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Research: Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus
- Nikolaos Vakirlis,
- Véronique Sarilar,
- Guénola Drillon,
- Aubin Fleiss,
- Nicolas Agier,
- Jean-Philippe Meyniel,
- Lou Blanpain,
- Alessandra Carbone,
- Hugo Devillers,
- Kenny Dubois,
- Alexandre Gillet-Markowska,
- Stéphane Graziani,
- Nguyen Huu-Vang,
- Marion Poirel,
- Cyrielle Reisser,
- Jonathan Schott,
- Joseph Schacherer,
- Ingrid Lafontaine,
- Bertrand Llorente,
- Cécile Neuvéglise,
- and Gilles Fischer
Genome Res. July 2016 26: 918-932; Published in Advance May 31, 2016, doi:10.1101/gr.204420.116
...Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus Nikolaos Vakirlis 1 , 6 , Véronique Sarilar 2 , 6 , Guénola Drillon 1 , 6 , Aubin Fleiss 1 , Nicolas Agier...
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ARTICLE: Evolution of Gene Order in the Genomes of Two Related Yeast Species
- Gilles Fischer,
- Cécile Neuvéglise,
- Pascal Durrens,
- Claude Gaillardin,
- and Bernard Dujon
Genome Res. December 1, 2001 11: 2009-2019; doi:10.1101/gr.212701
...of the chromosomal rearrangements that have lead to these differences were identified. We show that evolution of gene order in the s of these two yeast species is driven mainly by gene duplication onto different chromosomes followed by differential loss of the repeated copies. In addition, local gene inversions also...
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LETTER: Comparative Genomic Hybridization Provides New Insights Into the Molecular Taxonomy of the Saccharomyces Sensu Stricto Complex
- Laura C. Edwards-Ingram,
- Manda E. Gent,
- David C. Hoyle,
- Andrew Hayes,
- Lubomira I. Stateva,
- and Stephen G. Oliver
Genome Res. June 2004 14: 1043-1051; doi:10.1101/gr.2114704
...) or those telomeric or highly repeated sequences in yeast ( Fischer et al. 2000 ; Winzeler et al. 2003 ), would be avoided in these core groups. Whole- methods of phylogeny reconstruction are generally considered to avoid the limitations of constructing phylogenies from sequence data from just a few loci...
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Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
- Barbara Dunn,
- Chandra Richter,
- Daniel J. Kvitek,
- Tom Pugh,
- and Gavin Sherlock
Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
...are the most variable (Fig. 3); in addition, many discrete internally located regions with high copy number variation correspond to members of the Ty family of retrotransposons, or the Long Terminal Repeats (LTRs) that remain in the after transposition of these elements. Based on these observations, we...
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Article: Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium,
- Jean-Luc Souciet,
- Bernard Dujon,
- Claude Gaillardin,
- Mark Johnston,
- Philippe V. Baret,
- Paul Cliften,
- David J. Sherman,
- Jean Weissenbach,
- Eric Westhof,
- Patrick Wincker,
- Claire Jubin,
- Julie Poulain,
- Valérie Barbe,
- Béatrice Ségurens,
- François Artiguenave,
- Véronique Anthouard,
- Benoit Vacherie,
- Marie-Eve Val,
- Robert S. Fulton,
- Patrick Minx,
- Richard Wilson,
- Pascal Durrens,
- Géraldine Jean,
- Christian Marck,
- Tiphaine Martin,
- Macha Nikolski,
- Thomas Rolland,
- Marie-Line Seret,
- Serge Casarégola,
- 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 Fritsch,
- Lionel Frangeul,
- Adrien Goëffon,
- Nicolas Jauniaux,
- Rym Kachouri-Lafond,
- Célia Payen,
- Serge Potier,
- Lenka Pribylova,
- Christophe Ozanne,
- Guy-Franck Richard,
- Christine Sacerdot,
- Marie-Laure Straub,
- and Emmanuel Talla
Genome Res. October 2009 19: 1696-1709; Published in Advance June 12, 2009, doi:10.1101/gr.091546.109
...(Supplemental Table 7). Four full-length elements of this family (called Rover) were recognized in total. All carry a single CDS (between 631 and 867 codons), possess Terminal Inverted Repeats (TIR), and create 8-bp target site duplications. The presence of this element in four yeasts only, suggests an invasive...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...are the genomic regions adjacent to telomeres and often contain families of paralogous genes or pseudogenes, ribosomal DNA (rDNA) arrays, transposable elements, and other repeated sequences (Corcoran et al. 1988; Louis 1995; Kim et al. 1998; Fabre et al. 2005; Richard et al. 2013; Yue et al. 2017; Chaux-Jukic et...
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Letter: Unusual composition of a yeast chromosome arm is associated with its delayed replication
- Célia Payen,
- Gilles Fischer,
- Christian Marck,
- Caroline Proux,
- David James Sherman,
- Jean-Yves Coppée,
- Mark Johnston,
- Bernard Dujon,
- and Cécile Neuvéglise
Genome Res. October 2009 19: 1710-1721; Published in Advance July 10, 2009, doi:10.1101/gr.090605.108
...protein-encoding genes and 257 tRNA genes; it is ;900 kb larger than that of L. thermotolerans with about 300 more genes. The contains few transposable elements, with only one family of degenerate class II elements and two families of long-terminal repeat (LTR) retrotransposons. The major family, the Ty1...
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Research: Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe
- Sandrine Lenglez,
- Damien Hermand,
- and Anabelle Decottignies
Genome Res. September 2010 20: 1250-1261; Published in Advance August 5, 2010, doi:10.1101/gr.104513.109
...probability test, P = 0.0003) since, at most, 11% of S. pombe intergenic regions comprise a DNA replication origin (557 ORIs spread over 5000 intergenic regions) (Fig. 3A–C). Conversely, and in agreement with distinct mechanisms of integration, the 26 de novo insertion sites of the long terminal repeat...
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LETTER: Analysis of the VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure
- Lucio Marcello and
- J. David Barry
Genome Res. September 2007 17: 1344-1352; Published in Advance July 25, 2007, doi:10.1101/gr.6421207
...for VSGs of Trypanosoma congolense ( Bussler et al. 1998 ). VSG gene array architecture and evolution All of the VSG s analyzed here are located in subtelomeric arrays, with a sole exception. Tb927.5.3990 is interstitial, has none of the upstream 70-bp imperfect repeats characteristic of VSG s, and has...
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METHODS: LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics
- Steve Hampson,
- Aoife McLysaght,
- Brandon Gaut,
- and Pierre Baldi
Genome Res. May 1, 2003 13: 999-1010; Published in Advance April 14, 2003, doi:10.1101/gr.814403
...LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics Steve Hampson 2 , 5 , Aoife McLysaght 1 , 3 , 5 , Brandon Gaut 1 , 3 , 6 , and Pierre Baldi 2 , 4 1Institute for Genomics...

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