Comparative genomics of protoploid Saccharomycetaceae.
Jean-Luc Souciet,Bernard Dujon,Claude Gaillardin,Mark Johnston,Philippe Baret,Paul F. Cliften,David James Sherman,Jean Weissenbach,Eric Westhof,Patrick Wincker,Claire Jubin,Julie Poulain,Valérie Barbe,Béatrice Segurens,François Artiguenave,Véronique Anthouard,Benoit Vacherie,Marie-Eve Val,Robert S. Fulton,Patrick Minx,Richard K. Wilson,Pascal Durrens,Géraldine Jean,Christian Marck,Tiphaine Martin,Macha Nikolski,Thomas Rolland,Marie-Line Seret,Serge Casaregola,Laurence Despons,Cécile Fairhead,Gilles Fischer,Ingrid Lafontaine,Véronique Leh,Marc Lemaire,Jacky de Montigny,Cécile Neuvéglise,Agnès Thierry,Isabelle Blanc-Lenfle,Claudine Bleykasten,Julie Diffels,Emilie S. Fritsch,Lionel Frangeul,Adrien Goëffon,Nicolas Jauniaux,Rym Kachouri-Lafond,Celia Payen,Serge Potier,Lenka Pribylova,Christophe Ozanne,Guy-Franck Richard,Christine Sacerdot,Marie-Laure Straub,Emmanuel Talla +53 more
TLDR
Five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that are called "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication, are concentrated here on.Abstract:
Our knowledge of yeast genomes remains largely dominated by the extensive studies on Saccharomyces cerevisiae and the consequences of its ancestral duplication, leaving the evolution of the entire class of hemiascomycetes only partly explored. We concentrate here on five species of Saccharomycetaceae, a large subdivision of hemiascomycetes, that we call "protoploid" because they diverged from the S. cerevisiae lineage prior to its genome duplication. We determined the complete genome sequences of three of these species: Kluyveromyces (Lachancea) thermotolerans and Saccharomyces (Lachancea) kluyveri (two members of the newly described Lachancea clade), and Zygosaccharomyces rouxii. We included in our comparisons the previously available sequences of Kluyveromyces lactis and Ashbya (Eremothecium) gossypii. Despite their broad evolutionary range and significant individual variations in each lineage, the five protoploid Saccharomycetaceae share a core repertoire of approximately 3300 protein families and a high degree of conserved synteny. Synteny blocks were used to define gene orthology and to infer ancestors. Far from representing minimal genomes without redundancy, the five protoploid yeasts contain numerous copies of paralogous genes, either dispersed or in tandem arrays, that, altogether, constitute a third of each genome. Ancient, conserved paralogs as well as novel, lineage-specific paralogs were identified.read more
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Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118
Maite Novo,Frederic Bigey,Emmanuelle Beyne,Virginie Galeote,Frédérick Gavory,Sandrine Mallet,Brigitte Cambon,Jean Luc Legras,Patrick Wincker,Serge Casaregola,Sylvie Dequin +10 more
TL;DR: Overall, these data show that the wine yeast genome is subject to constant remodeling through the contribution of exogenous genes, and suggest that these processes are favored by ecologic proximity and are involved in the molecular adaptation of wine yeasts to conditions of high sugar, low nitrogen, and high ethanol concentrations.
Journal ArticleDOI
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.
Xing-Xing Shen,Dana A. Opulente,Dana A. Opulente,Jacek Kominek,Jacek Kominek,Xiaofan Zhou,Xiaofan Zhou,Jacob L. Steenwyk,Kelly V. Buh,Max A. B. Haase,Max A. B. Haase,Max A. B. Haase,Jennifer H. Wisecaver,Jennifer H. Wisecaver,Mingshuang Wang,Drew T. Doering,James T. Boudouris,Rachel M. Schneider,Rachel M. Schneider,Quinn K. Langdon,Moriya Ohkuma,Rikiya Endoh,Masako Takashima,Ri-ichiroh Manabe,Neža Čadež,Diego Libkind,Carlos A. Rosa,Jeremy DeVirgilio,Amanda Beth Hulfachor,Marizeth Groenewald,Cletus P. Kurtzman,Chris Todd Hittinger,Chris Todd Hittinger,Antonis Rokas +33 more
TL;DR: It is argued that reductive evolution is a major mode of evolutionary diversification and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them.
Journal ArticleDOI
Yeast evolutionary genomics
TL;DR: This Review summarizes recent progress in understanding the molecular mechanisms — such as gene duplication, mutation and acquisition of novel genetic material — that underlie yeast evolutionary genomics.
Journal ArticleDOI
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus
Devin R. Scannell,Oliver A. Zill,Antonis Rokas,Celia Payen,Maitreya J. Dunham,Michael B. Eisen,Michael B. Eisen,Jasper Rine,Mark Johnston,Mark Johnston,Chris Todd Hittinger,Chris Todd Hittinger +11 more
TL;DR: Improved genome sequences of three species of Saccharomyces sensu stricto yeasts are presented, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses, and genetically marked, stable haploid strains are generated for all three species.
Journal ArticleDOI
Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts
Lucia Morales,Bernard Dujon +1 more
TL;DR: Problems of meiotic fertility, ploidy constraint, gene and gene product compatibility, and nucleomitochondrial interactions are discussed and placed in the context of other known mechanisms of yeast genome evolution as a model for eukaryotes.
References
More filters
Journal ArticleDOI
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Journal ArticleDOI
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
TL;DR: A computerized method is presented that reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.
Journal ArticleDOI
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Journal ArticleDOI
MAFFT version 5: improvement in accuracy of multiple sequence alignment
TL;DR: Improvement in accuracy was generally observed for most methods, but remarkably large for the new options of MAFFT proposed here, which showed higher accuracy than currently available methods including TCoffee version 2 and CLUSTAL W in benchmark tests consisting of alignments of >50 sequences.
Journal ArticleDOI
The evolutionary fate and consequences of duplicate genes
Michael Lynch,John S. Conery +1 more
TL;DR: Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.
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