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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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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
...that maintenance of mRNA levels in cells is very important during the evolution of animal s and transcriptomes. In addition to expression reduction model, previously proposed models of duplicate gene retention include neofunctionalization and subfunctionalization (Force et al. 1999). To determine whichmodel...
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Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- Marco Mariotti,
- Didac Santesmasses,
- Salvador Capella-Gutierrez,
- Andrea Mateo,
- Carme Arnan,
- Rory Johnson,
- Salvatore D'Aniello,
- Sun Hee Yim,
- Vadim N. Gladyshev,
- Florenci Serras,
- Montserrat Corominas,
- Toni Gabaldón,
- and Roderic Guigó
Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
...in the reference set and in the extended set of 8263 s. Evolution of selenophosphate synthetases Genome Research 1257 www..org SelD genes were found in 26% of the reference prokaryotic s. A considerable fraction (19%) of the detected SelD genes encoded a protein with a Sec residue (always in the same position...
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Research: Intron evolution in Neurospora: the role of mutational bias and selection
- Yu Sun,
- Carrie A. Whittle,
- Pádraic Corcoran,
- and Hanna Johannesson
Genome Res. January 2015 25: 100-110; Published in Advance October 23, 2014, doi:10.1101/gr.175653.114
...from prokaryotic ancestors, whereas the ‘‘intron-late hypothesis’’ suggests phase 0 introns continuously emerged throughout eukaryotic evolution (Gilbert 1987; Logsdon 1998). By showing ongoing fixation of phase 0 introns in a recently Intron evolution in Neurospora Genome Research 107 www...
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Review: Origins, evolution, and phenotypic impact of new genes
- Henrik Kaessmann
Genome Res. October 2010 20: 1313-1326; Published in Advance July 22, 2010, doi:10.1101/gr.101386.109
...these copies after acquisition or evolution of promoters in their 59 flanking regions that may drive their transcription. (Pink rightangled arrow) TSS, (transparent pink box) additionally transcribed flanking sequence at the insertion site. 1314 Genome Research www..org Kaessmann Duplication of noncoding RNAs...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed...
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LETTER: Principles of transcriptional regulation and evolution of the metabolic system in E. coli
- Aswin S.N. Seshasayee,
- Gillian M. Fraser,
- M. Madan Babu,
- and Nicholas M. Luscombe
Genome Res. January 2009 19: 79-91; Published in Advance October 3, 2008, doi:10.1101/gr.079715.108
...Expression Unit, Heidelberg D-69117, Germany Abstract Organisms must adapt to make optimal use of the metabolic system in response to environmental changes. In the long-term, this involves evolution of the genomic repertoire of enzymes; in the short-term, transcriptional control ensures...
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LETTER: Comparative Analysis of Chloroplast Genomes: Functional Annotation, Genome-Based Phylogeny, and Deduced Evolutionary Patterns
- Javier De Las Rivas,
- Juan Jose Lozano,
- and Angel R. Ortiz
Genome Res. April 1, 2002 12: 567-583; doi:10.1101/gr.209402
...by a random process. However, by studying them it may be possible to infer what general environmental selective pressure could operate in the different lineages. From our analysis, one of the driving forces in the evolution of green algae and plant chloroplasts appear to be the acquisition of molecular...
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LETTER: Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution
- Dmitri M. Krylov,
- Yuri I. Wolf,
- Igor B. Rogozin,
- and Eugene V. Koonin
Genome Res. October 2003 13: 2229-2235; doi:10.1101/gr.1589103
...evolutionary genomics. Curr. Opin. Genet. Dev. 6 : 757 -762. ↵ Kumar, S., Tamura, K., and Nei, M. 1994 . MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. Comput. Appl. Biosci. 10 : 189 -191. ↵ Kunin, V. and Ouzounis, C.A. 2003 . The balance of driving forces during evolution...
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ARTICLE: Evolutionary Role of Restriction/Modification Systems as Revealed by Comparative Genome Analysis
- Eduardo P.C. Rocha,
- Antoine Danchin,
- and Alain Viari
Genome Res. June 1, 2001 11: 946-958; Published in Advance May 8, 2001, doi:10.1101/gr.153101
...in type III systems ( Redaschi and Bickle 1996 ). The protein is composed of two modules of which both are required for restriction but only one for methylation. Therefore, it is likely that parasitism is not (or is no longer) the driving force of these systems. The existence of systems for restricting...

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