Hemiascomycetous yeasts at the forefront of comparative genomics

Goffeau, 1996, Life with 6000 genes, Science, 274, 563, 10.1126/science.274.5287.546 Dujon, 2004, Genome evolution in yeasts, Nature, 430, 35, 10.1038/nature02579 Souciet, 2000, Genomic exploration of the hemiascomycetous yeasts, FEBS Lett, 487, 3, 10.1016/S0014-5793(00)02272-9 Cliften, 2003, Finding functional features in Saccharomyces genomes by phylogenetic footprinting, Science, 301, 71, 10.1126/science.1084337 Kellis, 2003, Sequencing and comparison of yeast species to identify genes and regulatory elements, Nature, 423, 241, 10.1038/nature01644 Fischer, 2001, Evolution of gene order in the genomes of two related yeast species, Genome Res, 11, 2009, 10.1101/gr.212701 Delneri, 2003, Engineering evolution to study speciation in yeasts, Nature, 422, 68, 10.1038/nature01418 Brachat, 2003, Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii, Genome Biol, 4, R45, 10.1186/gb-2003-4-7-r45 Kessler, 2003, Systematic discovery of new genes in the Saccharomyces cerevisiae genome, Genome Res, 13, 264, 10.1101/gr.232903 Harbison, 2004, Transcriptional regulatory code of a eukaryotic genome, Nature, 431, 99, 10.1038/nature02800 Zhang, 2005, Mapping of transcription start sites in Saccharomyces cerevisiae using 5′ SAGE, Nucleic Acids Res, 33, 2838, 10.1093/nar/gki583 Chiang, 2003, Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts, Genome Biol, 4, R43, 10.1186/gb-2003-4-7-r43 Li, 2005, Sampling motifs on phylogenetic trees, Proc Natl Acad Sci USA, 102, 9481, 10.1073/pnas.0501620102 Eddy, 2005, A model of the statistical power of comparative genome sequence analysis, PLoS Biol, 3, e10, 10.1371/journal.pbio.0030010 Gasch, 2004, Conservation and evolution of cis-regulatory systems in ascomycete fungi, PLoS Biol, 2, e398, 10.1371/journal.pbio.0020398 Berbee, 2001, Systematics and evolution, 229 Kellis, 2004, Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature, 428, 617, 10.1038/nature02424 Dietrich, 2004, The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome, Science, 304, 304, 10.1126/science.1095781 Jones, 2004, The diploid genome sequence of Candida albicans, Proc Natl Acad Sci USA, 101, 7329, 10.1073/pnas.0401648101 Braun, 2005, A human-curated annotation of the Candida albicans genome, PLoS Genetics, 1, e1, 10.1371/journal.pgen.0010001 Hittinger, 2004, Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts, Proc Natl Acad Sci USA, 101, 14144, 10.1073/pnas.0404319101 De Hertogh, 2003, Novel transporters from Hemiascomycete yeasts, J Mol Microbiol Biotechnol, 6, 19, 10.1159/000073405 Blank, 2005, Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts, FEMS Yeast Res, 5, 545, 10.1016/j.femsyr.2004.09.008 Richard, 2005, Comparative genomics in Hemiascomycete yeasts: genes involved in DNA replication, repair and recombination, Mol Biol Evol, 22, 1011, 10.1093/molbev/msi083 Fabre, 2005, Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing and subtelomeres, Mol Biol Evol, 22, 856, 10.1093/molbev/msi070 Butler, 2004, Evolution of the MAT locus and its Ho endonuclease in yeast species, Proc Natl Acad Sci USA, 101, 1632, 10.1073/pnas.0304170101 Logue, 2005, A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus, Eukaryot Cell, 4, 1009, 10.1128/EC.4.6.1009-1017.2005 Fairhead C, Dujon B: Structure of K. lactis subtelomeres: duplications and gene content. FEM Yeast Res 2005, in press. Wolfe, 1997, Molecular evidence for an ancient duplication of the entire yeast genome, Nature, 387, 708, 10.1038/42711 Andalis, 2004, Defects arising from whole-genome duplications in Saccharomyces cerevisiae, Genetics, 167, 1109, 10.1534/genetics.104.029256 Greig, 2002, Hybrid speciation in experimental populations of yeast, Science, 298, 1773, 10.1126/science.1076374 Lafontaine, 2004, Gene relics in the genome of the yeast Saccharomyces cerevisiae, Gene, 335, 1, 10.1016/j.gene.2004.03.028 Gu, 2005, Rapid evolution of expression and regulatory divergences after yeast gene duplication, Proc Natl Acad Sci USA, 102, 707, 10.1073/pnas.0409186102 Gao, 2004, Very low gene duplication rate in the yeast genome, Science, 306, 1367, 10.1126/science.1102033 Sugino, 2005, Estimating the time to the whole genome duplication and the duration of concerted evolution via gene conversion in yeast, Genetics, 10.1534/genetics.105.043869 Koszul, 2004, Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments, EMBO J, 23, 234, 10.1038/sj.emboj.7600024 Leh-Louis, 2004, Expansion and contraction of the DUP240 multigene family in Saccharomyces cerevisiae populations, Genetics, 167, 1611, 10.1534/genetics.104.028076 Schacherer, 2004, Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae, Genome Res, 14, 1291, 10.1101/gr.2363004 Pereira-Leal, 2005, Novel specificities emerge by stepwise duplication of functional modules, Genome Res, 15, 552, 10.1101/gr.3102105 Gojkovic, 2004, Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts, Mol Genet Genomics, 271, 387, 10.1007/s00438-004-0995-7 Hall, 2005, Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae, Eukaryot Cell, 4, 1102, 10.1128/EC.4.6.1102-1115.2005 Ihmels, 2005, Rewiring of the yeast transcriptional network through the evolution of motif usage, Science, 309, 938, 10.1126/science.1113833 Rokas, 2003, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 10.1038/nature02053 Boekhout, 2005, Gut feeling for yeasts, Nature, 434, 449, 10.1038/434449a Wood, 2002, The genome sequence of Schizosaccharomyces pombe, Nature, 415, 871, 10.1038/nature724 Loftus, 2005, The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans, Science, 307, 1321, 10.1126/science.1103773 Kurtzman, 2003, Phylogenetic circumscription of Saccharomyces, Kluveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora, FEMS Yeast Res, 4, 233, 10.1016/S1567-1356(03)00175-2 Diezmann, 2004, Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis, J Clin Microbiol, 42, 5624, 10.1128/JCM.42.12.5624-5635.2004 Nakao Y, Kodama Y, Nakamura N, Ito T, Hattori M, Shiba T, Ashikari T: Whole genome sequence of a lager brewing yeast. In Proceedings of the 29th European Brewery Convention Congress: 2003 May 17–22; Dublin:524-530. Ramezani-Rad, 2003, The Hansenula polymorpha (strain CBS4732) genome sequencing and analysis, FEMS Yeast Res, 4, 207, 10.1016/S1567-1356(03)00125-9