The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

<p>Abstract</p> <p>Background</p> <p>Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between <it>Paramecium tetraurelia </it>and all studied <it>Tetrahymena </it>species. This raises the question of whether the high mitochondrial G+C content observed in <it>P. tetraurelia </it>is a characteristic property of <it>Paramecium </it>mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of <it>Paramecium caudatum </it>and compared the gene content and sequence properties to the closely related <it>P. tetraurelia</it>.</p> <p>Results</p> <p>The guanine + cytosine content of the <it>P. caudatum </it>mitochondrial genome was significantly lower than that of <it>P. tetraurelia </it>(22.4% vs. 41.2%). This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within <it>P. caudatum </it>clearly A/T ending codons dominated, whereas for <it>P. tetraurelia </it>the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus <it>Paramecium </it>resembles that of <it>P. caudatum </it>and that the shift observed in <it>P. tetraurelia </it>is restricted to the <it>P. aurelia </it>species complex.</p> <p>Conclusions</p> <p>Surprisingly, the codon usage bias in the <it>P. caudatum </it>mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related <it>T. pyriformis </it>and other single-celled eukaryotes such as <it>Chlamydomonas</it>, than to the closely related <it>P. tetraurelia</it>. These differences in base composition and codon usage bias were, however, not reflected in the amino acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in <it>P. tetraurelia </it>mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.</p

Species of the Paramecium aurelia complex Sonneborn in Germany

The occurrence of species of the Paramecium aurelia complex was studied in material collected in 1995 in Baden-Wurtternberg, Germany. Also five strains collected previously in MOnster (Westphalia) and Stuttgart (Baden-Wurttemberg) were identified. Identification was carried out by mating the clones with the mating types of the standard strains of known species of the P. aurelia complex. The presence of P. biaurelia, P. triaurelia, P. sexaurelia, and P. novaurelia was revealed. All species were found in Stuttgart or in its neighbourhood (Baden-Wurttemberg), and two species (P. biaurelia and P. novaurelia) in the material from Monster (Westphalia). In some strains endosymbionts were found, Caedibacter sp. PREER, PREER, JURAND (1974) in the cytoplasm, and Holospora caryophila PREER and PREER (1982) in the macro-nucleus

Paramecium dodecaurelia strains from Hawaii

The presence of Paramecium dodecaurelia (three strains) was recorded in Hawaii

Molecular Polymorphism of Paramecium tetraurelia (Ciliophora, Protozoa) in Strains Originating from Different Continents

Abstract: Fragments of LSU rDNA and COI mtDNA genes were sequenced in Paramecium tetraurelia strains originating from different continents, i.e. from Australia (Sydney Europe (Spain. Poland). Asia (Israel, India, Japan) and North America (Indiana) in order to investigate intra-specific polymorphism in this species. Phylogenetic trees (based on analyses using, the NJ, MP and BI methods) revealed that P. tetraurelia strain.,, from Australia. Europe. North America and Asia (Israel, Japan) belong to one group divided into two main clusters, while a strain front India is separate and belongs to a different group. The Indian strain groups together with strains representing different species of the P. aurelia complex: P. septaurelia, P. octaurelia. and P. dodecaurelia. Polymorphism within P. tetraurelia was confirmed, however. it seems that the applied markers did not explain the ways of divergence of strains within Species (Indian strain and others), and also did not show correlations bet..

Strains of Paramecium quadecaurelia from Namibia, Africa; Genetic and molecular studies

Abstract: New strains of Paramecium quadecaurelia were found in Namibia, Africa. Previously, this species from the P. aurelia complex was known only from Australia, Emily Gap. Namibian strains were identified by mating reaction; their relationship with the Australian strain was studied by classical strain crosses (survival in F1 and F2 generations) and by comparison of cytosol-type hsp70 gene sequences. Phylogenetic trees of the Namibian and Australian strains of P. quadecaurelia and the other species of the P. aurelia complex were generated based on the maximum-likelihood method

Cytochrome b sequence data suggest rapid speciation within the Paramecium aurelia species complex

Abstract: We investigated mitochondrial Cytochrome b sequences from all 15 members of the enigmatic Paramecium aurelia species complex (Ciliophora). The analysis revealed high genetic distances between the different A aurelia species (6.1-19.8%) and a largely unresolved, star-like phylogenetic tree. This result strongly supports a rapid radiation in the evolutionary history of this species complex and it correlates well with the hypothesis that the extant species diversity may have originated from the neutral consequences of a whole genome duplication in the common ancestor of P. aurelia. (c) 2008 Elsevier Inc. All rights reserved

New European stands of Paramecium pentaurelia, Paramecium septaurelia, and Paramecium dodecaurelia, genetic and molecular studies

Abstract: New stands of Paramecium biaurelia, P. triaurelia, P. tetraurelia, P. pentaurelia, P. novaurelia, and P. dodecaurelia were recorded in Russia. Especially interesting, is the record of P. novaurelia in Vladivostok, Russian Far East, as it is a very rare species Outside of Europe. The distribution of species of the Paramecium aurelia complex in Eurasia with emphasis on findings in Russia is discussed