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Dieter Ammermann - One of the best experts on this subject based on the ideXlab platform.
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cell size and dorsal cilia are they useful features for the identification of Stylonychia mytilus ciliophora spirotrichea and its subpopulations
European Journal of Protistology, 2008Co-Authors: Dieter AmmermannAbstract:It was investigated whether (1) the number of cilia of the dorsal kineties 3 and 4 and (2) the cell length are species-specific characters which can be used to distinguish the sibling species S. mytilus and S. lemnae. The number of cilia of the dorsal kineties 3 and 4 is a relatively constant, reliable species-specific character in all investigated strains of both species and rather independent from the origin and the nutritional condition of the cells. The cell length is also a reliable species character, if strains of both species from Germany are compared (under identical nutritional conditions). However, all S. mytilus strains from China, Australia and Peru are significantly smaller forming one (or some) "small" subpopulations or subspecies, compared with a "big" subpopulation from Germany. The small ones cannot always be distinguished by size alone from S. lemnae cells. Thus the cell size in S. mytilus is not in all geographic regions a species character, but can be used to characterize subspecies.
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α-Tubulin Minichromosome Promoters in the Stichotrichous Ciliate Stylonychia lemnae
Eukaryotic Cell, 2006Co-Authors: Ilya N. Skovorodkin, Irina Raykhel, Alexander Pimenov, Bernd Schimanski, Dieter Ammermann, Arthur GünzlAbstract:Ciliated protists are model organisms for a number of molecular phenomena including telomerase function, self-splicing introns, and an RNA interference-related mechanism in programmed DNA elimination. Despite this relevance, our knowledge about promoters and transcriptional regulation in these organisms is very limited. The macronuclear genome of stichotrichous ciliates consists of minichromosomes which typically encode a single gene. The 5′ nontranscribed spacers are usually no longer than 400 bp and highly suitable for promoter characterizations. We used microinjection of two artificial and differently tagged α1 tubulin minichromosomes into the macronucleus of Stylonychia lemnae as a means to characterize in detail the corresponding promoter. Clonal cell lines that stably maintained both minichromosomes were generated, enabling comparative expression analysis by primer extension assays. Deletion and block substitution mutations of one of the minichromosomes revealed a TATA-like element, a putative initiator element, and two distinct upstream sequence elements (USEs). Determination of transcription initiation sites and a sequence alignment indicated that both TATA-like and initiator elements are conserved components of S. lemnae minichromosomes, whereas the USEs appear to be specific for the α1 tubulin minichromosome. The α2 tubulin minichromosome promoter is very short, comprising the two proximal elements but not the USEs. Despite the latter finding, up-regulation of α-tubulin expression in cells treated with concanavalin A activated the α2 but not the α1 tubulin promoter. These results therefore show that gene expression regulation in S. lemnae occurs at the level of transcription initiation on the basis of structurally different promoters.
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a pcr based method to distinguish the sibling species Stylonychia mytilus and Stylonychia lemnae ciliophora spirotrichea using isocitrate dehydrogenase gene sequences
Journal of Eukaryotic Microbiology, 2006Co-Authors: Madlen Haentzsch, Dieter Ammermann, Detlef Bernhard, Stephanie L Schmidt, Thomas U Berendonk, Martin SchlegelAbstract:A differentiation, based on morphological characters, between Stylonychia mytilus and Stylonychia lemnae is very difficult, especially for non-specialists. These two sibling species were considered as one species, S. mytilus, until detailed cytological and genetic studies could show the existence of two genetically isolated varieties. Further morphological and biochemical analyses verified the separation and finally in 1983 a new species S. lemnae was described. The examination of several isoenzymes revealed unambiguous differences in the banding pattern of isocitrate dehydrogenase (IDH) between these two species. Therefore, the IDH gene of 30 isolates of S. lemnae and S. mytilus coming from various regions all over the world were amplified and sequenced. The sequence analyses revealed intraspecific as well as interspecific substitutions, which were used for the development of species-specific PCR primers for both species. Application of these species-specific primer pairs now allows a very easy and clear identification of both sibling species.
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ACC
2006Co-Authors: Ilya N. Skovorodkin, Irina Raykhel, Arthur Günzl, Bernd Schimanski, Dieter Ammermann, Er Pimenov, Eukaryotic Cell Doi:. /ecAbstract:2 Ciliated protists are model organisms for a number of molecular phenomena including telomerase function, self-splicing introns and an RNA interference-related mechanism in programmed DNA elimination. Despite this relevance, our knowledge about promoters and transcriptional regulation in these organisms is very limited. The macronuclear genome of stichotrichous ciliates consists of minichromosomes which typically encode a single gene. The 5 ’ nontranscribed spacers are usually not longer than 400 bp and highly suitable for promoter characterizations. We used microinjection of two artificial and differently tagged 1 tubulin minichromosomes into the macronucleus of Stylonychia lemnae as a means to characterize in detail the corresponding promoter. Clonal cell lines were generated which stably maintained both minichromosomes enabling a comparative expression analysis by primer extension assays. Deletion and block substitution mutations of one of the minichromosomes revealed a TATA-like element, a putative initiator element, and two distinct upstream sequence elements (USEs). Determination of transcription initiation site
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minichromosomal dna replication in the macronucleus of the hypotrichous ciliate Stylonychia lemnae is independent of chromosome internal sequences
Chromosoma, 2001Co-Authors: Ilya N. Skovorodkin, Dieter Ammermann, Irina B Zassoukhina, Sigrid Hojak, Arthur GünzlAbstract:The origins of DNA replication in prokaryotes and eukaryotes are typically defined by cis-acting sequences. However, in ciliates, evidence suggests that the replication of short macronuclear minichromosomes may not require such determinants. In hypotrichous ciliates, macronuclei contain millions of gene-sized minichromosomes, which generally have a single protein-coding region, two short noncoding flanks and, on each end, a short telomere consisting of a double-stranded repeat region and a single-stranded 3′ overhang. Electron microscopic studies that showed that replication of minichromosomes initiates at or near telomeres and the discovery of a primase activity synthesizing RNA primers over the whole 3′ telomeric overhang in vitro suggested that minichromosome replication starts directly at telomeres. Conversely, many minichromosomes contain an AT-rich, semi-conserved, palindromic sequence motif in their subtelomeric regions and it has been proposed that this motif is involved in regulating minichromosomal replication. To analyze what sequences or structures of the minichromosomes are essential for DNA replication, we stably transfected genetically modified α1-tubulin-encoding minichromosomes into the hypotrichous ciliate Stylonychia lemnae. Cotransfection of mutated and control minichromosomes revealed that noncoding regions can be deleted or replaced with unrelated sequences without affecting minichromosome replication efficiency in vegetatively growing cells. Similarly, replacement of the coding region resulted in a minichromosome that was stably maintained in transfected cells at the same high copy number for many months. In contrast, α1-tubulin-encoding minichromosomes without telomeres were rapidly lost after transfection. Hence, DNA replication of the α1-tubulin-encoding minichromosome does not depend on chromosome-internal sequences but may depend on telomeres.
Laura F Landweber - One of the best experts on this subject based on the ideXlab platform.
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Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax.
Journal of Theoretical Biology, 2016Co-Authors: Jonathan Burns, Masahico Saito, Denys Kukushkin, Laura F Landweber, Xiao Chen, Nataša JonoskaAbstract:Abstract Some genera of ciliates, such as Oxytricha and Stylonychia, undergo massive genome reorganization during development and provide model organisms to study DNA rearrangement. A common feature of these ciliates is the presence of two types of nuclei: a germline micronucleus and a transcriptionally-active somatic macronucleus containing over 16,000 gene sized “nano-chromosomes”. During conjugation the old parental macronucleus disintegrates and a new macronucleus forms from a copy of the zygotic micronucleus. During this process, macronuclear chromosomes assemble through DNA processing events that delete 90–98% of the DNA content of the micronucleus. This includes the deletion of noncoding DNA segments that interrupt precursor DNA regions in the micronucleus, as well as transposons and other germline-limited DNA. Each macronuclear locus may be present in the micronucleus as several nonconsecutive, permuted, and/or inverted DNA segments. Here we investigate the genome-wide range of scrambled gene architectures that describe all precursor-product relationships in Oxytricha trifallax, the first completely sequenced scrambled genome. We find that five general, recurrent patterns in the sets of scrambled micronuclear precursor pieces can describe over 80% of Oxytricha's scrambled genes. These include instances of translocations and inversions, and other specific patterns characterized by alternating stretches of consecutive odd and even DNA segments. Moreover, we find that iterating patterns of alternating odd–even segments up to four times can describe over 96% of the scrambled precursor loci. Recurrence of these highly structured genetic architectures within scrambled genes presumably reflects recurrent evolutionary events that gave rise to over 3000 of scrambled loci in the germline genome.
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polymorphism recombination and alternative unscrambling in the dna polymerase alpha gene of the ciliate Stylonychia lemnae alveolata class spirotrichea
Genetics, 2003Co-Authors: Catherine A Lozupone, David H Ardell, Laura F LandweberAbstract:DNA polymerase alpha is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D.
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universal molecular computation in ciliates
2002Co-Authors: Laura F Landweber, Lila KariAbstract:How do cells and nature “compute”? They read and “rewrite” DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman’s elegant solution to a seven-city Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, ciliated protozoans of genus Oxytricha and Stylonychia had solved a potentially harder problem using DNA several million years earlier. The solution to this “problem”, which occurs during the process of gene unscrambling, represents one of nature’s ingenious solutions to the problem of the creation of genes. Here we develop a model for the guided homologous recombinations that take place during gene rearrangement and prove that such a model has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform at least any computation carried out by an electronic computer.
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Universal Molecular Computation in Ciliates
Springer, 2002Co-Authors: Laura F Landweber, Lila KariAbstract:How do cells and nature "compute"? They read and "rewrite" DNA all the time, by processes that modify sequences at the DNA or RNA level. In 1994, Adleman's elegant solution to a seven-city Directed Hamiltonian Path problem using DNA [1] launched the new field of DNA computing, which in a few years has grown to international scope. However, unknown to this field, ciliated protozoans of genus Oxytricha and Stylonychia had solved a potentially harder problem using DNA several million years earlier. The solution to this "problem", which occurs during the process of gene unscrambling, represents one of nature's ingenious solutions to the problem of the creation of genes. Here we develop a a model for the guided homologous recombinations that take place during gene rearrangement and prove that such a model has the computational power of a Turing machine, the accepted formal model of computation. This indicates that, in principle, these unicellular organisms may have the capacity to perform a..
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the molecular basis of nuclear genetic code change in ciliates
Current Biology, 2001Co-Authors: Catherine A Lozupone, Robin D Knight, Laura F LandweberAbstract:Abstract Background: The nuclear genetic code has changed in several lineages of ciliates. These changes, UAR to glutamine and UGA to cysteine, imply that eukaryotic release factor 1 (eRF1), the protein that recognizes stop codons and terminates translation, changes specificity. Here we test whether changes in eRF1 drive genetic code evolution. Results: Database sequence analysis reveals numerous genetic code alterations in ciliates, including UGA → tryptophan in Blepharisma americanum and the distantly related Colpoda. We sequenced eRF1 from four ciliates: B. americanum , a heterotrich that independently derived the same eRF1 specificity as Euplotes , and three spirotrichs, Stylonychia lemnae , S. mytilus , and Oxytricha trifallax , that independently derived the same genetic code as Tetrahymena (UAR → glutamine). Distantly related ciliates with similar codes show characteristic changes in eRF1. We used a sliding window analysis to test associations between changes in specific eRF1 residues and changes in the genetic code. The regions of eRF1 that display convergent substitutions are identical to those identified in a recently reported nonsense suppression mutant screen in yeast. Conclusions: Genetic code change by stop codon reassignment is surprisingly frequent in ciliates, with UGA → tryptophan occurring twice independently. This is the first description of this code, previously found only in bacteria and mitochondria, in a eukaryotic nuclear genome. eRF1 has evolved strikingly convergently in lineages with variant genetic codes. The strong concordance with biochemical data indicates that our methodology may be generally useful for detecting molecular determinants of biochemical changes in evolution.
Martin Schlegel - One of the best experts on this subject based on the ideXlab platform.
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a pcr based method to distinguish the sibling species Stylonychia mytilus and Stylonychia lemnae ciliophora spirotrichea using isocitrate dehydrogenase gene sequences
Journal of Eukaryotic Microbiology, 2006Co-Authors: Madlen Haentzsch, Dieter Ammermann, Detlef Bernhard, Stephanie L Schmidt, Thomas U Berendonk, Martin SchlegelAbstract:A differentiation, based on morphological characters, between Stylonychia mytilus and Stylonychia lemnae is very difficult, especially for non-specialists. These two sibling species were considered as one species, S. mytilus, until detailed cytological and genetic studies could show the existence of two genetically isolated varieties. Further morphological and biochemical analyses verified the separation and finally in 1983 a new species S. lemnae was described. The examination of several isoenzymes revealed unambiguous differences in the banding pattern of isocitrate dehydrogenase (IDH) between these two species. Therefore, the IDH gene of 30 isolates of S. lemnae and S. mytilus coming from various regions all over the world were amplified and sequenced. The sequence analyses revealed intraspecific as well as interspecific substitutions, which were used for the development of species-specific PCR primers for both species. Application of these species-specific primer pairs now allows a very easy and clear identification of both sibling species.
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fluorescence in situ hybridization with specific oligonucleotide rrna probes distinguishes the sibling species Stylonychia lemnae and Stylonychia mytilus ciliophora spirotrichea
Protist, 2006Co-Authors: Stephanie L Schmidt, Detlef Bernhard, Martin Schlegel, J FriedAbstract:Based on morphological and morphogenetic characters alone, the sibling species Stylonychia lemnae and Stylonychia mytilus, members of the Stylonychia mytilus complex, can hardly be distinguished. However, biochemical investigations of the isoenzyme pattern of different enzymes showed a distinct differentiation between these two species. In the last few years, fluorescence in situ hybridization (FISH) techniques have become a suitable and reliable tool for identification and differentiation of closely related species of protozoa, such as ciliates. To distinguish the sibling species, a set of specific oligonucleotide probes were developed. In the present study, the SSU rDNA of 7 clones of Stylonychia lemnae and 13 clones of Stylonychia mytilus, isolated from different geographic regions, were sequenced. Comparing all SSU rDNA sequences of both species, only one single difference within the whole gene was detected. Based on this difference, a set of two oligonucleotide probes, targeting the SSU rRNA of each species (Stylonychia mytilus and Stylonychia lemnae) was designed. These probes were successfully tested by applying the FISH techniques on preserved cells of different clones of both species.
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Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences.
Molecular phylogenetics and evolution, 2001Co-Authors: Detlef Bernhard, Dieter Ammermann, Alexandra Stechmann, Manuela Hehn, Martin SchlegelAbstract:Abstract The small subunit rDNAs of five species belonging to the Euplotidae and eight species of the Oxytrichidae were sequenced to obtain a more detailed picture of the phylogenetic relationships within the Spirotrichea (Ciliophora). Various tree reconstruction algorhythms yielded nearly identical topologies. All Euplotidae were separated from the other Spirotrichea by a deep split. Further, a large genetic distance between the marine genus Moneuplotes and the freshwater species of Euplotoides was found. Differences between the methods used occurred only within the Oxytrichidae. Whereas the monophyly of the Stylonychinae was supported in all trees, the monophyly of the Oxytrichinae was not. However, the molecular data support the morphological and ontogenetic evidence that the pattern of 18 frontal–ventral–transversal cirri evolved in the stemline of the Oxytrichidae and was modified several times independently. Our results are also in agreement with taxonomic revisions: the separation of both Sterkiella nova from Oxytricha and Tetmemena pustulata from Stylonychia.
Mikhail S. Gelfand - One of the best experts on this subject based on the ideXlab platform.
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Evolution of the Exon-Intron Structure in Ciliate Genomes.
PloS one, 2016Co-Authors: Vladyslav S. Bondarenko, Mikhail S. GelfandAbstract:A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n) are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively), but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33-35 bp, 47-51 bp, and 78-80 bp). In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short introns in various representatives of Ciliates.
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Depletion of 3n introns in Ichthyophthirius, Tetrahymena, Oxytricha, and Stylonychia.
2016Co-Authors: Vladyslav S. Bondarenko, Mikhail S. GelfandAbstract:Depletion of 3n introns in Ichthyophthirius, Tetrahymena, Oxytricha, and Stylonychia.
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Parameters of the weighted normal decomposition components of the introns length distributions of Ichthyophthirius, Tetrahymena, Oxytricha, and Stylonychia in the introns length interval 1–100 bp.
2016Co-Authors: Vladyslav S. Bondarenko, Mikhail S. GelfandAbstract:Parameters of the weighted normal decomposition components of the introns length distributions of Ichthyophthirius, Tetrahymena, Oxytricha, and Stylonychia in the introns length interval 1–100 bp.
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Evolution of the Exon-Intron Structure in Ciliate Genomes - Fig 6
2016Co-Authors: Vladyslav S. Bondarenko, Mikhail S. GelfandAbstract:A. The numbers of introns conserved between the orthologs of Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. B. Scatter-plots of orthologous introns length of Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. The intron length range up to 150 bp is shown. Red and blue lines separate classes of the intron lengths. C. L distributions of the conserved and young introns in orthologous genes for Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia (in the log2 scale). Conserved introns are significantly shorter than young introns in Ichthyophthirius, Oxytricha, and Stylonychia (by the Wilcoxon rank sum test, p-value < 2.2×10-16, < 10-4, and < 2.2×10-16, respectively).
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Evolution of the Exon-Intron Structure in Ciliate Genomes - Fig 2
2016Co-Authors: Vladyslav S. Bondarenko, Mikhail S. GelfandAbstract:A. Intron length distributions of Paramecium [5], Tetrahymena [6], Ichthyophthirius, Oxytricha [8], and Stylonychia. Introns containing “n” or “N” nucleotides were excluded. Pink and green colors show the numbers of 3n±1 and 3n introns, respectively. Blue and purple colors show the numbers of 3n±1 and 3n introns with in-frame stop codons, respectively. B. Decomposition of the intron length distributions of Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia in the length interval 1–100 bp into a sum of 2 or 3 weighted normal distributions. Histograms show the observed distributions without decomposition, whereas red, blue, and green curves denote the decomposed weighted normal distributions.
Detlef Bernhard - One of the best experts on this subject based on the ideXlab platform.
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a pcr based method to distinguish the sibling species Stylonychia mytilus and Stylonychia lemnae ciliophora spirotrichea using isocitrate dehydrogenase gene sequences
Journal of Eukaryotic Microbiology, 2006Co-Authors: Madlen Haentzsch, Dieter Ammermann, Detlef Bernhard, Stephanie L Schmidt, Thomas U Berendonk, Martin SchlegelAbstract:A differentiation, based on morphological characters, between Stylonychia mytilus and Stylonychia lemnae is very difficult, especially for non-specialists. These two sibling species were considered as one species, S. mytilus, until detailed cytological and genetic studies could show the existence of two genetically isolated varieties. Further morphological and biochemical analyses verified the separation and finally in 1983 a new species S. lemnae was described. The examination of several isoenzymes revealed unambiguous differences in the banding pattern of isocitrate dehydrogenase (IDH) between these two species. Therefore, the IDH gene of 30 isolates of S. lemnae and S. mytilus coming from various regions all over the world were amplified and sequenced. The sequence analyses revealed intraspecific as well as interspecific substitutions, which were used for the development of species-specific PCR primers for both species. Application of these species-specific primer pairs now allows a very easy and clear identification of both sibling species.
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fluorescence in situ hybridization with specific oligonucleotide rrna probes distinguishes the sibling species Stylonychia lemnae and Stylonychia mytilus ciliophora spirotrichea
Protist, 2006Co-Authors: Stephanie L Schmidt, Detlef Bernhard, Martin Schlegel, J FriedAbstract:Based on morphological and morphogenetic characters alone, the sibling species Stylonychia lemnae and Stylonychia mytilus, members of the Stylonychia mytilus complex, can hardly be distinguished. However, biochemical investigations of the isoenzyme pattern of different enzymes showed a distinct differentiation between these two species. In the last few years, fluorescence in situ hybridization (FISH) techniques have become a suitable and reliable tool for identification and differentiation of closely related species of protozoa, such as ciliates. To distinguish the sibling species, a set of specific oligonucleotide probes were developed. In the present study, the SSU rDNA of 7 clones of Stylonychia lemnae and 13 clones of Stylonychia mytilus, isolated from different geographic regions, were sequenced. Comparing all SSU rDNA sequences of both species, only one single difference within the whole gene was detected. Based on this difference, a set of two oligonucleotide probes, targeting the SSU rRNA of each species (Stylonychia mytilus and Stylonychia lemnae) was designed. These probes were successfully tested by applying the FISH techniques on preserved cells of different clones of both species.
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Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences.
Molecular phylogenetics and evolution, 2001Co-Authors: Detlef Bernhard, Dieter Ammermann, Alexandra Stechmann, Manuela Hehn, Martin SchlegelAbstract:Abstract The small subunit rDNAs of five species belonging to the Euplotidae and eight species of the Oxytrichidae were sequenced to obtain a more detailed picture of the phylogenetic relationships within the Spirotrichea (Ciliophora). Various tree reconstruction algorhythms yielded nearly identical topologies. All Euplotidae were separated from the other Spirotrichea by a deep split. Further, a large genetic distance between the marine genus Moneuplotes and the freshwater species of Euplotoides was found. Differences between the methods used occurred only within the Oxytrichidae. Whereas the monophyly of the Stylonychinae was supported in all trees, the monophyly of the Oxytrichinae was not. However, the molecular data support the morphological and ontogenetic evidence that the pattern of 18 frontal–ventral–transversal cirri evolved in the stemline of the Oxytrichidae and was modified several times independently. Our results are also in agreement with taxonomic revisions: the separation of both Sterkiella nova from Oxytricha and Tetmemena pustulata from Stylonychia.
