Phylogeny of parasitic parabasalia and free-living relatives inferred from conventional markers vs. Rpb1, a single-copy gene

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 1...

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Published in:	PloS one Vol. 6; no. 6; p. e20774
Main Authors:	Malik, Shehre-Banoo, Brochu, Cynthia D, Bilic, Ivana, Yuan, Jing, Hess, Michael, Logsdon, Jr, John M, Carlton, Jane M
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 09-06-2011 Public Library of Science (PLoS)
Subjects:	Amino acids Analysis Animals Biological evolution Biology Biosynthesis Cell culture Cloning Coding Commensals Data processing Dehydrogenases DNA-directed RNA polymerase Endosymbionts Enzymes Euglenozoa Eukaryotes Gene Dosage - genetics Gene duplication Genes Genes, Protozoan - genetics Genetic Markers Genomes Genomics Glyceraldehyde-3-phosphate dehydrogenase Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) - genetics Homology Humans Infections Intestine Molecular Sequence Data Morphology Nucleotide sequence Open Reading Frames - genetics Parabasalia Parabasalidea - genetics Parasites Parasites - genetics Parasitic diseases Parasitology Phosphopyruvate hydratase Phylogenetics Phylogeny Physiology Polymerase chain reaction Protozoan Proteins - genetics Public health Reproduction (copying) Reptiles & amphibians Ribonucleic acid Ribosomal RNA RNA RNA polymerase II RNA Polymerase II - genetics rRNA 18S Sediments Sexually transmitted diseases Species STD Termites Trichomonas gallinae Trichomonas vaginalis Tubulin Veterinary medicine Wood New York Iowa Austria Iowa City Iowa United States > US
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Summary:	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. 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. 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Current address: Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada Conceived and designed the experiments: S-BM JML JMC. Performed the experiments: S-BM CDB IB JY. Analyzed the data: S-BM. Contributed reagents/materials/analysis tools: MH JML JMC. Wrote the paper: S-BM CDB IB MH JML JMC.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0020774