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Research

Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germ line

¹ Universite Lyon 1 ; CNRS ; UMR 5558, Laboratoire de Biometrie et Biologie Evolutive; ² CNRS, Centre de Genetique Moleculaire; ³ 3GENOSCOPE (CEA) and UMR 8030 CNRS-GENOSCOPE-Universite d'Evry; ⁴ 4Laboratoire Genomes et Cancers, FRE 2939 CNRS, Institut Gustave Roussy; ⁵ CNRS, Centre de Genetique Moleculaireaire; ⁶ Laboratoire de Genetique Moleculaire, CNRS UMR 8541, Ecole Normale Superieure

Ciliates are the only unicellular eukaryotes known to separate germinal and somatic functions. Diploid but silent micronuclei transmit the genetic information to the next sexual generation. Polyploid macronuclei express the genetic information from a streamlined version of the genome, but are replaced at each sexual generation. The macronuclear genome of Paramecium tetraurelia was recently sequenced by a shotgun approach, providing access to the gene repertoire (Aury et al. 2006, Nature 444, 171-178). The 72 Mb assembly represents a consensus sequence for the somatic DNA, which is produced after sexual events by reproducible rearrangements of the zygotic genome involving elimination of repeated sequences, precise excision of unique-copy internal eliminated sequences (IES) and amplification of the cellular genes to high copy number. We report use of the shotgun sequencing data (>10E6 reads representing 13X coverage of a completely homozygous clone) to evaluate variability in the somatic DNA produced by these developmental genome rearrangements. Although DNA amplification appears uniform, both of the DNA elimination processes produce sequence heterogeneity. The variability that arises from IES excision allowed identification of hundreds of putative new IESs, compared to 42 that were previously known, and revealed cases of erroneous excision of segments of coding sequences. We demonstrate that IESs in coding regions are under selective pressure to introduce premature termination of translation in case of excision failure.

E-mail sperling{at}cgm.cnrs-gif.fr

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