C. Chan and B. Tye, Autonomously replicating sequences in Saccharomyces cerevisiae., Proceedings of the National Academy of Sciences, vol.77, issue.11, pp.6329-6362, 1980.
DOI : 10.1073/pnas.77.11.6329

B. Brewer and W. Fangman, The localization of replication origins on ARS plasmids in S. cerevisiae, Cell, vol.51, issue.3, pp.463-71, 1987.
DOI : 10.1016/0092-8674(87)90642-8

A. Poloumienko, A. Dershowitz, J. De, and C. Newlon, Completion of Replication Map of Saccharomyces cerevisiae Chromosome III, Molecular Biology of the Cell, vol.12, issue.11, pp.3317-3344, 2001.
DOI : 10.1091/mbc.12.11.3317

J. Donato, S. Chung, and B. Tye, Genome-Wide Hierarchy of Replication Origin Usage in Saccharomyces cerevisiae, PLoS Genetics, vol.11, issue.9, p.141, 2006.
DOI : 10.1371/journal.pgen.0020141.st001

I. Liachko, E. Tanaka, K. Cox, S. Chung, L. Yang et al., Novel features of ARS selection in budding yeast Lachancea kluyveri, BMC Genomics, vol.7, issue.12, p.633, 2011.
DOI : 10.1073/pnas.251530398

D. Rienzi, S. Lindstrom, K. Mann, T. Noble, W. Raghuraman et al., Maintaining replication origins in the face of genomic change, Genome Research, vol.22, issue.10, pp.1940-52, 2012.
DOI : 10.1101/gr.138248.112

I. Liachko, A. Bhaskar, C. Lee, S. Chung, B. Tye et al., A Comprehensive Genome-Wide Map of Autonomously Replicating Sequences in a Naive Genome, PLoS Genetics, vol.14, issue.5, p.1000946, 2010.
DOI : 10.1371/journal.pgen.1000946.s013

H. Tsai, J. Baller, I. Liachko, A. Koren, L. Burrack et al., Origin Replication Complex Binding, Nucleosome Depletion Patterns, and a Primary Sequence Motif Can Predict Origins of Replication in a Genome with Epigenetic Centromeres, mBio, vol.5, issue.5, pp.1703-01714, 2014.
DOI : 10.1128/mBio.01703-14

I. Liachko, R. Youngblood, K. Tsui, K. Bubb, C. Queitsch et al., GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris, PLoS Genetics, vol.11, issue.3, p.1004169, 2014.
DOI : 10.1371/journal.pgen.1004169.s015

C. Newlon and J. Theis, The structure and function of yeast ARS elements, Current Opinion in Genetics & Development, vol.3, issue.5, pp.752-760, 1993.
DOI : 10.1016/S0959-437X(05)80094-2

D. Fachinetti, R. Bermejo, A. Cocito, S. Minardi, Y. Katou et al., Replication Termination at Eukaryotic Chromosomes Is Mediated by Top2 and Occurs at Genomic Loci Containing Pausing Elements, Molecular Cell, vol.39, issue.4, pp.595-605, 2010.
DOI : 10.1016/j.molcel.2010.07.024

M. Raghuraman, E. Winzeler, D. Collingwood, S. Hunt, L. Wodicka et al., Replication Dynamics of the Yeast Genome, Science, vol.294, issue.5540, pp.115-136, 2001.
DOI : 10.1126/science.294.5540.115

N. Yabuki, H. Terashima, and K. Kitada, Mapping of early firing origins on a replication profile of budding yeast, Genes to Cells, vol.2, issue.6632 Suppl., pp.781-790, 2002.
DOI : 10.1046/j.1365-2443.2002.00559.x

C. Heichinger, C. Penkett, J. Bähler, and P. Nurse, Genome-wide characterization of fission yeast DNA replication origins, The EMBO Journal, vol.7, issue.21, pp.5171-5180, 2006.
DOI : 10.1038/sj.emboj.7601390

N. Agier, O. Romano, F. Touzain, C. Lagomarsino, M. Fischer et al., The Spatiotemporal Program of Replication in the Genome of Lachancea kluyveri, Genome Biology and Evolution, vol.5, issue.2
DOI : 10.1093/gbe/evt014

D. Gilbert, Evaluating genome-scale approaches to eukaryotic DNA replication, Nature Reviews Genetics, vol.4, issue.10, pp.673-84, 2010.
DOI : 10.1038/nrg2830

S. Vengrova and J. Dalgaard, DNA Replication: Methods and Protocols, 2009.

W. Feng, D. Collingwood, M. Boeck, L. Fox, G. Alvino et al., Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication, Nature Cell Biology, vol.15, issue.2, pp.148-55, 2006.
DOI : 10.1016/0092-8674(87)90643-X

C. Nieduszynski, Y. Knox, and A. Donaldson, Genome-wide identification of replication origins in yeast by comparative genomics, Genes & Development, vol.20, issue.14, pp.1874-1883, 2006.
DOI : 10.1101/gad.385306

C. Muller and C. Nieduszynski, Conservation of replication timing reveals global and local regulation of replication origin activity, Genome Research, vol.22, issue.10, pp.1953-62, 2012.
DOI : 10.1101/gr.139477.112

B. Dujon, Yeast evolutionary genomics, Nature Reviews Genetics, vol.104, issue.7, pp.512-536, 2010.
DOI : 10.1038/nrg2811

G. Bodey, M. Mardani, H. Hanna, M. Boktour, J. Abbas et al., The epidemiology of Candida glabrata and Candida albicans fungemia in immunocompromised patients with cancer, The American Journal of Medicine, vol.112, issue.5, pp.380-385, 2002.
DOI : 10.1016/S0002-9343(01)01130-5

B. Cormack, N. Ghori, and S. Falkow, An Adhesin of the Yeast Pathogen Candida glabrata Mediating Adherence to Human Epithelial Cells, Science, vol.285, issue.5427, pp.578-82, 1999.
DOI : 10.1126/science.285.5427.578

T. Gabaldon, T. Martin, M. Marcet-houben, P. Durrens, M. Bolotin-fukuhara et al., Comparative genomics of emerging pathogens in the Candida glabrata clade, BMC Genomics, vol.14, issue.1, p.623, 2013.
DOI : 10.1016/0097-8485(93)85006-X

URL : https://hal.archives-ouvertes.fr/inserm-00871184

A. Thierry, C. Bouchier, B. Dujon, and G. Richard, Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata, Nucleic Acids Research, vol.36, issue.18, pp.5970-82, 2008.
DOI : 10.1093/nar/gkn594

A. Thierry, B. Dujon, and G. Richard, Megasatellites: a new class of large tandem repeats discovered in the pathogenic yeast Candida glabrata, Cellular and Molecular Life Sciences, vol.48, issue.5, pp.671-677, 2009.
DOI : 10.1007/s00018-009-0216-y

URL : https://hal.archives-ouvertes.fr/pasteur-01370699

T. Rolland, B. Dujon, and G. Richard, Dynamic evolution of megasatellites in yeasts, Nucleic Acids Research, vol.38, issue.14, pp.4731-4740, 2010.
DOI : 10.1093/nar/gkq207

URL : https://hal.archives-ouvertes.fr/pasteur-01370686

F. Tekaia, B. Dujon, and G. Richard, Detection and Characterization of Megasatellites in Orthologous and Nonorthologous Genes of 21 Fungal Genomes, Eukaryotic Cell, vol.12, issue.6, pp.794-803, 2013.
DOI : 10.1128/EC.00001-13

URL : https://hal.archives-ouvertes.fr/pasteur-01370689

H. Muller, A. Thierry, J. Coppée, C. Gouyette, C. Hennequin et al., Genomic polymorphism in the population of Candida glabrata: Gene copy-number variation and chromosomal translocations, Fungal Genetics and Biology, vol.46, issue.3, 2009.
DOI : 10.1016/j.fgb.2008.11.006

S. Polakova, C. Blume, J. Zarate, M. Mentel, D. Jorck-ramberg et al., Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata, Proceedings of the National Academy of Sciences, vol.106, issue.8, pp.2688-93, 2009.
DOI : 10.1073/pnas.0809793106

H. Muller, C. Hennequin, J. Galland, B. Dujon, and C. Fairhead, The Asexual Yeast Candida glabrata Maintains Distinct a and ?? Haploid Mating Types, Eukaryotic Cell, vol.7, issue.5, pp.848-58, 2008.
DOI : 10.1128/EC.00456-07

M. Marbouty, C. Ermont, B. Dujon, G. Richard, and R. Koszul, species through an optimized centrifugal elutriation procedure, Yeast, vol.21, issue.5, pp.159-66, 2014.
DOI : 10.1002/yea.3005

URL : https://hal.archives-ouvertes.fr/pasteur-01420008

A. Kaykov and P. Nurse, The spatial and temporal organization of origin firing during the S-phase of fission yeast, Genome Research, vol.25, issue.3, pp.391-401, 2015.
DOI : 10.1101/gr.180372.114

L. Louis, V. Despons, L. Friedrich, A. Martin, T. Durrens et al., , an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization, G3: Genes|Genomes|Genetics, vol.2, issue.2, pp.299-311, 2012.
DOI : 10.1534/g3.111.000745

L. Morales and B. Dujon, Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts, Microbiology and Molecular Biology Reviews, vol.76, issue.4, pp.721-760, 2012.
DOI : 10.1128/MMBR.00022-12

J. Gordon, K. Byrne, and K. Wolfe, Mechanisms of Chromosome Number Evolution in Yeast, PLoS Genetics, vol.55, issue.4, 2011.
DOI : 10.1371/journal.pgen.1002190.s010

F. Chang, J. Theis, J. Miller, C. Nieduszynski, C. Newlon et al., Analysis of Chromosome III Replicators Reveals an Unusual Structure for the ARS318 Silencer Origin and a Conserved WTW Sequence within the Origin Recognition Complex Binding Site, Molecular and Cellular Biology, vol.28, issue.16, pp.5071-81, 2008.
DOI : 10.1128/MCB.00206-08

A. Ganley and T. Kobayashi, Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data, Genome Research, vol.17, issue.2, pp.184-91, 2007.
DOI : 10.1101/gr.5457707

S. James, O. Kelly, M. Carter, D. Davey, R. Van-oudenaarden et al., Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing, Genome Research, vol.19, issue.4
DOI : 10.1101/gr.084517.108

E. Proux-wera, K. Byrne, and K. Wolfe, Evolutionary Mobility of the Ribosomal DNA Array in Yeasts, Genome Biology and Evolution, vol.5, issue.3, pp.525-556, 2013.
DOI : 10.1093/gbe/evt022

D. Witten and W. Noble, On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements, Nucleic Acids Research, vol.40, issue.9, pp.3849-55, 2012.
DOI : 10.1093/nar/gks012

Z. Duan, M. Andronescu, K. Schutz, S. Mcilwain, Y. Kim et al., A three-dimensional model of the yeast genome, Nature, vol.465, issue.7296, pp.363-370, 2010.
DOI : 10.1073/pnas.0402766101

A. Cournac, H. Marie-nelly, M. Marbouty, R. Koszul, and J. Mozziconacci, Normalization of a chromosomal contact map, BMC Genomics, vol.13, issue.1, p.436, 2012.
DOI : 10.1186/gb-2009-10-3-r25

URL : https://hal.archives-ouvertes.fr/pasteur-00769663

G. Richard, A. Kerrest, I. Lafontaine, and B. Dujon, Comparative Genomics of Hemiascomycete Yeasts: Genes Involved in DNA Replication, Repair, and Recombination, Molecular Biology and Evolution, vol.22, issue.4, pp.1011-1034, 2005.
DOI : 10.1093/molbev/msi083

G. Richard, A. Kerrest, and B. Dujon, Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes, Microbiology and Molecular Biology Reviews, vol.72, issue.4, pp.686-727, 2008.
DOI : 10.1128/MMBR.00011-08

G. Sutherland, E. Baker, and R. Richards, Fragile sites still breaking, Trends in Genetics, vol.14, issue.12, pp.501-507, 1998.
DOI : 10.1016/S0168-9525(98)01628-X

A. Letessier, G. Millot, S. Koundrioukoff, A. Lachagès, N. Vogt et al., Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site, Nature, vol.45, issue.7332, pp.120-123, 2011.
DOI : 10.1038/nature09745

D. Yudkin, B. Hayward, M. Aladjem, D. Kumari, and K. Usdin, Chromosome fragility and the abnormal replication of the FMR1 locus in fragile X syndrome, Human Molecular Genetics, vol.23, issue.11, pp.2940-52, 2014.
DOI : 10.1093/hmg/ddu006

H. Fraser, Cell-cycle regulated transcription associates with DNA replication timing in yeast and human, Genome Biology, vol.14, issue.10, p.111, 2013.
DOI : 10.1101/gr.098947.109

L. Omberg, J. Meyerson, K. Kobayashi, L. Drury, J. Diffley et al., Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression, Molecular Systems Biology, vol.9, p.312, 2009.
DOI : 10.1186/1471-2164-7-276

A. Tsankov, D. Thompson, A. Socha, A. Regev, and O. Rando, The Role of Nucleosome Positioning in the Evolution of Gene Regulation, PLoS Biology, vol.34, issue.7, p.1000414, 2010.
DOI : 10.1371/journal.pbio.1000414.s025

S. Haase and S. Reed, Improved Flow Cytometric Analysis of the Budding Yeast Cell Cycle, Cell Cycle, vol.1, issue.2, pp.132-138, 2002.
DOI : 10.4161/cc.1.2.114

B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056

URL : https://hal.archives-ouvertes.fr/hal-00104411

. Génolevures, Complete Genomes

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.
DOI : 10.1093/bioinformatics/btp324

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352

G. Millot, Comprendre et réaliser les tests statistiques à l'aide de R, 2011.

W. Press, S. Teukolsky, W. Vetterling, and B. Flannery, Numerical recipes. The art of scientific computing, 2007.

W. Cleveland, LOWESS: A Program for Smoothing Scatterplots by Robust Locally Weighted Regression, The American Statistician, vol.35, issue.1, pp.54-58, 1981.
DOI : 10.2307/2683591

R. Brent, Algorithms for minimization without derivatives, 1973.

H. Inoue, H. Nojima, and H. Okayama, High efficiency transformation of Escherichia coli with plasmids, Gene, vol.96, issue.1, pp.23-31, 1990.
DOI : 10.1016/0378-1119(90)90336-P

J. Sambrook and D. Russell, The inoue method for preparation and transformation of competent E. coli: " ultra-competent " cells. CSH Protoc, 2006.

N. Annaluru, H. Muller, L. Mitchell, S. Ramalingam, G. Stracquadanio et al., Total Synthesis of a Functional Designer Eukaryotic Chromosome, Science, vol.344, issue.6179, pp.55-63, 2014.
DOI : 10.1126/science.1249252

URL : https://hal.archives-ouvertes.fr/pasteur-01420002

P. Ng and U. Keich, GIMSAN: a Gibbs motif finder with significance analysis, Bioinformatics, vol.24, issue.19, pp.2256-2263, 2008.
DOI : 10.1093/bioinformatics/btn408

T. Bailey and M. Gribskov, Combining evidence using p-values: application to sequence homology searches, Bioinformatics, vol.14, issue.1, pp.48-54, 1998.
DOI : 10.1093/bioinformatics/14.1.48

S. Engel, F. Dietrich, D. Fisk, G. Binkley, R. Balakrishnan et al., : Then and Now, G3: Genes|Genomes|Genetics, vol.4, issue.3, pp.389-98, 2014.
DOI : 10.1534/g3.113.008995

. Génolevures, Genomic Exploration of the Hemiascomycete Yeasts

H. Marie-nelly, M. Marbouty, A. Cournac, G. Liti, G. Fischer et al., Filling annotation gaps in yeast genomes using genome-wide contact maps, Bioinformatics, vol.30, issue.15, pp.2105-2118, 2014.
DOI : 10.1093/bioinformatics/btu162

URL : https://hal.archives-ouvertes.fr/pasteur-01488132

B. Langmead and S. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-366, 2012.
DOI : 10.1093/bioinformatics/btp352

M. Imakaev, G. Fudenberg, R. Mccord, N. Naumova, A. Goloborodko et al., Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nature Methods, vol.10, issue.10, pp.999-1003, 2012.
DOI : 10.1038/nmeth.2148

H. Muller, C. Hennequin, B. Dujon, and C. Fairhead, Ascomycetes: the Candida MAT locus: comparing MAT in the genomes of hemiascomycetous yeasts Sex in fungi: molecular determination and evolutionary implications, pp.247-63, 2007.