21 research outputs found

    Best tree of the Spirotrichea inferred by two-gene combined sequences (Atub-SSU).

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    <p>Bootstrap values for branches of the ML tree is given on nodes. The scale bar corresponds to 5 substitutions per 100 nucleotide positions. Dargyrome patterns and natural habitats are given after species name of euplotids by symbols. Clades I-IV for euplotids were designated according to Petroni <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040635#pone.0040635-Petroni1" target="_blank">[42]</a> and Yi et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040635#pone.0040635-Yi4" target="_blank">[38]</a>.</p

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

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    <div><p>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.</p> </div

    Euplotid Species for Which Alpha-Tubulin Genes Were Sequenced in the Present Work.

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    <p>Euplotid Species for Which Alpha-Tubulin Genes Were Sequenced in the Present Work.</p

    Intraspecific Distances Between/Among α-Tubulin Clones and Between/Among Paralogs.

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    <p>NOTE.<b>-</b><i>N,</i> number of clones; <i>d</i>, number of nucleotide substitutions per site calculated using Tamura-Nei model; <i>dA</i>, number of amino acid substitutions per site calculated using Dayhoff model; R/S, number of replacement site substitutions/number of synonymous substitutions among clones.</p>#<p>Fixed between paralogs.</p>**<p><i>Euplotes sinicus</i> population I: Clone 1–4; <i>E. sinicus</i> population II: Clone 5.</p

    Best tree of the Spirotrichea inferred by Maximum likelihood of Dataset Atub_n74.

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    <p>Species newly sequenced in the present study are shown in bold type. Bootstrap values for branches of the ML tree and posterior probability values for BI tree, respectively, are given on nodes. Fully supported (100%/1.00) branches are marked with solid circles. The scale bar corresponds to 10 substitutions per 100 nucleotide positions. Dargyrome patterns and natural habitats are given after species name of euplotids by symbols. Clades I-IV for euplotids were designated according to Petroni <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040635#pone.0040635-Petroni1" target="_blank">[42]</a> and Yi et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040635#pone.0040635-Yi4" target="_blank">[38]</a>.</p

    Representative euplotid species from live material and after protargol impregnation.

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    <p>Representative euplotid species from live material and after protargol impregnation.</p

    Accession numbers of the species used for the phylogenetic tree construction.

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    <p>Species newly sequenced in the present study are marked in bold. Species sequenced by the authors' group are maked by sterisks (*).</p

    Table S1 from Species delimitation for the molecular taxonomy and ecology of a widely distributed microbial eukaryotes genus <i>Euplotes</i> (Alveolata, Ciliophora)

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    Euplotes species analyzed in this study, and their reliability assessment based on rDNA sequences (Bold numbers were newly sequenced) and other integrated information

    Three group I introns in the small subunit ribosomal RNA gene of <i>Aegyriana oliva</i>.

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    <p><b>A.</b> Summary of reported group I introns in ciliates. The species reported in the present study are marked in bold. <b>B–D.</b> Secondary structure of three introns predicted by the GISSD database. <b>B.</b> Aol. S516. <b>C.</b> Aol. S943. <b>D.</b> Aol. S1506.</p
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