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

Malik SB, Brochu CD, Bilic I, Yuan J, Hess M, Logsdon JM, Carlton JM - PLoS ONE (2011)

Bottom Line: As a result, genetic studies of Parabasalia lag behind other organisms.These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data.These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America. sbmalik@dal.ca

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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Related in: MedlinePlus

Cartoon of parabasalid evolutionary relationships summarized from published phylogenies.The consensus backbone phylogenies shown are derived from (A) 18S rDNA [10], [37], and (B) concatenated 18S rDNA genes and enolase, GAPDH, α- and β-tubulin proteins [11]. Dotted lines indicate prior results without 18S rDNA [7].
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pone-0020774-g001: Cartoon of parabasalid evolutionary relationships summarized from published phylogenies.The consensus backbone phylogenies shown are derived from (A) 18S rDNA [10], [37], and (B) concatenated 18S rDNA genes and enolase, GAPDH, α- and β-tubulin proteins [11]. Dotted lines indicate prior results without 18S rDNA [7].

Mentions: Evolutionary relationships of parabasalids are under constant revision [8], [10], [11], [38]. Historically, genes encoding the 18S and 5.8S ribosomal RNA subunits (rDNA) have been used to infer parabasalid relationships at the greatest taxonomic breadth [39], [40], [41], but many parts of these molecular phylogenies are unresolved [9], [11], [42]. A cartoon consensus of recent 18S rDNA phylogenies of a number of parabasalids is summarized in Figure 1. Cloned degenerate polymerase chain reaction (PCR) products of several genes encoding proteins such as glyceraldehyde 3-phosphate dehydrogenase (GAPDH) [8], [9], [43], malate dehydrogenase (MDH) [44], enolase [45], α- and β-tubulin [7], [11], [46] have also been used to infer the evolutionary relationships, albeit of a less taxonomically-broad representation of the six parabasalid groups. However, these markers are not ideal: parabasalid enolase genes exhibit recombination [45], and MDH and GAPDH genes appear to be most closely related to bacterial homologs via lateral gene transfer [43], [44], [47], [48]. In contrast, α- and β-tubulin genes are more similar to eukaryotic homologs [7], [46], making these two and rDNA the only genes available until now for comparison of parabasalids to other eukaryotes. However, all of these protein-coding genes can be found duplicated in various parabasalid genera, and individually lack resolution at different taxonomic levels, while their phylogenies do not strongly corroborate one another [7], [43], [46], [49]. In spite of this, both GAPDH and 18S rRNA genes typically converge upon the same six monophyletic groups [8], [9] and thus probably contribute most of the signals to published analyses of concatenated parabasalid genes. These data suggest that an alternate eukaryotic protein-coding gene that has not undergone recombination, horizontal gene transfer, or duplication might be more useful to resolve the relationships within Parabasalia and between parabasalids and other eukaryotes.


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

Malik SB, Brochu CD, Bilic I, Yuan J, Hess M, Logsdon JM, Carlton JM - PLoS ONE (2011)

Cartoon of parabasalid evolutionary relationships summarized from published phylogenies.The consensus backbone phylogenies shown are derived from (A) 18S rDNA [10], [37], and (B) concatenated 18S rDNA genes and enolase, GAPDH, α- and β-tubulin proteins [11]. Dotted lines indicate prior results without 18S rDNA [7].
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3111441&req=5

pone-0020774-g001: Cartoon of parabasalid evolutionary relationships summarized from published phylogenies.The consensus backbone phylogenies shown are derived from (A) 18S rDNA [10], [37], and (B) concatenated 18S rDNA genes and enolase, GAPDH, α- and β-tubulin proteins [11]. Dotted lines indicate prior results without 18S rDNA [7].
Mentions: Evolutionary relationships of parabasalids are under constant revision [8], [10], [11], [38]. Historically, genes encoding the 18S and 5.8S ribosomal RNA subunits (rDNA) have been used to infer parabasalid relationships at the greatest taxonomic breadth [39], [40], [41], but many parts of these molecular phylogenies are unresolved [9], [11], [42]. A cartoon consensus of recent 18S rDNA phylogenies of a number of parabasalids is summarized in Figure 1. Cloned degenerate polymerase chain reaction (PCR) products of several genes encoding proteins such as glyceraldehyde 3-phosphate dehydrogenase (GAPDH) [8], [9], [43], malate dehydrogenase (MDH) [44], enolase [45], α- and β-tubulin [7], [11], [46] have also been used to infer the evolutionary relationships, albeit of a less taxonomically-broad representation of the six parabasalid groups. However, these markers are not ideal: parabasalid enolase genes exhibit recombination [45], and MDH and GAPDH genes appear to be most closely related to bacterial homologs via lateral gene transfer [43], [44], [47], [48]. In contrast, α- and β-tubulin genes are more similar to eukaryotic homologs [7], [46], making these two and rDNA the only genes available until now for comparison of parabasalids to other eukaryotes. However, all of these protein-coding genes can be found duplicated in various parabasalid genera, and individually lack resolution at different taxonomic levels, while their phylogenies do not strongly corroborate one another [7], [43], [46], [49]. In spite of this, both GAPDH and 18S rRNA genes typically converge upon the same six monophyletic groups [8], [9] and thus probably contribute most of the signals to published analyses of concatenated parabasalid genes. These data suggest that an alternate eukaryotic protein-coding gene that has not undergone recombination, horizontal gene transfer, or duplication might be more useful to resolve the relationships within Parabasalia and between parabasalids and other eukaryotes.

Bottom Line: As a result, genetic studies of Parabasalia lag behind other organisms.These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data.These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America. sbmalik@dal.ca

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.

Show MeSH
Related in: MedlinePlus