Journal ArticleDOI
The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome
Fred S. Dietrich,Fred S. Dietrich,Sylvia Voegeli,Sophie Brachat,Anita Lerch,Krista Gates,Sabine Steiner,Christine Mohr,Rainer Pöhlmann,Philippe P. Luedi,Philippe P. Luedi,Sangdun Choi,Rod A. Wing,Albert Flavier,Thomas Gaffney,Peter Philippsen +15 more
TLDR
The genome of the filamentous ascomycete Ashbya gossypii provided compelling evidence that the evolution of S. cerevisiae included a whole genome duplication orfusion of two related species and showed which of the duplicated genes lost one copy and which retained both copies.Abstract:
We have sequenced and annotated the genome of the filamentous ascomycete Ashbya gossypii. With a size of only 9.2 megabases, encoding 4718 protein-coding genes, it is the smallest genome of a free-living eukaryote yet characterized. More than 90% of A. gossypii genes show both homology and a particular pattern of synteny with Saccharomyces cerevisiae. Analysis of this pattern revealed 300 inversions and translocations that have occurred since divergence of these two species. It also provided compelling evidence that the evolution of S. cerevisiae included a whole genome duplication or fusion of two related species and showed, through inferred ancient gene orders, which of the duplicated genes lost one copy and which retained both copies.read more
Citations
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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Yupeng Wang,Haibao Tang,Jeremy D. DeBarry,Xu-fei Tan,Jingping Li,Xiyin Wang,Tae-Ho Lee,Huizhe Jin,Barry S. Marler,Hui Guo,Jessica C. Kissinger,Andrew H. Paterson +11 more
TL;DR: The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses.
Journal ArticleDOI
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
Olivier Jaillon,Jean-Marc Aury,Frédéric Brunet,Jean-Louis Petit,Nicole Stange-Thomann,Evan Mauceli,Laurence Bouneau,Cécile Fischer,Catherine Ozouf-Costaz,Alain Bernot,Sophie Nicaud,David M. Jaffe,Sheila Fisher,Georges Lutfalla,Carole Dossat,Béatrice Segurens,Corinne Dasilva,Marcel Salanoubat,Michael Levy,Nathalie Boudet,Sergi Castellano,Véronique Anthouard,Claire Jubin,Vanina Castelli,Michael Katinka,Benoit Vacherie,Christian Biémont,Zineb Skalli,Laurence Cattolico,Julie Poulain,Véronique de Berardinis,Corinne Cruaud,Simone Duprat,Philippe Brottier,Jean-Pierre Coutanceau,Jérôme Gouzy,Genís Parra,Guillaume Lardier,Charles Chapple,Kevin McKernan,Paul A. McEwan,Stephanie Bosak,Manolis Kellis,Jean-Nicolas Volff,Roderic Guigó,Michael C. Zody,Jill P. Mesirov,Kerstin Lindblad-Toh,Bruce W. Birren,Chad Nusbaum,Daniel Kahn,Marc Robinson-Rechavi,Vincent Laudet,Vincent Schächter,Francis Quetier,William Saurin,Claude Scarpelli,Patrick Wincker,Eric S. Lander,Eric S. Lander,Jean Weissenbach,Hugues Roest Crollius,Hugues Roest Crollius +62 more
TL;DR: Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish, and reconstructs much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
Journal ArticleDOI
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
Journal ArticleDOI
Genome evolution in yeasts
Bernard Dujon,David James 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 +66 more
TL;DR: 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.
Journal ArticleDOI
Population genomics of domestic and wild yeasts
Gianni Liti,David M. Carter,Alan M. Moses,Alan M. Moses,Jonas Warringer,Leopold Parts,Stephen A. James,Robert P. Davey,Ian N. Roberts,Austin Burt,Vassiliki Koufopanou,Isheng J. Tsai,Casey M. Bergman,Douda Bensasson,Michael J. T. O’Kelly,Alexander van Oudenaarden,David B. H. Barton,Elizabeth Bailes,Alex N. Nguyen,Matthew Jones,Michael A. Quail,Ian Goodhead,Ian Goodhead,Sarah Sims,Frances Smith,Anders Blomberg,Richard Durbin,Edward J. Louis +27 more
TL;DR: Rather than one or two domestication events leading to the extant baker’s yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
References
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Life with 6000 Genes
André Goffeau,Bart Barrell,Howard Bussey,Ronald W. Davis,Bernard Dujon,Horst Feldmann,Francis Galibert,J D Hoheisel,Claude Jacq,Mark Johnston,Edward J. Louis,Hans-Werner Mewes,Yasufumi Murakami,Peter Philippsen,Hervé Tettelin,Stephen G. Oliver +15 more
TL;DR: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration and provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history.
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Molecular evidence for an ancient duplication of the entire yeast genome
TL;DR: A model is proposed in which this species is a degenerate tetraploid resulting from a whole-genome duplication that occurred after the divergence of Saccharomyces from Kluyveromyces, and protein pairs derived from this duplication event make up 13% of all yeast proteins.
Journal ArticleDOI
The genome sequence of Schizosaccharomyces pombe
Valerie Wood,R. Gwilliam,Marie-Adèle Rajandream,M. Lyne,Rachel Lyne,A. Stewart,J. Sgouros,N. Peat,Jacqueline Hayles,Stephen Baker,D. Basham,Sharen Bowman,Karen Brooks,D. Brown,Steve D.M. Brown,Tracey Chillingworth,Carol Churcher,Mark O. Collins,R. Connor,Ann Cronin,P. Davis,Theresa Feltwell,Andrew G. Fraser,S. Gentles,Arlette Goble,N. Hamlin,David Harris,J. Hidalgo,Geoffrey M. Hodgson,S. Holroyd,T. Hornsby,S. Howarth,Elizabeth J. Huckle,Sarah E. Hunt,Kay Jagels,Kylie R. James,L. Jones,Matthew Jones,S. Leather,S. McDonald,J. McLean,P. Mooney,Sharon Moule,Karen Mungall,Lee Murphy,D. Niblett,C. Odell,Karen Oliver,Susan O'Neil,D. Pearson,Michael A. Quail,Ester Rabbinowitsch,Kim Rutherford,Simon Rutter,David L. Saunders,Kathy Seeger,Sarah Sharp,Jason Skelton,Mark Simmonds,R. Squares,S. Squares,K. Stevens,K. Taylor,Ruth Taylor,Adrian Tivey,S. Walsh,T. Warren,S. Whitehead,John Woodward,Guido Volckaert,Rita Aert,Johan Robben,B. Grymonprez,I. Weltjens,E. Vanstreels,Michael A. Rieger,M. Schafer,S. Muller-Auer,C. Gabel,M. Fuchs,C. Fritzc,E. Holzer,D. Moestl,H. Hilbert,K. Borzym,I. Langer,Alfred Beck,Hans Lehrach,Richard Reinhardt,Thomas M. Pohl,P. Eger,Wolfgang Zimmermann,H. Wedler,R. Wambutt,Bénédicte Purnelle,André Goffeau,Edouard Cadieu,Stéphane Dréano,Stéphanie Gloux,Valerie Lelaure,Stéphanie Mottier,Francis Galibert,Stephen J. Aves,Z. Xiang,Cherryl Hunt,Karen Moore,S. M. Hurst,M. Lucas,M. Rochet,Claude Gaillardin,Victor A. Tallada,Victor A. Tallada,Andrés Garzón,Andrés Garzón,G. Thode,Rafael R. Daga,Rafael R. Daga,L. Cruzado,Juan Jimenez,Juan Jimenez,Miguel del Nogal Sánchez,F. del Rey,J. Benito,Angel Domínguez,José L. Revuelta,Sergio Moreno,John Armstrong,Susan L. Forsburg,L. Cerrutti,Todd M. Lowe,W. R. McCombie,Ian T. Paulsen,Judith A. Potashkin,G. V. Shpakovski,David W. Ussery,Bart Barrell,Paul Nurse +136 more
TL;DR: The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote, is sequenced and highly conserved genes important for eukARYotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing are identified.
Journal ArticleDOI
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
Journal ArticleDOI
Three biotechnical processes using Ashbya gossypii, Candida famata, or Bacillus subtilis compete with chemical riboflavin production.
TL;DR: The production of riboflavin by the two fungi seems to be limited by precursor supply, as was concluded from feeding and gene-overexpression experiments, and the major limitation there seems to to be the rib oflavin pathway.
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