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Open Access Research article

The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus

Rob M de Graaf1, Theo A van Alen1, Bas E Dutilh2, Jan WP Kuiper14, Hanneke JAA van Zoggel15, Minh Bao Huynh15, Hans-Dieter Görtz3, Martijn A Huynen2 and Johannes HP Hackstein1*

Author Affiliations

1 Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands

2 Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands

3 Department of Zoology, Biological Institute, University of Stuttgart, Pfaffenwaldring 57, D-70569 Stuttgart, Germany

4 CIHR Group in Matrix Dynamics, University of Toronto, 150 College Street, Toronto, Ontario, Canada M5S 3E2

5 Laboratoire de Recherche sur la Croissance Cellulaire, la Réparation et la Régénération Tissulaires (CRRET), EAC 7149 CNRS, Université Paris EST, 61, Avenue du Général de Gaulle, 94010 Créteil Cedex, France

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BMC Genomics 2009, 10:514  doi:10.1186/1471-2164-10-514

Published: 6 November 2009

Abstract

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.

Conclusion

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.