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Phylogeny of Parasitic Parabasalia and Free-Living Relatives Inferred from Conventional Markers vs. Rpb1, a Single-Copy Gene

By Shehre-Banoo Malik, Cynthia D. Brochu, Ivana Bilic, Jing Yuan, Michael Hess, John M. Logsdon and Jane M. Carlton
Topics: Research Article
Publisher: Public Library of Science
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Provided by: PubMed Central

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  1. (2007). A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer.
  2. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
  3. (2005). A potentially functional mariner transposable element in the protist Trichomonas vaginalis.M o l
  4. (2008). A rapid bootstrap algorithm for the RAxML Web servers.
  5. (2010). A review of the clinical presentation of Dientamoebiasis.
  6. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
  7. (2009). AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.
  8. (2008). An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis.
  9. (2008). An improved general amino acid replacement matrix.
  10. (2002). Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang.
  11. (1962). Axenic cultivation of Trichomonas tenax, the oral flagellate of man. I. Establishment of cultures.
  12. (2009). Axenization and optimization of in vitro growth of clonal cultures of Tetratrichomonas gallinarum and Trichomonas gallinae.
  13. (1969). Behavior and pathogenicity of Tritrichomonas foetus in chick liver cell cultures.
  14. (2010). Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.
  15. (2006). Clonal cultures of Histomonas meleagridis, Tetratrichomonas gallinarum and a Blastocystis sp. established through micromanipulation.
  16. (1995). Clustered alpha-amanitin resistance mutations in mouse.
  17. (2008). Comparative analysis of trichomonad genome sizes and karyotypes.
  18. (1997). Comparative sequence analysis of 5.8S rRNA genes and internal transcribed spacer (ITS) regions of trichomonadid protozoa.
  19. (2007). Comparison of four protein phylogeny of parabasalian symbionts in termite guts.
  20. (2010). Comparison of microscopy, two xenic culture techniques, conventional and real-time PCR for the detection of Dientamoeba fragilis in clinical stool samples.
  21. (1999). Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.
  22. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees.
  23. (2004). Critical analysis of the topology and rooting of the parabasalian 16S rRNA tree.
  24. (2010). Critical taxonomic revision of Parabasalids with description of one new genus and three new species.
  25. (1995). Cryopreservation and storage of parasitic protozoa in liquid nitrogen.
  26. (2010). Cryptic diversity of free-living parabasalids, Pseudotrichomonas keilini and Lacusteria cypriaca n. g., n. sp., as inferred from small subunit rDNA sequences.
  27. (2005). Cryptic species within the Tetratrichomonas gallinarum species complex revealed by molecular polymorphism.
  28. (2003). Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota).
  29. (2007). Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.
  30. (2004). Emerging from obscurity: biological, clinical, and diagnostic aspects of Dientamoeba fragilis. Clin Microbiol Rev 17: 553–570. table of contents.
  31. (2009). Estimating maximum likelihood phylogenies with PhyML.
  32. (1991). Experimental infections in chickens with Chilomastix gallinarum, Tetratrichomonas gallinarum,a n dTritrichomonas eberthi.
  33. (1971). Fine structure of the mastigont system in Tritrichomonas foetus (Riedmu ¨ller)*.
  34. (1972). Fine structure of Trichomitus batrachorum (Perty).
  35. (1988). Fine-structure genetics of ama-1, an essential gene encoding the amanitin-binding subunit of RNA polymerase II in Caenorhabditis elegans.
  36. (2010). Fluorescence in situ hybridization (FISH) mapping of single copy genes on Trichomonas vaginalis chromosomes. Mol Biochem Parasitol.
  37. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
  38. (2007). Global eukaryote phylogeny: Combined small- and large-subunit ribosomal DNA trees support monophyly of Rhizaria, Retaria and Excavata.
  39. (2008). Histomoniasis (Blackhead) and other protozoan diseases of the intestinal tract. In: Saif
  40. (2007). Identification of Pentatrichomonas hominis in feline fecal samples by polymerase chain reaction assay.
  41. (2008). Implications of the new eukaryotic systematics for parasitologists.
  42. (2005). Inference of the phylogenetic position of oxymonads based on nine genes: Support for Metamonada and Excavata.
  43. (2009). Inheritance and diversification of symbiotic trichonymphid flagellates from a common ancestor of termites and the cockroach Cryptocercus.
  44. (1987). Isolation of a stable clone of the ameboidadherent (AA) variant of Trichomonas vaginalis.
  45. (1990). Jakoba libera (Ruinen,
  46. (2008). Lateral transfer of the gene for a widely used marker, alpha-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata).
  47. (1988). Lethal and amanitinresistance mutations in the Caenorhabditis elegans ama-1 and ama-2 genes.
  48. (1987). Localization of an alpha-amanitin resistance mutation in the gene encoding the largest subunit of mouse RNA polymerase II.
  49. (1941). Macroscopic differentiation of lesions of histomoniasis and trichomoniasis in turkeys.
  50. (1999). Malawimonas jakobiformis n. gen., n. sp. (Malawimonadidae n. fam.): A Jakoba-like heterotrophic nanoflagellate with discoidal mitochondrial cristae.
  51. (2007). Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses.
  52. (2011). Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite.
  53. (2010). Molecular analysis of clonal trichomonad isolates indicate the existence of heterogenic species present in different birds and within the same host.
  54. (2009). Molecular characterization of a new Tetratrichomonas species in a patient with empyema.
  55. (2008). Molecular characterization of the Trichomonas gallinae morphologic complex in the United States.
  56. (2005). Molecular characterization of trichomonads from feces of dogs with diarrhea.
  57. (1996). Molecular data suggest an early acquisition of the mitochondrion endosymbiont.
  58. (2007). Molecular identity and heterogeneity of trichomonad parasites in a closed avian population.
  59. (2004). Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees. Mol Phylogenet Evol 31: 572–580. Evaluation of Markers for Parabasalid Phylogeny PLoS
  60. (2009). Molecular phylogeny of parabasalids with emphasis on the order Cristamonadida and its complex morphological evolution.
  61. (2007). Morphological and molecular identification of non-Tritrichomonas foetus trichomonad protozoa from the bovine preputial cavity.
  62. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models.
  63. (2001). MRBAYES: Bayesian inference of phylogenetic trees.
  64. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
  65. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput.
  66. (1990). Mutant Caenorhabditis elegans RNA polymerase II with a 20,000-fold reduced sensitivity to alpha-amanitin.
  67. (1998). New insights into the phylogeny of trichomonads inferred from small subunit rRNA sequences.
  68. (2007). Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups. Gene 394: 78–86. Evaluation of Markers for Parabasalid Phylogeny PLoS
  69. (2001). On core jakobids and excavate taxa: The ultrastructure of Jakoba incarcerata.
  70. (2009). Partial sequence of the beta-tubulin of Histomonas meleagridis and the activity of benzimidazoles against H. meleagridis in vitro.
  71. (2005). PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). 4.0b10 ed. SunderlandMassachusetts: Sinauer Associates.
  72. (2006). PCR for the identification and differentiation of Histomonas meleagridis, Tetratrichomonas gallinarum and Blastocystis spp.
  73. (1999). Phylogenetic affinities of Diplonema within the Euglenozoa as inferred from the SSU rRNA gene and partial COI protein sequences.
  74. (2008). Phylogenetic mixture models for proteins.
  75. (2010). Phylogenetic position and morphology of Spirotrichosomidae (Parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus.
  76. (1998). Phylogenetic relationships of the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase, from parabasalid flagellates.
  77. (2009). Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘‘supergroups’’.
  78. (1995). Phylogeny of trichomonads inferred from small-subunit rRNA sequences.
  79. (2000). Phylum Parabasalia. In:
  80. (2004). Polymorphic insertions and deletions in parabasalian enolase genes.
  81. (2007). Pulmonary superinfection by trichomonads in the course of acute respiratory distress syndrome.
  82. (1989). Rapid one-step characterization of recombinant vectors by direct analysis of transformed Escherichia coli colonies.
  83. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
  84. (2008). Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation.
  85. (2001). Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.
  86. (1969). Structure of Hypotrichomonas acosta (Moskowitz) (Monocercomonadidae, Trichomonadida) as revealed by electron microscopy.
  87. (1972). Structure of Monocercomonas sp. as revealed by electron microscopy.
  88. (1968). Structure of Pentatrichomonas hominis (Davaine) as revealed by electron microscopy.
  89. (2009). Studies of trichomonad protozoa in free ranging songbirds: prevalence of Trichomonas gallinae in house finches (Carpodacus mexicanus) and corvids and a novel trichomonad in mockingbirds (Mimus polyglottos).
  90. (1974). Study of Dientamoeba fragilis Jepps & Dobell. I. Electronmicroscopic observations of the binucleate stages. II. Taxonomic position and revision of the genus.
  91. (2010). Systematic position of Histomonas meleagridis based on four protein genes.
  92. (2005). Tetratrichomonads from the oral cavity and respiratory tract of humans.
  93. (2009). The CIPRES Portals.
  94. (1993). The divergence of Trichomonas vaginalis virus RNAs among various isolates of Trichomonas vaginalis.
  95. (1957). The establishment of various trichomonads of animals and man in axenic cultures.
  96. (1920). The flagellate character and reclassification of the parasite producing ‘‘blackhead’’ in turkeys – Histomonas (gen. nov.) meleagridis (Smith).
  97. (2010). The genome of Trichomonas vaginalis. In:
  98. (2006). The gut flagellate community of the termite Neotermes cubanus with special reference to Staurojoenina and Trichocovina hrdyi nov.
  99. (2009). The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont Coronympha.
  100. (2005). The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.
  101. (2009). The protist Trichomonas vaginalis harbors multiple lineages of transcriptionally active Mutator-like elements.
  102. (1996). Transcription in the early diverging eukaryote Trichomonas vaginalis: an unusual RNA polymerase II and alpha-amanitin-resistant transcription of protein-coding genes.
  103. (1962). Trichomonad canker in the Inca dove, Scardafella inca (Lesson).
  104. (1962). Trichomonads from poikilotherms: Nutritional and physiological notes.
  105. (2009). Trichomonal sinusitis in an adolescent patient with multiple trauma.
  106. (1954). Trichomonas gallinae: A review.
  107. (2003). Tritrichomonas foetus and not Pentatrichomonas hominis is the etiologic agent of feline trichomonal diarrhea.
  108. (2001). Unusual diversity in alphaamanitin sensitivity of RNA polymerases in trichomonads.