonoides and Trichomonoides, may belong to the genus Tetratrichomonas. Tetratrichomonas isolates were divided into 16 robust host-specific and monophyletic groups that probably represent separate, mostly new, species. As only five Tetratrichomonas species were described from the examined host taxa so far, our study uncovered considerable species diversity within the genus. The wide host range, high level of species-specific host specificity, and newly revealed biodiversity make the genus Tetratrichomonas a valuable model for studying evolution of parasites.
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Affiliation(s)
- Ivan Cepicka
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic.
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Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H. An Empirical Assessment of Long-Branch Attraction Artefacts in Deep Eukaryotic Phylogenomics. Syst Biol 2005; 54:743-57. [PMID: 16243762 DOI: 10.1080/10635150500234609] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
In the context of exponential growing molecular databases, it becomes increasingly easy to assemble large multigene data sets for phylogenomic studies. The expected increase of resolution due to the reduction of the sampling (stochastic) error is becoming a reality. However, the impact of systematic biases will also become more apparent or even dominant. We have chosen to study the case of the long-branch attraction artefact (LBA) using real instead of simulated sequences. Two fast-evolving eukaryotic lineages, whose evolutionary positions are well established, microsporidia and the nucleomorph of cryptophytes, were chosen as model species. A large data set was assembled (44 species, 133 genes, and 24,294 amino acid positions) and the resulting rooted eukaryotic phylogeny (using a distant archaeal outgroup) is positively misled by an LBA artefact despite the use of a maximum likelihood-based tree reconstruction method with a complex model of sequence evolution. When the fastest evolving proteins from the fast lineages are progressively removed (up to 90%), the bootstrap support for the apparently artefactual basal placement decreases to virtually 0%, and conversely only the expected placement, among all the possible locations of the fast-evolving species, receives increasing support that eventually converges to 100%. The percentage of removal of the fastest evolving proteins constitutes a reliable estimate of the sensitivity of phylogenetic inference to LBA. This protocol confirms that both a rich species sampling (especially the presence of a species that is closely related to the fast-evolving lineage) and a probabilistic method with a complex model are important to overcome the LBA artefact. Finally, we observed that phylogenetic inference methods perform strikingly better with simulated as opposed to real data, and suggest that testing the reliability of phylogenetic inference methods with simulated data leads to overconfidence in their performance. Although phylogenomic studies can be affected by systematic biases, the possibility of discarding a large amount of data containing most of the nonphylogenetic signal allows recovering a phylogeny that is less affected by systematic biases, while maintaining a high statistical support.
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Affiliation(s)
- Henner Brinkmann
- Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de Biochimie, Université de Montréal, Succursale Centre-Ville, Montréal, Québec H3C3J7, Canada
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Ohkuma M, Iida T, Ohtoko K, Yuzawa H, Noda S, Viscogliosi E, Kudo T. Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Hypermastigea. Mol Phylogenet Evol 2005; 35:646-55. [PMID: 15878133 DOI: 10.1016/j.ympev.2005.02.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 02/03/2005] [Accepted: 02/21/2005] [Indexed: 10/25/2022]
Abstract
Small subunit rRNA gene sequences were identified without cultivation from parabasalid symbionts of termites belonging to the hypermastigid orders Trichonymphida (the genera Hoplonympha, Staurojoenina, Teranympha, and Eucomonympha) and Spirotrichonymphida (Spirotrichonymphella), and from four yet-unidentified parabasalid symbionts of the termite Incisitermes minor. All these new sequences were analyzed by Bayesian, likelihood, and parsimony methods in a broad phylogeny including all identified parabasalid sequences available in databases and some as yet unidentified sequences probably derived from hypermastigids. A salient point of our study focused on hypermastigids was the polyphyly of this class. We also noted a clear dichotomy between Trichonymphida and the other parabasalid taxa. However, this hypermastigid order was apparently polyphyletic, probably reflecting its morphological diversity. Among Trichonymphida, Teranympha (Teranymphidae) grouped together with the members of the family Eucomonymphidae, suggesting that its family status is ambiguous. The monophyletic lineage composed by Spirotrichonymphida exhibited a narrower branching pattern than Trichonymphida. The root of parabasalids was examined but could not be discerned accurately.
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Affiliation(s)
- Moriya Ohkuma
- Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan.
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Hackstein JHP. Eukaryotic Fe-hydrogenases – old eukaryotic heritage or adaptive acquisitions? Biochem Soc Trans 2005; 33:47-50. [PMID: 15667261 DOI: 10.1042/bst0330047] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All eukaryotes seem to possess proteins that most probably evolved from an ancestral Fe-hydrogenase. These proteins, known as NARF or Nar, do not produce hydrogen. Notably, a small group of rather unrelated unicellular anaerobes and a few algae possess Fe-hydrogenases, which produce hydrogen. In most, but not all organisms, hydrogen production occurs in membrane-bounded organelles, i.e. hydrogenosomes or plastids. Whereas plastids are monophyletic, hydrogenosomes evolved repeatedly and independently from mitochondria or mitochondria-like organelles. A systematic analysis of the various hydrogenosomes and their hydrogenases will contribute to an understanding of the evolution of the eukaryotic cell, and provide clues to the evolutionary origin(s) of the Fe-hydrogenase.
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Affiliation(s)
- J H P Hackstein
- Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Hackstein JHP, Yarlett N. Hydrogenosomes and symbiosis. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2005; 41:117-42. [PMID: 16623392 DOI: 10.1007/3-540-28221-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Johannes H P Hackstein
- Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands.
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