The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.
BACKGROUND
There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia) are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial) genome.


RESULTS
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.


CONCLUSIONS
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.
de Graaf
Rob M
RM
Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, The Netherlands. exorest@science.ru.nl
van Alen
Theo A
TA
Dutilh
Bas E
BE
Kuiper
Jan W P
JW
van Zoggel
Hanneke J A A
HJ
Huynh
Minh Bao
MB
Görtz
Hans-Dieter
HD
Huynen
Martijn A
MA
Hackstein
Johannes H P
JH
D004579:Electron Transport; D003576:Electron Transport Complex IV / Q000235:genetics; D016812:Euplotes / Q000235:genetics* / Q000378:metabolism; D054629:Genome, Mitochondrial / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D012269:Ribosomal Proteins / Q000235:genetics
D012269:Ribosomal Proteins; D012343:RNA, Transfer; D003576:Electron Transport Complex IV