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Eukaryotic Cell, June 2002, p. 341-352, Vol. 1, No. 3
1535-9778/02/$04.00+0     DOI: 10.1128/EC.1.3.341-352.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Random Sequencing of Paramecium Somatic DNA{dagger}

Linda Sperling,1* Philippe Dessen,2 Marek Zagulski,3 Ron E. Pearlman,4 Andrzey Migdalski,3 Robert Gromadka,3 Marine Froissard,1 Anne-Marie Keller,1 and Jean Cohen1

Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette Cedex,1 Laboratoire de Génétique Oncologique, UMR1599 CNRS, Institut Gustave Roussy, F-94805 Villejuif Cedex, France,2 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, DNA Sequencing Laboratory, Pawinskiego 5a, 02-106 Warsaw, Poland,3 Department of Biology, Core Molecular Biology Facility, York University, Toronto, Ontario, Canada M3J 1P34

Received 26 November 2001/ Accepted 15 February 2002

We report a random survey of 1 to 2% of the somatic genome of the free-living ciliate Paramecium tetraurelia by single-run sequencing of the ends of plasmid inserts. As in all ciliates, the germ line genome of Paramecium (100 to 200 Mb) is reproducibly rearranged at each sexual cycle to produce a somatic genome of expressed or potentially expressed genes, stripped of repeated sequences, transposons, and AT-rich unique sequence elements limited to the germ line. We found the somatic genome to be compact (>68% coding, estimated from the sequence of several complete library inserts) and to feature uniformly small introns (18 to 35 nucleotides). This facilitated gene discovery: 722 open reading frames (ORFs) were identified by similarity with known proteins, and 119 novel ORFs were tentatively identified by internal comparison of the data set. We determined the phylogenetic position of Paramecium with respect to eukaryotes whose genomes have been sequenced by the distance matrix neighbor-joining method by using random combined protein data from the project. The unrooted tree obtained is very robust and in excellent agreement with accepted topology, providing strong support for the quality and consistency of the data set. Our study demonstrates that a random survey of the somatic genome of Paramecium is a good strategy for gene discovery in this organism.

* Corresponding author. Mailing address: Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette Cedex, France. Phone: 33(0)1 69-82-32-09. Fax: 33(0)1 69-82-31-50. E-mail: sperling{at}cgm.cnrs-gif.fr.

{dagger} Dedicated to the memory of André Adoutte.

Eukaryotic Cell, June 2002, p. 341-352, Vol. 1, No. 3
1535-9778/02/$04.00+0     DOI: 10.1128/EC.1.3.341-352.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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