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2. Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

Author

Tekaia, Fredj, Blandin, Gaëlle, Malpertuy, Alain, Llorente, Bertrand, Durrens, Pascal, Toffano-Nioche, Claire, Ozier-Kalogeropoulos, Odile, Bon, Elisabeth, Gaillardin, Claude, Aigle, Michel, Bolotin-Fukuhara, Monique, Casarégola, Serge, de Montigny, Jacky, Lépingle, Andrée, Neuvéglise, Cécile, Potier, Serge, Souciet, Jean-Luc, Wésolowski-Louvel, Micheline, and Dujon, Bernard

Published
2000
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3. Genomic Exploration of the Hemiascomycetous Yeasts: 21. Comparative functional classification of genes

Author

Gaillardin, Claude, Duchateau-Nguyen, Guillemette, Tekaia, Fredj, Llorente, Bertrand, Casaregola, Serge, Toffano-Nioche, Claire, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, de Montigny, Jacky, Dujon, Bernard, Durrens, Pascal, Lépingle, Andrée, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Termier, Michel, Wésolowski-Louvel, Micheline, Wincker, Patrick, Souciet, Jean-Luc, and Weissenbach, Jean

Published
2000
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4. Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

Author

Malpertuy, Alain, Tekaia, Fredj, Casarégola, Serge, Aigle, Michel, Artiguenave, Francois, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, de Montigny, Jacky, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Neuvéglise, Cécile, Ozier-Kalogeropoulos, Odile, Potier, Serge, Saurin, William, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, Weissenbach, Jean, Souciet, Jean-Luc, and Dujon, Bernard

Published
2000
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5. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

Author

Llorente, Bertrand, Durrens, Pascal, Malpertuy, Alain, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, Dujon, Bernard, de Montigny, Jacky, Lépingle, Andrée, Neuvéglise, Cécile, Ozier-Kalogeropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, Weissenbach, Jean, Souciet, Jean-Luc, and Gaillardin, Claude

Published
2000
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7. Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited

Author

Blandin, Gaëlle, Durrens, Pascal, Tekaia, Fredj, Aigle, Michel, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Casarégola, Serge, de Montigny, Jacky, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogeropoulos, Odile, Perrin, Arnaud, Potier, Serge, Souciet, Jean-Luc, Talla, Emmanuel, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Marck, Christian, and Dujon, Bernard

Published
2000
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8. Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies

Author

Souciet, Jean-Luc, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, de Montigny, Jacky, Dujon, Bernard, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, and Weissenbach, Jean

Published
2000
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9. Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae

Author

Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, de Montigny, Jacky, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, Weissenbach, Jean, Souciet, Jean-Luc, and Dujon, Bernard

Published
2000
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14. Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny withSaccharomyces cerevisiae

Author

Llorente, Bertrand, primary, Malpertuy, Alain, additional, Neuvéglise, Cécile, additional, de Montigny, Jacky, additional, Aigle, Michel, additional, Artiguenave, François, additional, Blandin, Gaëlle, additional, Bolotin-Fukuhara, Monique, additional, Bon, Elisabeth, additional, Brottier, Philippe, additional, Casaregola, Serge, additional, Durrens, Pascal, additional, Gaillardin, Claude, additional, Lépingle, Andrée, additional, Ozier-Kalogéropoulos, Odile, additional, Potier, Serge, additional, Saurin, William, additional, Tekaia, Fredj, additional, Toffano-Nioche, Claire, additional, Wésolowski-Louvel, Micheline, additional, Wincker, Patrick, additional, Weissenbach, Jean, additional, Souciet, Jean-Luc, additional, and Dujon, Bernard, additional

Published
2000
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17. Genomic Exploration of the Hemiascomycetous Yeasts: 14. Debaryomyces hanseniivar. hansenii

Author

Lépingle, Andrée, Casaregola, Serge, Neuvéglise, Cécile, Bon, Elisabeth, Nguyen, Huu-Vang, Artiguenave, François, Wincker, Patrick, and Gaillardin, Claude

Abstract

By analyzing 2830 random sequence tags (RSTs), totalling 2.7 Mb, we explored the genome of the marine, osmo‐ and halotolerant yeast, Debaryomyces hansenii. A contig 29 kb in length harbors the entire mitochondrial genome. The genes encoding Cox1, Cox2, Cox3, Cob, Atp6, Atp8, Atp9, several subunits of the NADH dehydrogenase complex 1 and 11 tRNAs were unambiguously identified. An equivalent number of putative transposable elements compared to Saccharomyces cerevisiaewere detected, the majority of which are more related to higher eukaryote copiaelements. BLASTX comparisons of RSTs with databases revealed at least 1119 putative open reading frames with homology to S. cerevisiaeand 49 to other genomes. Specific functions, including transport of metabolites, are clearly over‐represented in D. hanseniicompared to S. cerevisiae, consistent with the observed difference in physiology of the two species. The sequences have been deposited with EMBL under the accession numbers AL436045–AL438874.

Published
2000
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18. Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies11Sequences and annotations are accessible at: Génoscope (http://www.genoscope.cns.fr), FEBS Letters Website (http://www.elsevier.nl/febs/show/), Bordeaux (http://cbi.genopole-bordeaux.fr/Genolevures) and were deposited into the EMBL database (accession number from AL392203 to AL441602)

Author

Souciet, Jean-Luc, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, de Montigny, Jacky, Dujon, Bernard, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, and Weissenbach, Jean

Subjects
Phylogenetics, Random sequencing, Bioinformatics, Comparative genomics, Saccharomyces cerevisiae
Abstract

The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast-specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’.

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