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Background  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  Paramecium tetraurelia  and all studied  Tetrahymena  species. This raises the question of whether the high mitochondrial G+C content observed in  P. tetraurelia  is a characteristic property of  Paramecium  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  Paramecium caudatum  and compared the gene content and sequence properties to the closely related  P. tetraurelia .    Results  The guanine + cytosine content of the  P. caudatum  mitochondrial genome was significantly lower than that of  P. tetraurelia  (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  P. caudatum  clearly A/T ending codons dominated, whereas for  P. tetraurelia  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  Paramecium  resembles that of  P. caudatum  and that the shift observed in  P. tetraurelia  is restricted to the  P. aurelia  species complex.    Conclusions  Surprisingly, the codon usage bias in the  P. caudatum  mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related  T. pyriformis  and other single-celled eukaryotes such as  Chlamydomonas , than to the closely related  P. tetraurelia . 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  P. tetraurelia  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.

bmc genomics

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