Literature DB >> 16524829

Comparative genomics and genome evolution in yeasts.

Kenneth H Wolfe1.   

Abstract

Yeasts provide a powerful model system for comparative genomics research. The availability of multiple complete genome sequences from different fungal groups--currently 18 hemiascomycetes, 8 euascomycetes and 4 basidiomycetes--enables us to gain a broad perspective on genome evolution. The sequenced genomes span a continuum of divergence levels ranging from multiple individuals within a species to species pairs with low levels of protein sequence identity and no conservation of gene order. One of the most interesting emerging areas is the growing number of events such as gene losses, gene displacements and gene relocations that can be attributed to the action of natural selection.

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Year:  2006        PMID: 16524829      PMCID: PMC1609344          DOI: 10.1098/rstb.2005.1799

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  39 in total

1.  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

2.  The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.

Authors:  Brendan J Loftus; Eula Fung; Paola Roncaglia; Don Rowley; Paolo Amedeo; Dan Bruno; Jessica Vamathevan; Molly Miranda; Iain J Anderson; James A Fraser; Jonathan E Allen; Ian E Bosdet; Michael R Brent; Readman Chiu; Tamara L Doering; Maureen J Donlin; Cletus A D'Souza; Deborah S Fox; Viktoriya Grinberg; Jianmin Fu; Marilyn Fukushima; Brian J Haas; James C Huang; Guilhem Janbon; Steven J M Jones; Hean L Koo; Martin I Krzywinski; June K Kwon-Chung; Klaus B Lengeler; Rama Maiti; Marco A Marra; Robert E Marra; Carrie A Mathewson; Thomas G Mitchell; Mihaela Pertea; Florenta R Riggs; Steven L Salzberg; Jacqueline E Schein; Alla Shvartsbeyn; Heesun Shin; Martin Shumway; Charles A Specht; Bernard B Suh; Aaron Tenney; Terry R Utterback; Brian L Wickes; Jennifer R Wortman; Natasja H Wye; James W Kronstad; Jennifer K Lodge; Joseph Heitman; Ronald W Davis; Claire M Fraser; Richard W Hyman
Journal:  Science       Date:  2005-01-13       Impact factor: 47.728

3.  Updated map of duplicated regions in the yeast genome.

Authors:  C Seoighe; K H Wolfe
Journal:  Gene       Date:  1999-09-30       Impact factor: 3.688

4.  Nicotinic acid limitation regulates silencing of Candida adhesins during UTI.

Authors:  Renee Domergue; Irene Castaño; Alejandro De Las Peñas; Margaret Zupancic; Virginia Lockatell; J Richard Hebel; David Johnson; Brendan P Cormack
Journal:  Science       Date:  2005-03-17       Impact factor: 47.728

5.  Birth of a metabolic gene cluster in yeast by adaptive gene relocation.

Authors:  Simon Wong; Kenneth H Wolfe
Journal:  Nat Genet       Date:  2005-06-12       Impact factor: 38.330

6.  The genome sequence of the rice blast fungus Magnaporthe grisea.

Authors:  Ralph A Dean; Nicholas J Talbot; Daniel J Ebbole; Mark L Farman; Thomas K Mitchell; Marc J Orbach; Michael Thon; Resham Kulkarni; Jin-Rong Xu; Huaqin Pan; Nick D Read; Yong-Hwan Lee; Ignazio Carbone; Doug Brown; Yeon Yee Oh; Nicole Donofrio; Jun Seop Jeong; Darren M Soanes; Slavica Djonovic; Elena Kolomiets; Cathryn Rehmeyer; Weixi Li; Michael Harding; Soonok Kim; Marc-Henri Lebrun; Heidi Bohnert; Sean Coughlan; Jonathan Butler; Sarah Calvo; Li-Jun Ma; Robert Nicol; Seth Purcell; Chad Nusbaum; James E Galagan; Bruce W Birren
Journal:  Nature       Date:  2005-04-21       Impact factor: 49.962

7.  The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.

Authors:  Kevin P Byrne; Kenneth H Wolfe
Journal:  Genome Res       Date:  2005-09-16       Impact factor: 9.043

8.  Lineage-specific loss and divergence of functionally linked genes in eukaryotes.

Authors:  L Aravind; H Watanabe; D J Lipman; E V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  2000-10-10       Impact factor: 11.205

9.  Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae.

Authors:  Charles Hall; Sophie Brachat; Fred S Dietrich
Journal:  Eukaryot Cell       Date:  2005-06

10.  Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae.

Authors:  Zhenglong Gu; Lior David; Dmitri Petrov; Ted Jones; Ronald W Davis; Lars M Steinmetz
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-12       Impact factor: 11.205

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  30 in total

1.  Introduction. Bioinformatics: from molecules to systems.

Authors:  David T Jones; Michael J E Sternberg; Janet M Thornton
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-03-29       Impact factor: 6.237

Review 2.  Cellular hyperproliferation and cancer as evolutionary variables.

Authors:  Alejandro Sánchez Alvarado
Journal:  Curr Biol       Date:  2012-09-11       Impact factor: 10.834

3.  Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments.

Authors:  Seán S OhÉigeartaigh; David Armisén; Kevin P Byrne; Kenneth H Wolfe
Journal:  BMC Genomics       Date:  2011-07-26       Impact factor: 3.969

4.  Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces.

Authors:  Jennifer E G Gallagher; Joshua E Babiarz; Leonid Teytelman; Kenneth H Wolfe; Jasper Rine
Journal:  Genetics       Date:  2009-01-26       Impact factor: 4.562

5.  PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.

Authors:  Chris Stark; Ting-Cheng Su; Ashton Breitkreutz; Pedro Lourenco; Matthew Dahabieh; Bobby-Joe Breitkreutz; Mike Tyers; Ivan Sadowski
Journal:  Database (Oxford)       Date:  2010-01-28       Impact factor: 3.451

6.  Ends-in vs. ends-out targeted insertion mutagenesis in Saccharomyces castellii.

Authors:  Eimantas Astromskas; Marita Cohn
Journal:  Curr Genet       Date:  2009-05-13       Impact factor: 3.886

7.  Enhancer of decapping proteins 1 and 2 are important for translation during heat stress in Saccharomyces cerevisiae.

Authors:  Daniel W Neef; Dennis J Thiele
Journal:  Mol Microbiol       Date:  2009-08-04       Impact factor: 3.501

8.  Cdc28-Clb5 (CDK-S) and Cdc7-Dbf4 (DDK) collaborate to initiate meiotic recombination in yeast.

Authors:  Lihong Wan; Hengyao Niu; Bruce Futcher; Chao Zhang; Kevan M Shokat; Simon J Boulton; Nancy M Hollingsworth
Journal:  Genes Dev       Date:  2008-02-01       Impact factor: 11.361

9.  Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae.

Authors:  Dina A Faddah; Eric W Ganko; Caroline McCoach; Joseph K Pickrell; Sean E Hanlon; Frederick G Mann; Joanna O Mieczkowska; Corbin D Jones; Jason D Lieb; Todd J Vision
Journal:  PLoS Genet       Date:  2009-06-05       Impact factor: 5.917

10.  SNUGB: a versatile genome browser supporting comparative and functional fungal genomics.

Authors:  Kyongyong Jung; Jongsun Park; Jaeyoung Choi; Bongsoo Park; Seungill Kim; Kyohun Ahn; Jaehyuk Choi; Doil Choi; Seogchan Kang; Yong-Hwan Lee
Journal:  BMC Genomics       Date:  2008-12-04       Impact factor: 3.969

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