title: Random sequencing of Paramecium somatic DNA.
abstract: 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.
authors.affiliation: Centre de Génétique Moléculaire, CNRS, 91198 Gif-sur-Yvette Cedex, France. sperling@cgm.cnrs-gif.fr
authors.forename: Linda
authors.initials: L
authors.lastname: Sperling
authors.forename: Philippe
authors.initials: P
authors.lastname: Dessen
authors.forename: Marek
authors.initials: M
authors.lastname: Zagulski
authors.forename: Ron E
authors.initials: RE
authors.lastname: Pearlman
authors.forename: Andrzey
authors.initials: A
authors.lastname: Migdalski
authors.forename: Robert
authors.initials: R
authors.lastname: Gromadka
authors.forename: Marine
authors.initials: M
authors.lastname: Froissard
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Keller
authors.forename: Jean
authors.initials: J
authors.lastname: Cohen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D016054:DNA, Protozoan / Q000235:genetics*; D030561:Databases, Nucleic Acid; D018503:Genome, Protozoan; D007438:Introns; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D016805:Paramecium tetraurelia / Q000235:genetics*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D020543:Proteome; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D003062:Codon; D016054:DNA, Protozoan; D020543:Proteome; D015800:Protozoan Proteins