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  • 1
    Electronic Resource
    Electronic Resource
    Transkingdom transfer of the phosphoglucose isomerase gene (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 453-459 
    Details
    ISSN: 1432-1432
    Keywords: Phosphoglucose isomerase ; Lateral gene transfer ; Ancient gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Previous analysis of the gene encoding phosphoglucose isomerase (Pgi) suggests that this gene may have been transferred between a eukaryote and a bacterium. However, excluding the alternative hypothesis of ancient gene duplication has proven difficult because of both insufficient sampling of taxa and an earlier misidentification of a bacterialPgi sequence. This paper presents a phylogenetic analysis of published completePgi sequences together with analysis of new partialPgi sequences from six species of bacteria. The data identify a group of bacterialPgi sequences, including sequences fromEscherichia coli andHaemophilus influenzae, which are more closely related to eukaryoticPgi sequences than to other bacterial sequences. The topology of gene trees constructed using several different methods are all consistent with the hypothesis of lateral gene transfer andnot ancient gene duplication. Furthermore, an estimate of a molecular clock forPgi dates the divergence of theE. coli andH. influenzae sequences from the animal sequences to between 470 and 650 million years ago, well after other estimates of the divergence between eukaryotes and bacteria. This study provides the most convincing evidence to date of the transkingdom transfer of a nuclear gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02337517
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  • 2
    Electronic Resource
    Electronic Resource
    Transkingdom Transfer of the Phosphoglucose Isomerase Gene (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 453-459 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Phosphoglucose isomerase — Lateral gene transfer — Ancient gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Previous analysis of the gene encoding phosphoglucose isomerase (Pgi) suggests that this gene may have been transferred between a eukaryote and a bacterium. However, excluding the alternative hypothesis of ancient gene duplication has proven difficult because of both insufficient sampling of taxa and an earlier misidentification of a bacterial Pgi sequence. This paper presents a phylogenetic analysis of published complete Pgi sequences together with analysis of new partial Pgi sequences from six species of bacteria. The data identify a group of bacterial Pgi sequences, including sequences from Escherichia coli and Haemophilus influenzae, which are more closely related to eukaryotic Pgi sequences than to other bacterial sequences. The topology of gene trees constructed using several different methods are all consistent with the hypothesis of lateral gene transfer and not ancient gene duplication. Furthermore, an estimate of a molecular clock for Pgi dates the divergence of the E. coli and H. influenzae sequences from the animal sequences to between 470 and 650 million years ago, well after other estimates of the divergence between eukaryotes and bacteria. This study provides the most convincing evidence to date of the transkingdom transfer of a nuclear gene.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006106
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  • 3
    Electronic Resource
    Electronic Resource
    In the land of the blind, one-eye is king: ecology of the mixotrophic ciliates Strombidium oculatum and Strombidium stylifer (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Strombidium oculatum and Strombidium stylifer live in tide pools at mid-latitudes on both sides of the North Atlantic Ocean. These “green” ciliates obtain chloroplasts from macroalgae, in particular from members of the Ulvophyceae, which they use for photosynthesis. Both ciliates also contain orange-pigmented granules that are organized into an eyespot. These granules are probably also obtained from their prey, the motile swarmer cells of the algae. Strombidium stylifer has been cultivated in our laboratory on pieces of Ulva, as well as a variety of microalgae. Strombidium oculatum has resisted cultivation to date. S. stylifer is an obligate mixotroph, incapable of sustained growth either starved in the light or fed in the dark. The presence in the ciliates of algal-derived organelles of photosynthesis and photodetection raises interesting questions about the behavior of both predator and prey, with light possibly being a critical integrating cue for their interaction.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_59.x
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  • 4
    Electronic Resource
    Electronic Resource
    Understanding genome complexity and protein evolution in ciliates: insights from mitchondria and nuclei (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We are exploring the evolutionary implications of genome duality in ciliates. Ciliates possess both a somatic macronucleus (MAC) and a germline micronucleus (MIC). Only the MAC is transcriptionally active, and divides by amitosis rather than mitosis and meiosis. We have previously hypothesized that genome duality is the driving force behind the heterogeneous and unusually elevated rates of amino acid substitutions we find in some protein coding genes. Does the dimorphic nature of the ciliate genome allow them to “cross the valleys in the adaptive landscape” of protein evolution? To test this hypothesis, we are analyzing additional protein genes as well as mitochondrial genes. Mitochondrial genes serve as an excellent comparison to those of the nucleus because phylogenetic information lost by the rapidly evolving nuclear genome may be retained in the mitochondria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_74.x
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  • 5
    Electronic Resource
    Electronic Resource
    Frontiers in Genomics: Insights into Protist Evolutionary Biology, University of Iowa, May 19–21, 2004 (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract. Protists constitute the bulk of eukaryotic diversity yet their genomes remain relatively unexplored. To address this issue, a workshop entitled, “Frontiers in Genomics: Insights into Protist Evolutionary Biology”, was convened at the University of Iowa on June 19–21, 2004. The specific aims of the workshop were to define the role of genomics in the eukaryotic tree of life, to identify challenges in characterizing protist (i.e. microbial eukaryote) genomes, and in proposing specific solutions to these challenges. The findings of the workshop are presented here and in a white paper that provide a set of guidelines for organizing the protist community and for planning and executing a protist genome project.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05-3355.x
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  • 6
    Electronic Resource
    Electronic Resource
    Phylogenetic Position of Sorogena stoianovitchae and Relationships within the Class Colpodea (Ciliophora) Based on SSU rDNA Sequences (2001)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 48 (2001), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . The ciliate Sorogena stoianovitchae, which can form a multicellular fruiting body, has been classified based upon its ultrastructure and morphology: the oral and somatic infraciliature of S. stoianovitchae most closely resemble those of members of the order Cyrtolophosidida in the class Colpodea. We characterized the small subunit ribosomal DNA (SSU rDNA) gene sequence from S. stoianovitchae and compared this sequence with those from representatives of all ciliate classes. These analyses placed S. stoianovitchae as either sister to members of the class Nassophorea or Colpodea. In an in-group analysis, including all SSU rDNA sequences from members of the classes Nassophorea and Colpodea and representatives of appropriate outgroups, S. stoianovitchae was always sister to Platyophrya vorax (class Colpodea, order Cyrtolophosidida). However, our analyses failed to support the monophyly ot the class Colpodea. Instead, our data suggest that there are essentially three unresolved clades: (1) the class Nassophorea; (2) Bresslaua vorax, Colpoda inflata, Pseudoplatyophrya nana, and Bursaria truncatella (class Colpodea); and (3) P. vorax and S. stoianovitchae (class Colpodea).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2001.tb00197.x
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  • 7
    Electronic Resource
    Electronic Resource
    Developmental genome processing and protein evolution in the ciliate Chilodonella uncinata (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Ciliates are microbial eukaryotes with dual genomes, one present in the transcriptionally inactive germline micronucleus (MIC) and the other in the somatic macronucleus (MAC). In the development of the MAC from the MIC, ciliates process their genomes by chromosomal fragmentation, excision of internal excised sequences (IESs), and amplification of chromosomes. Chilodonella uncinata is in a class of ciliates, Phyllopharyngea, that undergo extensive processing to generate MACs containing thousands of gene-sized chromosomes. Previous analyses suggest that sequences involved in this processing are highly variable among ciliate lineages. In this study, we examine cis-acting signals involved in the elimination of IESs in C. uncinata in order to understand the phylogenetic level at which processing signals are conserved. In addition, we are testing the hypothesis that the differential selection on dual genomes in ciliates allows unusually rapid divergence among paralogs of protein coding genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_84.x
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  • 8
    Electronic Resource
    Electronic Resource
    Evolution and implications of genome rearrangements in ciliates (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We are exploring genome evolution in diverse ciliates to assess whether patterns of protein evolution correspond to the presence of genome duality, and to levels of genome rearrangements among ciliates. Ciliate genomes contain an estimated 25,000–35,000 genes, a number higher than that of other characterized microbial eukaryotes and on a similar scale to that of humans and Arabidopsis thaliana. We have previously hypothesized that the divergence among ciliate proteins, and the accumulation of paralogs within ciliate taxa, is due to differential selection on the functional macronucleus and the transcriptionally inactive micronucleus. To assess this hypothesis, we are expanding our analyses of protein-coding gene sequences to compare the fate of proteins in ciliates to that of other eukaryotes, and to test whether the most divergent ciliate proteins are found in ciliates with extensively processed genomes. These analyses, combined with a phylogenetic perspective that reveals multiple origins of extensive fragmentation in ciliates, provide a possible explanation for the large genome size and diversity of proteins in ciliates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_39.x
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular markers for assessing community diversity of coastal ciliates (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Biogeography of microbial eukaryotes is widely debated. While some claim that all microbial organisms have a cosmopolitan distribution, other data suggest evidence of endemism. To assess these hypotheses for the distribution of ciliates in the orders Choreotrichia and Oligotrichia, coastal community samples were taken from Long Island Sound. We are obtaining sequences of SSU rRNA, ITS rRNA, and mitochondrial genes to use as molecular markers for assessing gene flow across time and space. These data will serve as a basis for continued study of phylogeographic distribution of Choreotrichia and Oligotrichia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_21.x
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular Phylogeny of Phyllopharyngean Ciliates and their Group I Introns (2004)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 51 (2004), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: We analyzed small subunit ribosomal DNA (ssu-rDNA) sequences to evaluate both the monophyly of the ciliate class Phyllopharyngea de Puytorac et al. (1974), and relationships among subclasses. Classifications based on morphology and ultrastructure divide the Phyllopharyngea into four subclasses, the Phyllopharyngia, Chonotrichia, Rhynchodia, and Suctoria. Our analyses of ssu-rDNA genealogies derived from sequence data collected from diverse members representing three of the four subclasses of Phyllopharyngea (Suctoria: Ephelota spp., Prodiscophyra collini, Acineta sp.; Phyllopharyngia: Chlamydodon exocellatus, Chlamydodon triquetrus, Dysteria sp.; and Chonotrichia: Isochona sp.) provide strong support for the monophyly of the Phyllopharyngea, and show that the Chonotrichia emerge from within the Phyllopharyngia. Based on this initial sampling, suctorian budding types are monophyletic, and exogenous budding appears to be basal to evaginative and endogenous budding. Further, we report the discovery of a group I intron at position 891 in the Suctoria Acineta sp. and Tokophrya lemnarum, and a second group I intron at position 1506 in T. lemnarum. These introns represent only the second examples of group I introns in a ciliate ribosomal gene, since the discovery of ribozymes in the LSU rRNA gene of Tetrahymena thermophila. Phylogenetic analyses of Group I introns suggest a complex evolutionary history involving either multiple loses or gains of introns within endogenously budding Suctoria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2004.tb00392.x
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