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2. A human-curated annotation of the Candida albicans genome.

Author

Braun, Burkhard R, van Het Hoog, Marco, d'Enfert, Christophe, Martchenko, Mikhail, Dungan, Jan, Kuo, Alan, Inglis, Diane O, Uhl, M Andrew, Hogues, Hervé, Berriman, Matthew, Lorenz, Michael, Levitin, Anastasia, Oberholzer, Ursula, Bachewich, Catherine, Harcus, Doreen, Marcil, Anne, Dignard, Daniel, Iouk, Tatiana, Zito, Rosa, Frangeul, Lionel, Tekaia, Fredj, Rutherford, Kim, Wang, Edwin, Munro, Carol A, Bates, Steve, Gow, Neil A, Hoyer, Lois L, Köhler, Gerwald, Morschhäuser, Joachim, Newport, George, Znaidi, Sadri, Raymond, Martine, Turcotte, Bernard, Sherlock, Gavin, Costanzo, Maria, Ihmels, Jan, Berman, Judith, Sanglard, Dominique, Agabian, Nina, Mitchell, Aaron P, Johnson, Alexander D, Whiteway, Malcolm, and Nantel, André

Subjects
Genetics, Developmental Biology
Abstract

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

Published
2005

4. Protection against Mycobacterium ulcerans lesion development by exposure to aquatic insect saliva

Author

Marsollier, Laurent, Deniaux, Estelle, Brodin, Priscille, Marot, Agnes, Wondje, Christelle Mbondji, Saint-Andre, Jean-Paul, Chauty, Annick, Johnson, Christian, Tekaia, Fredj, Yeramian, Edouard, Legras, Pierre, Carbonnelle, Bernard, Reysset, Gilles, Eyangoh, Sara, Milon, Genevieve, Cole, Stewart T., and Aubry, Jacques

Subjects
Mycobacterial infections -- Prevention, Skin -- Ulcers, Skin -- Prevention, West Africa -- Health aspects
Abstract

ABSTRACT Background Buruli ulcer is a severe human skin disease caused by Mycobacterium ulcerans. This disease is primarily diagnosed in West Africa with increasing incidence. Antimycobacterial drug therapy is relatively [...]

Published
2007

5. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., Pain, Arnab, Anderson, Michael J., Wortman, Jennifer R., Kim, H. Stanley, Arroyo, Javier, Berriman, Matthew, Abe, Keietsu, Archer, David B., Bermejo, Clara, Bennett, Joan, Bowyer, Paul, Chen, Dan, Collins, Matthew, Coulsen, Richard, Davies, Robert, Dyer, Paul S., Farman, Mark, Fedorova, Nadia, Fedorova, Natalie, Feldblyum, Tamara V., Fischer, Reinhard, Fosker, Nigel, Fraser, Audrey, Garcia, Jose L., Garcia, Maria J., Goble, Arlette, Goldman, Gustavo H., Gomi, Katsuya, Griffith-Jones, Sam, Gwilliam, Ryan, Haas, Brian, Haas, Hubertus, Harris, David, Horiuchi, H., Huang, Jiaqi, Humphray, Sean, Jimenez, Javier, Keller, Nancy, Khouri, Hoda, Kitamoto, Katsuhiko, Kobayashi, Tetsuo, Konzack, Sven, Kulkarni, Resham, Kumagai, Toshitaka, Lafton, Anne, Latge, Jean-Paul, Li, Weixi, Lord, Angela, Lu, Charles, Majoros, William H., May, Gregory S., Miller, Bruce L., Mohamoud, Yasmin, Molina, Maria, Monod, Michel, Mouyna, Isabelle, Mulligan, Stephanie, Murphy, Lee, O'Neil, Susan, Paulsen, Ian, Penalva, Miguel A., Pertea, Mihaela, Price, Claire, Pritchard, Bethan L., Quail, Michael A., Rabbinowitsch, Ester, Rawlins, Neil, Rajandream, Marie-Adele, Reichard, Utz, Renauld, Hubert, Robson, Geoffrey D., de Cordoba, Santiago Rodriguez, Rodriguez-Pena, Jose M., Ronning, Catherine M., Rutter, Simon, Salzberg, Steven L., Sanchez, Miguel, Sanchez-Ferrero, Juan C., Saunders, David, Seeger, Kathy, Squares, Rob, Squares, Steven, Takeuchi, Michio, Tekaia, Fredj, Turner, Geoffrey, de Aldana, Carlos R. Vazquez, Weidman, Janice, White, Owen, Woodward, John, Yu, Jae-Hyuk, Fraser, Claire, Galagan, James E., Asai, Kiyoshi, Machida, Masayuki, Hall, Neil, Barrell, Bart, and Denning, David W.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): William C. Nierman (corresponding author) [1]; Arnab Pain [2]; Michael J. Anderson [3]; Jennifer R. Wortman [1]; H. Stanley Kim [1]; Javier Arroyo [4]; Matthew Berriman [2]; Keietsu Abe [...]

Published
2005
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6. Genome evolution in yeasts

Author

Dujon, Bernard, Sherman, David, Fischer, Gilles, Durrens, Pascal, Casaregola, Serge, Lafontaine, Ingrid, de Montigny, Jacky, Marck, Christian, Neuveglise, Cecile, Talla, Emmanuel, Goffard, Nicolas, Frangeul, Lionel, Aigle, Michel, Anthouard, Veronique, Babour, Anna, Barbe, Valerie, Barnay, Stephanie, Blanchin, Sylvie, Beckerich, Jean-Marie, Beyne, Emmanuelle, Bleykasten, Claudine, Boisrame, Anita, Boyer, Jeanne, Cattolico, Laurence, Confanioleri, Fabrice, de Daruvar, Antoine, Despons, Laurence, Fabre, Emmanuelle, Fairhead, Cecile, Ferry-Dumazet, Helene, Groppi, Alexis, Hantraye, Florence, Hennequin, Christophe, Jauniaux, Nicolas, Joyet, Philippe, Kachouri, Rym, Kerrest, Alix, Koszul, Romain, Lemaire, Marc, Lesur, Isabelle, Ma, Laurence, Muller, Heloise, Nicaud, Jean-Marc, Nikolski, Macha, Oztas, Sophie, Ozier-Kalogeropoulos, Odile, Pellenz, Stefan, Potier, Serge, Richard, Guy-Franck, Straub, Marie-Laure, Suleau, Audrey, Swennen, Dominique, Tekaia, Fredj, Wesolowski-Louvel, Micheline, Westhof, Eric, Wirth, Benedicte, Zeniou-Meyer, Maria, Zivanovic, Ivan, Bolotin-Fukuhara, Monique, Thierry, Agnes, Bouchier, Christiane, Caudron, Bernard, Scarpelli, Claude, Gaillardin, Claude, Weissenbach, Jean, Wincker, Patrick, and Souciet, Jean-Luc

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Bernard Dujon (corresponding author) [1]; David Sherman [5, 6]; Gilles Fischer [1]; Pascal Durrens [6, 7]; Serge Casaregola [8]; Ingrid Lafontaine [1]; Jacky de Montigny [9]; Christian Marck [10]; [...]

Published
2004
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10. Evolution of proteomes: fundamental signatures and global trends in amino acid compositions

Author

Yeramian Edouard and Tekaia Fredj

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level. Results In this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are compared with various inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment. Conclusion A simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.

Published
2006
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11. A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization

Author

Brino Laurent, Dujon Bernard, Tekaia Fredj, and Talla Emmanuel

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data. Results We present here a novel design of Saccharomyces cerevisiae microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences. Conclusions A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors.

Published
2003
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13. 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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14. 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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15. 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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16. 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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18. 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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19. 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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20. 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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22. SuperPartitions: Detection and classification of orthologs

Author

Tekaia, Fredj, Yeramian, Edouard, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Bioinformatique Structurale, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur (PTR No 264 and 370), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Evolution, Paralogs, fungi, Conservation profiles, Genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Clustering
Abstract

International audience; The proper detection of orthologs is crucial for evolutionary studies of genes and species. Despite large efforts to solve this problem the methodological situation appears unsettled to a large extent and the "quest for orthologs" is still an ongoing task in large-scale genome comparisons. Here, we introduce a simple operational framework for the detection of orthologs and their classification. The operational framework relies on well-established principles, optimizing their implementation for the considered purposes, and chaining components in coherent procedures: 1) We take advantage of the efficiency and simplicity of the Reciprocal Best Hit (RBH) detections, remedying (by design) the drawback concerning the limitations in terms of 1:1 detections. The procedure is based on the partitioning of Reciprocal Best Hits, with the further merging of partitions including members of the same paralogous classes ("SuperPartition of Orthologs" (SPOs)). 2) We then resort to the conservation profiles of the obtained clusters, allowing simple detection of SPOs containing duplicated members. Based on accepted evolutionary principles, such members can be further tagged as in-paralogs (co-orthologs) or out-paralogs. The method is illustrated and validated by extensive genomic analyses. The performances of the overall approach are characterized in global terms for three sets of species (Chlamydiae, Mycobacteria, Aspergilli), showing that at least 75% of the sets of orthologs contain at most one protein from a given species. The sets including more than one protein from a given species are shown to contain in-paralogs in proportions varying from 28% to 58%. The characterizations also show that the large majority of SPOs are associated with ancestral motifs, and accordingly not prone to chaining effects that might be triggered by multi-domain proteins. Further the SPO formulation is compared to other similarity based ortholog detection methods. Beyond core common results, significant differences are observed between various methods, which can be accounted for to a large extent on conceptual grounds, relative to the different merging schemes involved. Such comparisons highlight a major advantage of the SPO approach concerning the proper clustering of associated paralogs, which appear to be often dispatched spuriously into distinct orthologous classes. Finally the perspectives for future applications and elaborations of SPO-based compositional analyses are discussed.

Published
2011
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25. Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)

Author

Morales, Lucia, primary, Noel, Benjamin, additional, Porcel, Betina, additional, Marcet-Houben, Marina, additional, Hullo, Marie-Francoise, additional, Sacerdot, Christine, additional, Tekaia, Fredj, additional, Leh-Louis, Véronique, additional, Despons, Laurence, additional, Khanna, Varun, additional, Aury, Jean-Marc, additional, Barbe, Valérie, additional, Couloux, Arnaud, additional, Labadie, Karen, additional, Pelletier, Eric, additional, Souciet, Jean-Luc, additional, Boekhout, Teun, additional, Gabaldon, Toni, additional, Wincker, Patrick, additional, and Dujon, Bernard, additional

Published
2013
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29. Novel transporters from hemiascomycete yeasts.

Author

UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, De Hertogh, Benoît, Talla, Emmanuel, Tekaia, Fredj, Beyne, Emmanuelle, Sherman, David, Baret, Philippe, Dujon, Bernard, Goffeau, André, UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, De Hertogh, Benoît, Talla, Emmanuel, Tekaia, Fredj, Beyne, Emmanuelle, Sherman, David, Baret, Philippe, Dujon, Bernard, and Goffeau, André

Abstract

We screened nearly one thousand random sequenced targets obtained by partial sequencing of 13 hemiascomycete genomes identified by higher amino acid sequence similarity to a non-Saccharomyces cerevisiae protein than to a S. Cerevisiae protein. Among those sequences we have identified 36 novel phylogenetic clusters of putative transporters which, according to the Transport Commission system (TC-DB, 2002; http:// tcdb.ucsd.edu/tcdb), do not belong to acknowledged S. Cerevisiae protein families [De Hertogh et al.: Funct. Integr. Genomics 2002;2:154-170; http://cbi.labri.u-bordeaux.fr/Genolevures]. These novel hemiascomycete transporters comprise 3 channels, 23 secondary transporters, 5 primary transporters and 5 membrane proteins of unknown function.

Published
2003

30. Use of Fine-Needle Aspiration for Diagnosis of Mycobacterium ulcerans Infection

Author

Cassisa, Viviane, primary, Chauty, Annick, additional, Marion, Estelle, additional, Ardant, Marie Françoise, additional, Eyangoh, Sara, additional, Cottin, Jane, additional, Aubry, Jacques, additional, Koussemou, Hugues, additional, Lelièvre, Bénédicte, additional, Férec, Séverine, additional, Tekaia, Fredj, additional, Johnson, Christian, additional, and Marsollier, Laurent, additional

Published
2010
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32. Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., Pain, Arnab, Anderson, Michael J., Wortman, Jennifer R., Kim, H. Stanley, Arroyo, Javier, Berriman, Matthew, Abe, Keietsu, Archer, David B., Bermejo, Clara, Bennett, Joan, Bowyer, Paul, Chen, Dan, Collins, Matthew, Coulsen, Richard, Davies, Robert, Dyer, Paul S., Farman, Mark, Fedorova, Nadia, Fedorova, Natalie, Feldblyum, Tamara V., Fischer, Reinhard, Fosker, Nigel, Fraser, Audrey, Garcia, Jose L., Garcia, Maria J., Goble, Arlette, Goldman, Gustavo H., Gomi, Katsuya, Griffith-Jones, Sam, Gwilliam, Ryan, Haas, Brian, Haas, Hubertus, Harris, David, Horiuchi, H., Huang, Jiaqi, Humphray, Sean, Jimenez, Javier, Keller, Nancy, Khouri, Hoda, Kitamoto, Katsuhiko, Kobayashi, Tetsuo, Konzack, Sven, Kulkarni, Resham, Kumagai, Toshitaka, Lafon, Anne, Latge, Jean-Paul, Li, Weixi, Lord, Angela, Lu, Charles, Majoros, William H., May, Gregory S., Miller, Bruce L., Mohamoud, Yasmin, Molina, Maria, Monod, Michel, Mouyna, Isabelle, Mulligan, Stephanie, Murphy, Lee, O'Neil, Susan, Paulsen, Ian, Penalva, Miguel A., Pertea, Mihaela, Price, Claire, Pritchard, Bethan L., Quail, Michael A., Rabbinowitsch, Ester, Rawlins, Neil, Rajandream, Marie-Adele, Reichard, Utz, Renauld, Hubert, Robson, Geoffrey D., de Cordoba, Santiago Rodriguez, Rodriguez-Pena, Jose M., Ronning, Catherine M., Rutter, Simon, Salzberg, Steven L., Sanchez, Miguel, Sanchez-Ferrero, Juan C., Saunders, David, Seeger, Kathy, Squares, Rob, Squares, Steven, Takeuchi, Michio, Tekaia, Fredj, Turner, Geoffrey, de Aldana, Carlos R. Vazquez, Weidman, Janice, White, Owen, Woodward, John, Yu, Jae-Hyuk, Fraser, Claire, Galagan, James E., Asai, Kiyoshi, Machida, Masayuki, Hall, Neil, Barrell, Bart, and Denning, David W.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): William C. Nierman; Arnab Pain; Michael J. Anderson; Jennifer R. Wortman; H. Stanley Kim; Javier Arroyo; Matthew Berriman; Keietsu Abe; David B. Archer; Clara Bermejo; Joan Bennett; Paul Bowyer; [...]

Published
2006
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33. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

Author

Stinear, Timothy P., primary, Seemann, Torsten, additional, Pidot, Sacha, additional, Frigui, Wafa, additional, Reysset, Gilles, additional, Garnier, Thierry, additional, Meurice, Guillaume, additional, Simon, David, additional, Bouchier, Christiane, additional, Ma, Laurence, additional, Tichit, Magali, additional, Porter, Jessica L., additional, Ryan, Janine, additional, Johnson, Paul D.R., additional, Davies, John K., additional, Jenkin, Grant A., additional, Small, Pamela L.C., additional, Jones, Louis M., additional, Tekaia, Fredj, additional, Laval, Françoise, additional, Daffé, Mamadou, additional, Parkhill, Julian, additional, and Cole, Stewart T., additional

Published
2007
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35. Erratum: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., primary, Pain, Arnab, additional, Anderson, Michael J., additional, Wortman, Jennifer R., additional, Kim, H. Stanley, additional, Arroyo, Javier, additional, Berriman, Matthew, additional, Abe, Keietsu, additional, Archer, David B., additional, Bermejo, Clara, additional, Bennett, Joan, additional, Bowyer, Paul, additional, Chen, Dan, additional, Collins, Matthew, additional, Coulsen, Richard, additional, Davies, Robert, additional, Dyer, Paul S., additional, Farman, Mark, additional, Fedorova, Nadia, additional, Fedorova, Natalie, additional, Feldblyum, Tamara V., additional, Fischer, Reinhard, additional, Fosker, Nigel, additional, Fraser, Audrey, additional, García, Jose L., additional, García, Maria J., additional, Goble, Arlette, additional, Goldman, Gustavo H., additional, Gomi, Katsuya, additional, Griffith-Jones, Sam, additional, Gwilliam, Ryan, additional, Haas, Brian, additional, Haas, Hubertus, additional, Harris, David, additional, Horiuchi, H., additional, Huang, Jiaqi, additional, Humphray, Sean, additional, Jiménez, Javier, additional, Keller, Nancy, additional, Khouri, Hoda, additional, Kitamoto, Katsuhiko, additional, Kobayashi, Tetsuo, additional, Konzack, Sven, additional, Kulkarni, Resham, additional, Kumagai, Toshitaka, additional, Lafon, Anne, additional, Latgé, Jean-Paul, additional, Li, Weixi, additional, Lord, Angela, additional, Lu, Charles, additional, Majoros, William H., additional, May, Gregory S., additional, Miller, Bruce L., additional, Mohamoud, Yasmin, additional, Molina, Maria, additional, Monod, Michel, additional, Mouyna, Isabelle, additional, Mulligan, Stephanie, additional, Murphy, Lee, additional, O'Neil, Susan, additional, Paulsen, Ian, additional, Peñalva, Miguel A., additional, Pertea, Mihaela, additional, Price, Claire, additional, Pritchard, Bethan L., additional, Quail, Michael A., additional, Rabbinowitsch, Ester, additional, Rawlins, Neil, additional, Rajandream, Marie-Adele, additional, Reichard, Utz, additional, Renauld, Hubert, additional, Robson, Geoffrey D., additional, de Córdoba, Santiago Rodriguez, additional, Rodríguez-Peña, Jose M., additional, Ronning, Catherine M., additional, Rutter, Simon, additional, Salzberg, Steven L., additional, Sanchez, Miguel, additional, Sánchez-Ferrero, Juan C., additional, Saunders, David, additional, Seeger, Kathy, additional, Squares, Rob, additional, Squares, Steven, additional, Takeuchi, Michio, additional, Tekaia, Fredj, additional, Turner, Geoffrey, additional, de Aldana, Carlos R. Vazquez, additional, Weidman, Janice, additional, White, Owen, additional, Woodward, John, additional, Yu, Jae-Hyuk, additional, Fraser, Claire, additional, Galagan, James E., additional, Asai, Kiyoshi, additional, Machida, Masayuki, additional, Hall, Neil, additional, Barrell, Bart, additional, and Denning, David W., additional

Published
2006
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39. Expressed Sequence Tag Analysis of the Human Pathogen Paracoccidioides brasiliensis Yeast Phase: Identification of Putative Homologues of Candida albicans Virulence and Pathogenicity Genes

Author

Goldman, Gustavo H., primary, dos Reis Marques, Everaldo, additional, Duarte Ribeiro, Diógenes Custódio, additional, de Souza Bernardes, Luciano Ângelo, additional, Quiapin, Andréa Carla, additional, Vitorelli, Patrícia Marostica, additional, Savoldi, Marcela, additional, Semighini, Camile P., additional, de Oliveira, Regina C., additional, Nunes, Luiz R., additional, Travassos, Luiz R., additional, Puccia, Rosana, additional, Batista, Wagner L., additional, Ferreira, Leslie Ecker, additional, Moreira, Júlio C., additional, Bogossian, Ana Paula, additional, Tekaia, Fredj, additional, Nobrega, Marina Pasetto, additional, Nobrega, Francisco G., additional, and Goldman, Maria Helena S., additional

Published
2003
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42. 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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46. Otoancorin, an inner ear protein restricted to the interface between the apical surface of sensory epithelia and their overlying acellular gels, is defective in a autosomal recessive deafness DFNB22.

Author

Zwaenepoel, Ingrid, Mustapha, Mirna, Leibovici, Michel, Verpy, Elisabeth, Goodyear, Richard, Xue Zhong Liu, Nouaile, Sylvie, Nance, Walter E., Kanaan, Moien, Avraham, Karen B., Tekaia, Fredj, Loiselet, Jacques, Lathrop, March, Richardson, Guy, and Petit, Christine

Subjects
EPITHELIAL cells, IMMUNOFLUORESCENCE
Abstract

Examines the interface between the apical surface of sensory epithelia and overlying acellular gels. Components of otoancorin; Distribution of otoancorin in the mouse cochlea by immunofluorescence microscopy; Role of mesothelin in cell to substrate adhesion.

Published
2002
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48. Expressed Sequence Tag Analysis of the Human Pathogen Paracoccidioides brasiliensisYeast Phase: Identification of Putative Homologues of Candida albicansVirulence and Pathogenicity Genes

Author

Goldman, Gustavo H., dos Reis Marques, Everaldo, Duarte Ribeiro, Dio´genes Custo´dio, de Souza Bernardes, Luciano A^ngelo, Quiapin, Andre´a Carla, Vitorelli, Patri´cia Marostica, Savoldi, Marcela, Semighini, Camile P., de Oliveira, Regina C., Nunes, Luiz R., Travassos, Luiz R., Puccia, Rosana, Batista, Wagner L., Ferreira, Leslie Ecker, Moreira, Ju´lio C., Bogossian, Ana Paula, Tekaia, Fredj, Nobrega, Marina Pasetto, Nobrega, Francisco G., and Goldman, Maria Helena S.

Abstract

ABSTRACTParacoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of the prevalent systemic mycosis in Latin America, paracoccidioidomycosis. We present here a survey of expressed genes in the yeast pathogenic phase of P. brasiliensis. We obtained 13,490 expressed sequence tags from both 5' and 3' ends. Clustering analysis yielded the partial sequences of 4,692 expressed genes that were functionally classified by similarity to known genes. We have identified several Candida albicansvirulence and pathogenicity homologues in P. brasiliensis. Furthermore, we have analyzed the expression of some of these genes during the dimorphic yeast-mycelium-yeast transition by real-time quantitative reverse transcription-PCR. Clustering analysis of the mycelium-yeast transition revealed three groups: (i) RBT, hydrophobin, and isocitrate lyase; (ii) malate dehydrogenase, contigs Pb1067 and Pb1145, GPI, and alternative oxidase; and (iii) ubiquitin, delta-9-desaturase, HSP70, HSP82, and HSP104. The first two groups displayed high mRNA expression in the mycelial phase, whereas the third group showed higher mRNA expression in the yeast phase. Our results suggest the possible conservation of pathogenicity and virulence mechanisms among fungi, expand considerably gene identification in P. brasiliensis, and provide a broader basis for further progress in understanding its biological peculiarities.

Published
2003
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49. Genomic Exploration of the Hemiascomycetous Yeasts: 8. Zygosaccharomyces rouxii11The sequences have been deposited with EMBL under the accession numbers AL392203–AL397138

Author

de Montigny, Jacky, Straub, Marie-Laure, Potier, Serge, Tekaia, Fredj, Dujon, Bernard, Wincker, Patrick, Artiguenave, François, and Souciet, Jean-Luc

Subjects
Comparative genomics, Hemiascomycete, Saccharomyces cerevisiae, Random sequence tag
Abstract

This paper reports the genomic analysis of strain CBS732 of Zygosaccharomyces rouxii, a homothallic diploid yeast. We explored the sequences of 4934 random sequencing tags of about 1 kb in size and compared them to the Saccharomyces cerevisiae gene products. Approximately 2250 nuclear genes, 57 tRNAs, the rDNA locus, the endogenous pSR1 plasmid and 15 mitochondrial genes were identified. According to 18S and 25S rRNA cladograms and to synteny analysis, Z. rouxii could be placed among the S. cerevisiae sensu lato yeasts.

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50. 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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