Random Sequencing of Paramecium Somatic DNA†
| Autor: | Robert Gromadka, Marine Froissard, Anne-Marie Keller, Marek Zagulski, Jean Cohen, Linda Sperling, Ron E. Pearlman, Andrzey Migdalski, Philippe Dessen |
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| Jazyk: | angličtina |
| Rok vydání: | 2002 |
| Předmět: |
Transposable element
Models Molecular Proteome Sequence analysis Molecular Sequence Data Protozoan Proteins Microbiology Genome Article Open Reading Frames Animals Paramecium Amino Acid Sequence ORFS Codon Molecular Biology Gene Phylogeny Genetics biology Base Sequence General Medicine Sequence Analysis DNA DNA Protozoan biology.organism_classification Introns Protein Structure Tertiary Paramecium tetraurelia Databases Nucleic Acid Genome Protozoan |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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