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  • 1
    Electronic Resource
    Electronic Resource
    Phylogeny of Ultra-Rapidly Evolving Dinoflagellate Chloroplast Genes: A Possible Common Origin for Sporozoan and Dinoflagellate Plastids (2000)
    Springer
    Journal of molecular evolution 51 (2000), S. 26-40 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Dinoflagellate — Sporozoa — Chloroplast — Ribosomal RNA —psbA— Red alga — Chromist — Phylogeny — Alveolates — Mutation pressure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002390010064
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  • 2
    Electronic Resource
    Electronic Resource
    Mitochondrial DNA of the Coral Sarcophyton glaucum Contains a Gene for a Homologue of Bacterial MutS: A Possible Case of Gene Transfer from the Nucleus to the Mitochondrion (1998)
    Springer
    Journal of molecular evolution 46 (1998), S. 419-431 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Sarcophyton glaucum— Soft coral — Cnidaria — Mitochondrial genes — Nucleotide sequences —MutS gene — Mismatch repair — Phylogenetic analysis — Genetic code — Transfer RNA gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The nucleotide sequences of two segments of 6,737 ntp and 258 ntp of the 18.4-kb circular mitochondrial (mt) DNA molecule of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains the 3′ 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5′ terminal 1,124 ntp of the gene for the large subunit rRNA (l-rRNA). These genes are arranged in the order given and all are transcribed from the same strand of the molecule. The smaller segment contains the 3′ terminal 134 ntp of the ND4 gene and a complete tRNAf-Met gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan rather than termination. Also, as in M. senile the mt-tRNAf-Met gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and TψC loop sequences, and a mismatched nucleotide pair at the top of the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006321
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  • 3
    Electronic Resource
    Electronic Resource
    Sequence Analysis of the Mitochondrial Genome of Sarcophyton glaucum: Conserved Gene Order Among Octocorals (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 697-708 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Sarcophyton glaucum— Cnidaria — Mitochondrial DNA — Nucleotide sequence — Genetic code — Gene order
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The nucleotide sequence for an 11,715-bp segment of the mitochondrial genome of the octocoral Sarcophyton glaucum is presented, completing the analysis of the entire genome for this anthozoan member of the phylum Cnidaria. The genome contained the same 13 protein-coding and 2 ribosomal RNA genes as in other animals. However, it also included an unusual mismatch repair gene homologue reported previously and codes for only a single tRNA gene. Intermediate in length compared to two other cnidarians (17,443 and 18,911 bp), this organellar genome contained the smallest amount of noncoding DNA (428, compared to 1283 and 781 nt, respectively), making it the most compact one found for the phylum to date. The mitochondrial genes of S. glaucum exhibited an identical arrangement to that found in another octocoral, Renilla kolikeri, with five protein-coding genes in the same order as has been found in insect and vertebrate mitochondrial genomes. Although gene order appears to be highly conserved among octocorals, compared to the hexacoral, Metridium senile, few similarities were found. Like other metazoan mitochondrial genomes, the A + T composition was elevated and a general bias against codons ending in G or C was observed. However, an exception to this was the infrequent use of TGA compared to TGG to code for tryptophan. This divergent codon bias is unusual but appears to be a conserved feature among two rather distantly related anthozoans.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006429
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  • 4
    Electronic Resource
    Electronic Resource
    Concept of a bacterium still valid in prokaryote debate (2007)
    [s.l.] : Nature Publishing Group
    Nature 446 (2007), S. 257-257 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Sir Nigel Goldenfeld and Carl Woese, in their Connections Essay “Biology's next revolution” (Nature 445, 369; 2007), seek a change in concepts of 'organism, species and evolution' because of the prevalence of lateral ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/446257c
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  • 5
    Electronic Resource
    Electronic Resource
    The highly reduced genome of an enslaved algal nucleus (2001)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 410 (2001), S. 1091-1096 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Chromophyte algae differ fundamentally from plants in possessing chloroplasts that contain chlorophyll c and that have a more complex bounding-membrane topology. Although chromophytes are known to be evolutionary chimaeras of a red alga and a non-photosynthetic host, which gave rise to their ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35074092
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  • 6
    Electronic Resource
    Electronic Resource
    Evolution and Diversity of Zooflagellates (1993)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 40 (1993), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1993.tb06115.x
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  • 7
    Electronic Resource
    Electronic Resource
    The Protozoan Phylum Opalozoa (1993)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 40 (1993), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . The recently established protozoan phylum Opalozoa Cavalier-Smith 1991 includes all those zooflagellates with tubular mitochondrial cristae that never have cortical alveoli or rigid tubular ciliary hairs (retronemes), and also the opalinids, proteomyxids sensu stricto, and plasmodiophorids. Opalozoa totally lack plastids but usually (though not invariably) have peroxisomes. They always have well-developed Golgi dictyosomes. The trophic phase is a unicellular ciliated phagotroph except in the only intracellular parasites, the plasmodiophorids, where it is a non-phagotrophic and non-ciliated microplasmodium, and in the proteomyxids where it is an amoeboflagellate (which may sometimes be nonciliated) or a multicellular meroplasmodium. Unlike the phagotrophic Mycetozoa, opalozoans do not form aerial fruiting bodies, but encystation is common. The first detailed classification of the phylum is presented here. It is divided into four subphyla (three new), eight classes (four new, one emended), three subclasses (all new), three superorders (all new) and 22 orders of which 12 are new and one is emended. Diagnoses of these taxa are given, as well as lists of the 31 families (11 new) and 62 genera included within them. Opalozoa, which include Cercomonas and Heterornita, the commonest soil flagellates, are ecologically and evolutionarily important.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1993.tb06117.x
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular evolution of eukaryotes using structural genomic data (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: One of the most challenging evolutionary problems is locating the root of the eukaryote tree. We know that the root lies somewhere within the kingdom Protozoa, but the widespread view that early eukaryotes were amitochondrial has recently been dramatically overturned. Systematic biases in sequence evolution prevent the reliable inference of the eukaryote root from single-gene trees. Concatenated sequence trees should be more reliable, but leave many possibilities open. In principle deletions/insertions or gene fusions should be superior for this purpose whenever ancestral and derived states are clearly distinguishable. Using a derived gene fusion between dihydrofolate reductase (DHFR) and thymidylate synthase (TS), genes we were able to greatly narrow down the position of the root. This gene fusion clearly divides eukaryotes into two clades: Amoebozoa plus opisthokonts (unikonts, which are ancestrally uniciliate) and bikonts, which are ancestrally biciliate. Another gene fusion between the first three enzymes of the six enzyme pyrimidine synthesis pathway supports this division. This derived three gene fusion is seen in Amoebozoa and opisthokonts (unikonts) but not in bikonts. A third gene fusion in the phosphofructokinse gene which is so far only found in opisthokonts and Amoebozoa further lends support to the eukaryote unikont/bikont divide. Independent support comes from sequence trees based on concatenated protein alignments. Our results show that the primary divergence of eukaryotes was probably between unikonts (animals, Fungi, Choanozoa and Amoebozoa) and bikonts (plants, chromists, all other Protozoa: alveolates, excavates, Rhizaria, Apusozoa) and that the root of the eukaryote tree lies between these two groups.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_75.x
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  • 9
    Electronic Resource
    Electronic Resource
    Evolutionary Origins of Hsp90 Chaperones and a Deep Paralogy in their Bacterial Ancestors (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: . The 82–90 kD family of molecular chaperone proteins has homologs in eukaryotes (Hsp90) and many eubacteria (HtpG) but not in Archaebacteria. We used representatives of all four different eukaryotic paralogs (cytosolic, endoplasmic reticulum (ER), chloroplast, mitochondrial) together with numerous eubacterial HtpG proteins for phylogenetic analyses to investigate their evolutionary origins. Our trees confirm that none of the organellar Hsp90s derives from the endosymbionts of early eukaryotes. Contrary to previous suggestions of distant origins through lateral gene transfer (LGT) all eukaryote Hsp90s are related to Gram-positive eubacterial HtpG proteins. The nucleocytosolic, ER and chloroplast Hsp90 paralogs are clearly mutually related. The origin of mitochondrial Hsp90 is more obscure, as these sequences are deeply nested within eubacteria. Our trees also reveal a deep split within eubacteria into a group of mainly long-branching sequences (including the eukaryote mitochondrial Hsp90s) and another group comprising exclusively short-branching HtpG proteins, from which the cytosolic/ER versions probably arose. Both versions are present in several eubacterial phyla, suggesting gene duplication very early in eubacterial evolution and multiple independent losses thereafter. We identified one probable case of LGT within eubacteria. However, multiple losses can simply explain the evolutionary pattern of the eubacterial HtpG paralogs and predominate over LGT. We suggest that the actinobacterial ancestor of eukaryotes harbored genes for both eubacterial HtpG paralogs, as the actinobacterium Streptomyces coelicolor still does; one could have given rise to the mitochondrial Hsp90 and the other, following another duplication event in the ancestral eukaryote, to the cytosolic and ER Hsp90 homologs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2004.tb00580.x
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  • 10
    Electronic Resource
    Electronic Resource
    Ribosomal RNA Phylogeny of Bodonid and Diplonemid Flagellates and the Evolution of Euglenozoa (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: Euglenozoa is a major phylum of excavate protozoa (comprising euglenoids, kinetoplastids, and diplonemids) with highly unusual nuclear, mitochondrial, and chloroplast genomes. To improve understanding of euglenozoan evolution, we sequenced nuclear small-subunit rRNA genes from 34 bodonids (Bodo, Neobodo, Parabodo, Dimastigella-like, Rhynchobodo, Rhynchomonas, and unidentified strains), nine diplonemids (Diplonema, Rhynchopus), and a euglenoid (Entosiphon). Phylogenetic analysis reveals that diplonemids and bodonids are more diverse than previously recognised, but does not clearly establish the branching order of kinetoplastids, euglenoids, and diplonemids. Rhynchopus is holophyletic; parasitic species arose from within free-living species. Kinetoplastea (bodonids and trypanosomatids) are robustly holophyletic and comprise a major clade including all trypanosomatids and most bodonids (‘core bodonids’) and a very divergent minor one including Ichthyobodo. The root of the major kinetoplastid clade is probably between trypanosomatids and core bodonids. Core bodonids have three distinct subclades. Clade 1 has two distinct Rhynchobodo-like lineages; a lineage comprising Dimastigella and Rhynchomonas; and another including Cruzella and Neobodo. Clade 2 comprises Cryptobial Trypanoplasma, Procryptobia, and Parabodo. Clade 3 is an extensive Bodo saltans species complex. Neobodo designis is a vast genetically divergent species complex with mutually exclusive marine and freshwater subclades. Our analysis supports three phagotrophic euglenoid orders: Petalomonadida (holophyletic), Ploeotiida (probably holophyletic), Peranemida (paraphyletic).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2004.tb00387.x
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