PubMed Health⌕ Search
Home/Archive/PubMed

PubMed · 15229592

Genome evolution in yeasts.

Bernard Dujon·David Sherman·Gilles Fischer·Pascal Durrens·Serge Casaregola·Ingrid Lafontaine·Jacky De Montigny·Christian Marck·Cécile Neuvéglise·Emmanuel Talla·Nicolas Goffard·Lionel Frangeul·Michel Aigle·Véronique Anthouard·Anna Babour·Valérie Barbe·Stéphanie Barnay·Sylvie Blanchin·Jean-Marie Beckerich·Emmanuelle Beyne·Claudine Bleykasten·Anita Boisramé·Jeanne Boyer·Laurence Cattolico·Fabrice Confanioleri·Antoine De Daruvar·Laurence Despons·Emmanuelle Fabre·Cécile Fairhead·Hélène Ferry-Dumazet·Alexis Groppi·Florence Hantraye·Christophe Hennequin·Nicolas Jauniaux·Philippe Joyet·Rym Kachouri·Alix Kerrest·Romain Koszul·Marc Lemaire·Isabelle Lesur·Laurence Ma·Héloïse Muller·Jean-Marc Nicaud·Macha Nikolski·Sophie Oztas·Odile Ozier-Kalogeropoulos·Stefan Pellenz·Serge Potier·Guy-Franck Richard·Marie-Laure Straub·Audrey Suleau·Dominique Swennen·Fredj Tekaia·Micheline Wésolowski-Louvel·Eric Westhof·Bénédicte Wirth·Maria Zeniou-Meyer·Ivan Zivanovic·Monique Bolotin-Fukuhara·Agnès Thierry·Christiane Bouchier·Bernard Caudron·Claude Scarpelli·Claude Gaillardin·Jean Weissenbach·Patrick Wincker·Jean-Luc Souciet
View original source ↗Export metadata ↓

Abstract

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss.

Explore related subjects

Chromosomes, FungalConserved SequenceEvolution, MolecularGene DuplicationGenes, FungalGenome, FungalMolecular Sequence DataRNA, RibosomalRNA, TransferSaccharomyces cerevisiae ProteinsSyntenyTandem Repeat SequencesYeastsJournal ArticleResearch Support, Non-U.S. Gov't

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Bernard Dujon, David Sherman, Gilles Fischer, Pascal Durrens, Serge Casaregola, Ingrid Lafontaine, Jacky De Montigny, Christian Marck, Cécile Neuvéglise, Emmanuel Talla, Nicolas Goffard, Lionel Frangeul, Michel Aigle, Véronique Anthouard, Anna Babour, Valérie Barbe, Stéphanie Barnay, Sylvie Blanchin, Jean-Marie Beckerich, Emmanuelle Beyne, Claudine Bleykasten, Anita Boisramé, Jeanne Boyer, Laurence Cattolico, Fabrice Confanioleri, Antoine De Daruvar, Laurence Despons, Emmanuelle Fabre, Cécile Fairhead, Hélène Ferry-Dumazet, Alexis Groppi, Florence Hantraye, Christophe Hennequin, Nicolas Jauniaux, Philippe Joyet, Rym Kachouri, Alix Kerrest, Romain Koszul, Marc Lemaire, Isabelle Lesur, Laurence Ma, Héloïse Muller, Jean-Marc Nicaud, Macha Nikolski, Sophie Oztas, Odile Ozier-Kalogeropoulos, Stefan Pellenz, Serge Potier, Guy-Franck Richard, Marie-Laure Straub, Audrey Suleau, Dominique Swennen, Fredj Tekaia, Micheline Wésolowski-Louvel, Eric Westhof, Bénédicte Wirth, Maria Zeniou-Meyer, Ivan Zivanovic, Monique Bolotin-Fukuhara, Agnès Thierry, Christiane Bouchier, Bernard Caudron, Claude Scarpelli, Claude Gaillardin, Jean Weissenbach, Patrick Wincker, Jean-Luc Souciet. 2004-07-01. Genome evolution in yeasts.. https://doi.org/10.1038/nature02579

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Hi-C calibration by chemically induced chromosomal interactions.

The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within 10-60 kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in 5-10% of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.

Chromosomes, Fungal↗
PubMed2006

Single Holliday junctions are intermediates of meiotic recombination.

Crossing-over between homologous chromosomes facilitates their accurate segregation at the first division of meiosis. Current models for crossing-over invoke an intermediate in which homologs are connected by two crossed-strand structures called Holliday junctions. Such double Holliday junctions are a prominent intermediate in Saccharomyces cerevisiae meiosis, where they form preferentially between homologs rather than between sister chromatids. In sharp contrast, we find that single Holliday junctions are the predominant intermediate in Schizosaccharomyces pombe meiosis. Furthermore, these single Holliday junctions arise preferentially between sister chromatids rather than between homologs. We show that Mus81 is required for Holliday junction resolution, providing further in vivo evidence that the structure-specific endonuclease Mus81-Eme1 is a Holliday junction resolvase. To reconcile these observations, we present a unifying recombination model applicable for both meiosis and mitosis in which single Holliday junctions arise from single- or double-strand breaks, lesions postulated by previous models to initiate recombination.

Chromosomes, Fungal↗
PubMed2006

PROPHECY--a yeast phenome database, update 2006.

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics--the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale--connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at http://prophecy.lundberg.gu.se. Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics.

Chromosomes, Fungal↗