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Literature DB >> 14681422

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.

David Sherman¹, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet.

Abstract

The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides data and tools to facilitate comparative genomic studies on hemiascomycetous yeasts. Now, four complete genome sequences recently determined (Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, Yarrowia lipolytica) have been added to the partial sequences of 13 species previously analysed by a random approach. The database also includes the reference genome Saccharomyces cerevisiae. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes a community area for specific studies by members of the international community.

Entities: Species

Mesh：

Year: 2004 PMID： 14681422 PMCID： PMC308825 DOI： 10.1093/nar/gkh091

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

12 in total

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

2. An efficient algorithm for large-scale detection of protein families.

Authors: A J Enright; S Van Dongen; C A Ouzounis
Journal: Nucleic Acids Res Date: 2002-04-01 Impact factor: 16.971

3. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.

Authors: Klaas Vandepoele; Yvan Saeys; Cedric Simillion; Jeroen Raes; Yves Van De Peer
Journal: Genome Res Date: 2002-11 Impact factor: 9.043

4. The generic genome browser: a building block for a model organism system database.

Authors: Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal: Genome Res Date: 2002-10 Impact factor: 9.043

5. MIPS: a database for genomes and protein sequences.

Authors: H W Mewes; D Frishman; U Güldener; G Mannhaupt; K Mayer; M Mokrejs; B Morgenstern; M Münsterkötter; S Rudd; B Weil
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

6. Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.

Authors: F Tekaia; G Blandin; A Malpertuy; B Llorente; P Durrens; C Toffano-Nioche; O Ozier-Kalogeropoulos; E Bon; C Gaillardin; M Aigle; M Bolotin-Fukuhara; S Casarégola; J de Montigny; A Lépingle; C Neuvéglise; S Potier; J Souciet; M Wésolowski-Louvel; B Dujon
Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

7. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae.

Authors: B Llorente; A Malpertuy; C Neuvéglise; J de Montigny; M Aigle; F Artiguenave; G Blandin; M Bolotin-Fukuhara; E Bon; P Brottier; S Casaregola; P Durrens; C Gaillardin; A Lépingle; O Ozier-Kalogéropoulos; S Potier; W Saurin; F Tekaia; C Toffano-Nioche; M Wésolowski-Louvel; P Wincker; J Weissenbach; J Souciet; B Dujon
Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

8. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes.

Authors: C Gaillardin; G Duchateau-Nguyen; F Tekaia; B Llorente; S Casaregola; C Toffano-Nioche; M Aigle; F Artiguenave; G Blandin; M Bolotin-Fukuhara; E Bon; P Brottier; J de Montigny; B Dujon; P Durrens; A Lépingle; A Malpertuy; C Neuvéglise; O Ozier-Kalogéropoulos; S Potier; W Saurin; M Termier; M Wésolowski-Louvel; P Wincker; J Souciet; J Weissenbach
Journal: FEBS Lett Date: 2000-12-22 Impact factor: 4.124

9. Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

Authors: Paul Cliften; Priya Sudarsanam; Ashwin Desikan; Lucinda Fulton; Bob Fulton; John Majors; Robert Waterston; Barak A Cohen; Mark Johnston
Journal: Science Date: 2003-05-29 Impact factor: 47.728

10. Sequencing and comparison of yeast species to identify genes and regulatory elements.

Authors: Manolis Kellis; Nick Patterson; Matthew Endrizzi; Bruce Birren; Eric S Lander
Journal: Nature Date: 2003-05-15 Impact factor: 49.962

22 in total

1. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.

Authors: Roland Barriot; Jérôme Poix; Alexis Groppi; Aurélien Barré; Nicolas Goffard; David Sherman; Isabelle Dutour; Antoine de Daruvar
Journal: Nucleic Acids Res Date: 2004-07-07 Impact factor: 16.971

2. Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae.

Authors: Zhihong Zhang; Fred S Dietrich
Journal: Curr Genet Date: 2005-09-14 Impact factor: 3.886

3. Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica.

Authors: Kevin B Reed; James M Wagner; Simon d'Oelsnitz; Joshua M Wiggers; Hal S Alper
Journal: J Ind Microbiol Biotechnol Date: 2019-08-19 Impact factor: 3.346

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

2. An efficient algorithm for large-scale detection of protein families.

3. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice.

4. The generic genome browser: a building block for a model organism system database.

5. MIPS: a database for genomes and protein sequences.

6. Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.

7. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae.

8. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes.

9. Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

10. Sequencing and comparison of yeast species to identify genes and regulatory elements.

1. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.

2. Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae.

3. Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica.

4. A molecular chaperone for mitochondrial complex I assembly is mutated in a progressive encephalopathy.

5. Fungal Genomes and Insights into the Evolution of the Kingdom.

Review 6. Biology of the pathogenic yeast Candida glabrata.

7. Salt-dependent expression of ammonium assimilation genes in the halotolerant yeast, Debaryomyces hansenii.

8. Mitochondria from the salt-tolerant yeast Debaryomyces hansenii (halophilic organelles?).

9. Integrated assessment of genomic correlates of protein evolutionary rate.

10. Sugar metabolism, redox balance and oxidative stress response in the respiratory yeast Kluyveromyces lactis.