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Open Access Research article

Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

Guénola Ricard1, Rob M de Graaf2, Bas E Dutilh1, I Duarte1, Theo A van Alen2, Angela HAM van Hoek2, Brigitte Boxma2, Georg WM van der Staay2, Seung Yeo Moon-van der Staay2, Wei-Jen Chang3, Laura F Landweber3, Johannes HP Hackstein2 and Martijn A Huynen14*

Author Affiliations

1 Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, the Netherlands

2 Department of Evolutionary Microbiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands

3 Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA

4 Laboratoire de Biometrie et Biologie Evolutive, University de Lyon University de Lyon 1, CNRS, 43 boulevard du 11 novembre 1918, Villeurbanne F-69622, France

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BMC Genomics 2008, 9:587  doi:10.1186/1471-2164-9-587

Published: 5 December 2008

Abstract

Background

Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement.

Results

We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21–29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway.

Conclusion

The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.