Protein Coding Gene Trees in Ciliates: Comparison with rRNA-Based Phylogenies

Tourancheau, Anne Baroin; Villalobo, Eduardo; Tsao, Nora; Torres, Antonio; Pearlman, Ronald E.

doi:10.1006/mpev.1998.0534

Cited by 36 publications

(27 citation statements)

References 24 publications

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“…All aligned positions were included in the analyses, even if certain regions were excluded by the original authors (as was done by Kanai et al, 1997;Budin and Philippe, 1998;Burmester et al, 1998;Downie et al, 1998;Tourancheau et al, 1998). Gaps in DNA sequence matrices were manually coded by using WinClada (Nixon, 1999).…”

Section: Methodsmentioning

confidence: 99%

“…intron trnL-trnF intron and spacer 1152 164 16 Downie et al (1998) intron rpoC1 intron 949 136 17 Krakauer et al (1998) exon-DNA prion precursor protein 896 36 18 Budin and Philippe (1998) exon-AA Hsp70 817 123 19 Tourancheau et al (1998) exon-AA phosphoglycerate kinase 492 34 20 Kanai et al (1997) exon-AA photolyase-blue-light photoreceptor family 838 132 21 Burmester et al (1998) exon-AA hexamerins and hemocyanins 971 189 22 Saurin et al (1999) exon-AA ABC transporters 416 53 23 Brown et al (1997) exon-AA trytophanyl-and tyrosyl-tRNA synthetases 184 33 24 Bonci et al (1997) exon …”

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confidence: 99%

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Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

2001

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

2001

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“…However, protein-coding genes can possess paralogs that might bias phylogenetic trees [27], [28]. Among these protein-coding genes, alpha-tubulin is one of the mostly used gene makers for ciliated phylogeny [8], [11], [13], [15], [20], [21], [29], and its duplication in ciliates has been previously studied only with sparse taxon sampling [15], [30]. Therefore, alpha-tubulin is a promising candidate for testing whether protein-coding genes are suitable for phylogeny construction of ciliates.…”

Section: Introductionmentioning

confidence: 99%

Assessing Whether Alpha-Tubulin Sequences Are Suitable for Phylogenetic Reconstruction of Ciliophora with Insights into Its Evolution in Euplotids

Katz

Song

2012

PLoS ONE

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The current understanding of ciliate phylogeny is mainly based on analyses of a single gene, the small subunit ribosomal RNA (SSU-rDNA). However, phylogenetic trees based on single gene sequence are not reliable estimators of species trees, and SSU-rDNA genealogies are not useful for resolution of some branches within Ciliophora. Since congruence between multiple loci is the best tool to determine evolutionary history, we assessed the usefulness of alpha-tubulin gene, a protein-coding gene that is frequently sequenced, for ciliate phylogeny. Here, we generate alpha-tubulin gene sequences of 12 genera and 30 species within the order Euplotida, one of the most frequently encountered ciliate clades with numerous apparently cosmopolitan species, as well as four genera within its putative sister order Discocephalida. Analyses of the resulting data reveal that: 1) the alpha-tubulin gene is suitable phylogenetic marker for euplotids at the family level, since both nucleotide and amino acid phylogenies recover all monophyletic euplotid families as defined by both morphological criteria and SSU-rDNA trees; however, alpha-tubulin gene is not a good marker for defining species, order and subclass; 2) for seven out of nine euplotid species for which paralogs are detected, gene duplication appears recent as paralogs are monophyletic; 3) the order Euplotida is non-monophyletic, and the family Uronychiidae with sequences from four genera, is non-monophyletic; and 4) there is more genetic diversity within the family Euplotidae than is evident from dargyrome (geometrical pattern of dorsal “silverline system” in ciliates) patterns, habit and SSU-rDNA phylogeny, which indicates the urgent need for taxonomic revision in this area.

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“…AF003250), the related genus Spirostomum (Accession No. AF003251) [11] and sequences from Paramecium tetraurelia (Accession Nos. X99490 and X99489) and Paramecium caudatum (Accession No.…”

Section: Resultsmentioning

confidence: 99%

A rapid and simple method of detection of Blepharisma japonicum using PCR and immobilisation on FTA paper

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Hughes

McNuff³

2003

BMC Ecol

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BackgroundThe rapid expansion in the availability of genome and DNA sequence information has opened up new possibilities for the development of methods for detecting free-living protozoa in environmental samples. The protozoan Blepharisma japonicum was used to investigate a rapid and simple detection system based on polymerase chain reaction amplification (PCR) from organisms immobilised on FTA paper.ResultsUsing primers designed from the α-tubulin genes of Blepharisma, specific and sensitive detection to the equivalent of a single Blepharisma cell could be achieved. Similar detection levels were found using water samples, containing Blepharisma, which were dried onto Whatman FTA paper.ConclusionThis system has potential as a sensitive convenient detection system for Blepharisma and could be applied to other protozoan organisms.

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Protein Coding Gene Trees in Ciliates: Comparison with rRNA-Based Phylogenies

Cited by 36 publications

References 24 publications

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

Assessing Whether Alpha-Tubulin Sequences Are Suitable for Phylogenetic Reconstruction of Ciliophora with Insights into Its Evolution in Euplotids

A rapid and simple method of detection of Blepharisma japonicum using PCR and immobilisation on FTA paper

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