The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus

The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region) piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals.The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial genes from other sources.Ciliates, unicellular eukaryotes, are extremely species-rich and colonize a very broad spectrum of ecological niches. They are characterized by complexes of cilia, used for swimming and food capturing and by a nuclear dimorphism that is unique for ciliates. All members possess a micronuclear genome, which is active in sexual reproduction, and a macronuclear genome that is transcriptionally active during somatic development and maintenance. In addition to the macronuclear and micronuclear genomes, aerobic ciliates also possess a mitochondrial genome. Although there are thousands o