M. Clamp, Ensembl 2002: accommodating comparative genomics, Nucleic Acids Research, vol.31, issue.1, pp.38-42, 2003.
DOI : 10.1093/nar/gkg083

M. Halling-brown, A Fugu-Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genes, Nucleic Acids Research, vol.32, issue.8, pp.2618-2622, 2004.
DOI : 10.1093/nar/gkh573

C. Hitte, Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping, Nature Reviews Genetics, vol.68, issue.8, pp.643-648, 2005.
DOI : 10.1101/gr.2663304

W. J. Murphy, Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps, Science, vol.309, issue.5734, pp.613-617, 2005.
DOI : 10.1126/science.1111387

O. 'brien and S. J. , Anchored reference loci for comparative genome mapping in mammals, Nat. Genet, vol.2, pp.103-112, 1993.

X. Pan, SynBrowse: a synteny browser for comparative sequence analysis, Bioinformatics, vol.21, issue.17, pp.3461-3468, 2005.
DOI : 10.1093/bioinformatics/bti555

. G. Pavesi, GeneSyn: a tool for detecting conserved gene order across genomes, Bioinformatics, vol.20, issue.9, pp.1472-1474, 2004.
DOI : 10.1093/bioinformatics/bth102

G. Tesler, GRIMM: genome rearrangements web server, Bioinformatics, vol.18, issue.3, pp.492-493, 2002.
DOI : 10.1093/bioinformatics/18.3.492

J. Bouck, W. Miller, J. H. Gorrell, D. Muzny, and R. A. Gibbs, Analysis of the quality and utility of random shotgun sequencing at low redundancies, Genome Res, vol.8, pp.1074-1084, 1998.

E. F. Kirkness, The Dog Genome: Survey Sequencing and Comparative Analysis, Science, vol.301, issue.5641, pp.1898-1903, 2003.
DOI : 10.1126/science.1086432

E. H. Margulies, An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing, Proc. Natl Acad. Sci. USA, pp.4795-4800, 2005.
DOI : 10.1073/pnas.0409882102

E. A. Ostrander and E. Giniger, Semper Fidelis: What Man's Best Friend Can Teach Us about Human Biology and Disease, The American Journal of Human Genetics, vol.61, issue.3, pp.475-480, 1997.
DOI : 10.1086/515522

F. Galibert, The importance of the canine model in medical genetics, Bull. Acad. Natl Med, vol.182, pp.811-821, 1998.

F. Galibert, C. Andre, and C. Hitte, Le chien, un mod??le pour la g??n??tique des mammif??res, m??decine/sciences, vol.20, issue.8-9, pp.761-766, 2004.
DOI : 10.1051/medsci/2004208-9761

N. B. Sutter and E. A. Ostrander, Dog star rising: the canine genetic system, Nature Reviews Genetics, vol.25, issue.12, pp.900-910, 2004.
DOI : 10.1038/nrg777

K. Chase, Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton, Proc. Natl Acad. Sci. USA 99, pp.9930-9935, 2002.
DOI : 10.1073/pnas.152333099

D. Patterson, Companion Animal Medicine in the Age of Medical Genetics, Journal of Veterinary Internal Medicine, vol.193, issue.Suppl, pp.1-9, 2000.
DOI : 10.1111/j.1939-1676.2000.tb01492.x

M. Breen, An integrated 4249 marker FISH/RH map of the canine genome, BMC Genomics, vol.5, pp.1-11, 2004.

R. Guyon, Building Comparative Maps Using 1.5x Sequence Coverage: Human Chromosome 1p and the Canine Genome, Cold Spring Harbor Symposia on Quantitative Biology, vol.44, issue.0, pp.171-177, 2003.
DOI : 10.1006/geno.1999.5989

N. B. Sutter, Extensive and breed-specific linkage disequilibrium in Canis familiaris, Genome Research, vol.14, issue.12, pp.2388-2396, 2004.
DOI : 10.1101/gr.3147604

R. Guyon, A 1-Mb resolution radiation hybrid map of the canine genome, Proc. Natl Acad. Sci. USA, pp.5296-5301, 2003.
DOI : 10.1073/pnas.0831002100

M. Breen, Chromosome-Specific Single-Locus FISH Probes Allow Anchorage of an 1800-Marker Integrated Radiation-Hybrid/Linkage Map of the Domestic Dog Genome to All Chromosomes, Genome Research, vol.11, issue.10, pp.1784-1795, 2001.
DOI : 10.1101/gr.189401

C. S. Mellersh, An integrated linkage-radiation hybrid map of the canine genome, Mammalian Genome, vol.11, issue.2, pp.120-130, 2000.
DOI : 10.1007/s003350010024

C. Priat, A Whole-Genome Radiation Hybrid Map of the Dog Genome, Genomics, vol.54, issue.3, pp.361-378, 1998.
DOI : 10.1006/geno.1998.5602

C. S. Mellersh, A Linkage Map of the Canine Genome, Genomics, vol.46, issue.3, pp.326-336, 1997.
DOI : 10.1006/geno.1997.5098

D. R. Cox, Radiation hybrid mapping, Cytogenetic and Genome Research, vol.59, issue.2-3, pp.80-81, 1992.
DOI : 10.1159/000133205

F. Vignaux, Construction and optimization of a dog whole-genome radiation hybrid panel, Mammalian Genome, vol.10, issue.9, pp.888-894, 1999.
DOI : 10.1007/s003359901109

R. Agarwala, D. L. Applegate, D. Maglott, G. D. Schuler, and A. A. Schaffer, A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy, Genome Research, vol.10, issue.3, pp.350-364, 2000.
DOI : 10.1101/gr.10.3.350

C. Hitte, Comparison of MultiMap and TSP/CONCORDE for Constructing Radiation Hybrid Maps, Journal of Heredity, vol.94, issue.1, pp.9-13, 2003.
DOI : 10.1093/jhered/esg012

T. C. Matise, M. Perlin, and A. Chakravarti, Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map, Nature Genetics, vol.21, issue.4, pp.384-390, 1994.
DOI : 10.1016/0165-4608(92)90171-4

M. Boehnke, K. Lange, and D. R. Cox, Statistical methods for multipoint radiation hybrid mapping, Am. J. Hum. Genet, vol.49, pp.1174-1188, 1991.

T. Schiex and C. Gaspin, CARTHAGENE: constructing and joining maximum likelihood genetic maps, Proc. Int. Conf. Intell. Syst. Mol. Biol, vol.5, pp.258-267, 1997.

A. Ben-dor and B. Chor, On Constructing Radiation Hybrid Maps, Journal of Computational Biology, vol.4, issue.4, pp.517-533, 1997.
DOI : 10.1089/cmb.1997.4.517

D. Applegate, R. Bixby, V. Chvatal, and W. Cook, On the solution of traveling salesman problems, Documenta Mathematica ? Extra, vol.3, pp.645-656, 1998.

S. G. Gregory, A physical map of the mouse genome, Nature, vol.266, issue.6899, pp.743-750, 2002.
DOI : 10.1101/GR.214802

R. A. Gibbs, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol.428, pp.493-521, 2004.

R. A. Gibbs and G. M. Weinstock, Evolving Methods for the Assembly of Large Genomes, Cold Spring Harbor Symposia on Quantitative Biology, vol.7, issue.0, pp.189-194, 2003.
DOI : 10.1038/nature01262

S. F. Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

R. H. Waterston, Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-562, 2002.

S. Zhao, Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation, Genome Research, vol.14, issue.10a
DOI : 10.1101/gr.2663304

J. Ashurst, C. Chen, J. Gilbert, K. Jekosch, S. Keenan et al., The Vertebrate Genome Annotation (Vega) database, Nucleic Acids Research, vol.33, issue.Database issue, pp.459-465, 2005.
DOI : 10.1093/nar/gki135

. Chenz-q, . Lautenbergerja, L. Lyons, O. Mckenziel, and . Briensj, A human genome map of comparative anchor tagged sequences, J Hered, vol.90, pp.477-484, 1999.

T. Derrien, C. Andre, F. Galibert, and C. Hitte, AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps, Bioinformatics, vol.23, issue.4, pp.498-499, 2007.
DOI : 10.1093/bioinformatics/btl618

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

G. Fischer, C. Neuveglise, P. Durrens, C. Gaillardin, and B. Dujon, Evolution of Gene Order in the Genomes of Two Related Yeast Species, Genome Research, vol.11, issue.12, pp.2009-2028, 2001.
DOI : 10.1101/gr.212701
URL : https://hal.archives-ouvertes.fr/hal-00306595

R. Gibbs, G. Weinstock, M. Metzker, D. Muzny, E. Sodergren et al., Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol.428, pp.493-521, 2004.

P. Goodstadtl, Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human, PLoS Computational Biology, vol.49, issue.9, p.133, 2006.
DOI : 1434-5161(2004)049[0548:ADTPAI]2.0.CO;2

R. Hardison, Comparative genomics, PLoS Biol, vol.2, p.58, 2003.

L. Hillier, W. Miller, E. Birney, W. Warren, R. Hardison et al., Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, vol.194, issue.7018, pp.695-716, 2004.
DOI : 10.1101/gr.794803

C. Hitte, J. Madeoy, E. Kirkness, C. Priat, T. Lorentzen et al., Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping, Nature Reviews Genetics, vol.68, issue.8, pp.643-648, 2005.
DOI : 10.1101/gr.2663304

O. Jaillon, J. Aury, F. Brunet, J. Petit, N. Stange-thomann et al., Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol.10, issue.7011, pp.946-957, 2004.
DOI : 10.1016/S0014-5793(00)02273-0
URL : https://hal.archives-ouvertes.fr/hal-00427605

D. Karolchik, A. Hinrichs, T. Furey, K. Roskin, C. Sugnet et al., The UCSC Table Browser data retrieval tool, Nucleic Acids Research, vol.32, issue.90001, pp.493-496, 2004.
DOI : 10.1093/nar/gkh103

A. Kasprzyk, D. Keefe, D. Smedley, D. London, W. Spooner et al., EnsMart: A Generic System for Fast and Flexible Access to Biological Data, Genome Research, vol.14, issue.1, pp.160-169, 2004.
DOI : 10.1101/gr.1645104

W. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202. Article published online before March 2002

E. Kirkness, V. Bafna, A. Halpern, S. Levy, R. K. Rusch et al., The Dog Genome: Survey Sequencing and Comparative Analysis, Science, vol.301, issue.5641, pp.1898-1903, 2003.
DOI : 10.1126/science.1086432

E. Lander, L. Linton, B. Birren, C. Nusbaum, M. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.6, issue.6822, pp.860-921, 2001.
DOI : 10.1038/35057062

D. Liangc, InGeno?anintegratedgenomeandorthologviewer for improved genome to genome comparisons, BMC Bioinformatics, vol.7, issue.1, p.461, 2006.
DOI : 10.1186/1471-2105-7-461

K. Lindblad-toh, C. Wade, T. Mikkelsen, E. Karlsson, D. Jaffe et al., Genome sequence, comparative analysis and haplotype structure of the domestic dog, Nature, vol.426, issue.7069, pp.803-819, 2005.
DOI : 10.1038/nature04338

E. Margulies, J. Vinson, W. Miller, D. Jaffe, K. Lindblad-toh et al., An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing, Proceedings of the National Academy of Sciences, vol.102, issue.13, pp.4795-4800, 2005.
DOI : 10.1073/pnas.0409882102

W. Murphy, D. Larkin, A. Everts-van-der-wind, G. Bourque, G. Tesler et al., Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps, Science, vol.309, issue.5734, pp.613-617, 2005.
DOI : 10.1126/science.1111387

O. Brien, S. Womack, J. Lyons, L. Moore, K. Jenkins et al., Anchored reference loci for comparative genome mapping in mammals, Nat Genet, vol.2, pp.103-112, 1993.

X. Pan, L. Stein, and V. Brendel, SynBrowse: a synteny browser for comparative sequence analysis, Bioinformatics, vol.21, issue.17, pp.3461-3468, 2005.
DOI : 10.1093/bioinformatics/bti555

P. Pevzner and G. Tesler, Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes, Genome Research, vol.13, issue.1, pp.37-45, 2003.
DOI : 10.1101/gr.757503

R. Waterston, K. Lindblad-toh, E. Birney, J. Rogers, J. Abril et al., Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-562, 2002.

X. Zheng, F. Lu, Z. Wang, F. Zhong, J. Hoover et al., Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs, Bioinformatics, vol.21, issue.6, pp.703-710, 2005.
DOI : 10.1093/bioinformatics/bti045

. Derrien, Analysis of the Unassembled Part of the Dog Genome Sequence, pp.678-401

R. Busca and R. Ballotti, Cyclic AMP a Key Messenger in the Regulation of Skin Pigmentation, Pigment Cell Research, vol.13, issue.2, pp.60-69, 2000.
DOI : 10.1034/j.1600-0749.2000.130203.x

H. Widlund and D. Fisher, Microphthalamia-associated transcription factor: a critical regulator of pigment cell development and survival, Oncogene, vol.22, issue.20, pp.3035-3041, 1957.
DOI : 10.1038/sj.onc.1206443

D. Sponenberg and M. Rothschild, Genetics of coat colour and hair texture In The Genetics of the Dog Ruvinsky A , Sampson J edition, pp.61-685

R. Everts, J. Rothuizen, and B. Van-oost, Identification of a premature stop codon in the melanocyte-stimulating hormone receptor gene (MC1R) in Labrador and Golden retrievers with yellow coat colour, Animal Genetics, vol.15, issue.3, pp.194-199, 2000.
DOI : 10.1016/0167-4781(96)00100-5

J. Newton, A. Wilkie, L. He, S. Jordan, D. Metallinos et al., Melanocortin 1 receptor variation in the domestic dog, Mammalian Genome, vol.11, issue.1, pp.24-30, 2000.
DOI : 10.1007/s003350010005

S. Schmutz, T. Berryere, N. Ellinwood, J. Kerns, and G. Barsh, MC1R Studies in Dogs With Melanistic Mask or Brindle Patterns, Journal of Heredity, vol.94, issue.1, pp.69-73, 2003.
DOI : 10.1093/jhered/esg014

T. Berryere, J. Kerns, G. Barsh, and S. Schmutz, Association of an Agouti allele with fawn or sable coat color in domestic dogs, Mammalian Genome, vol.91, issue.Suppl 8
DOI : 10.1007/s00335-004-2445-6

J. Kerns, J. Newton, T. Berryere, E. Rubin, J. Cheng et al., Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs, Mammalian Genome, vol.34, issue.10, pp.798-808, 2004.
DOI : 10.1007/s00335-004-2377-1

S. Schmutz, T. Berryere, and A. Goldfinch, TYRP1 and MC1R genotypes and their effects on coat color in dogs, Mammalian Genome, vol.13, issue.7, pp.380-387, 2002.
DOI : 10.1007/s00335-001-2147-2

U. Philipp, H. Hamann, L. Mecklenburg, S. Nishino, E. Mignot et al., Polymorphisms within the canine MLPH gene are associated with dilute coat color in dogs, BMC Genetics, vol.6, issue.1, p.34, 2005.
DOI : 10.1186/1471-2156-6-34

R. Guyon, T. Lorentzen, C. Hitte, L. Kim, E. Cadieu et al., A 1-Mb resolution radiation hybrid map of the canine genome, Proceedings of the National Academy of Sciences, vol.100, issue.9, pp.5296-5301, 2003.
DOI : 10.1073/pnas.0831002100

M. Breen, C. Hitte, T. Lorentzen, R. Thomas, E. Cadieu et al., An integrated 4249 marker FISH/RH map of the canine genome, BMC Genomics, vol.5, issue.1, p.65, 2004.
DOI : 10.1186/1471-2164-5-65

A. Akcan and W. Wegner, Changes in the visual pathways and visual centers in Merle syndrome in the dog, Z Versuchstierkd, vol.25, pp.91-99, 1983.

K. Gelatt, N. Powell, and K. Huston, Inheritance of microphthalmia with coloboma in the Australian shepherd dog, Am J Vet Res, vol.42, pp.1686-1690, 1981.

G. Strain, Congenital Deafness and its Recognition, Veterinary Clinics of North America: Small Animal Practice, vol.29, issue.4, pp.895-907, 1999.
DOI : 10.1016/S0195-5616(99)50079-X

D. Sponenberg, Germinal reversion of the merle allele In Australian shepherd dogs, Journal of Heredity, vol.75, issue.1, p.78, 1984.
DOI : 10.1093/oxfordjournals.jhered.a109874

S. Schmutz, T. Berryere, and C. Sharp, KITLG maps to canine chromosome 15 and is excluded as a candidate gene for merle in dogs, Animal Genetics, vol.20, issue.1, pp.75-76, 2003.
DOI : 10.1006/geno.1999.5947

A. Hansdottir, K. Palsdottir, J. Favor, A. Neuhauser-klaus, H. Fuchs et al., The novel mouse microphthalmia mutations Mitfmi-enu5 and Mitfmi-bcc2 produce dominant negative Mitf proteins, Genomics, vol.83, issue.5, pp.932-935, 2004.
DOI : 10.1016/j.ygeno.2003.10.013

E. Steingrimsson, H. Arnheiter, J. Hallsson, M. Lamoreux, N. Copeland et al., Interallelic complementation at the mouse Mitf locus, Genetics, vol.163, pp.267-276, 2003.

M. Tassabehji, V. Newton, and A. Read, Waardenburg syndrome type 2 caused by mutations in the human microphthalmia (MITF) gene, Nature Genetics, vol.26, issue.3, pp.251-255, 1994.
DOI : 10.1016/0165-4608(93)90050-V

S. Potterf, M. Furumura, K. Dunn, H. Arnheiter, and W. Pavan, Transcription factor hierarchy in Waardenburg syndrome

A. Watanabe, K. Takeda, B. Ploplis, and M. Tachibana, Epistatic relationship between Waardenburg Syndrome genes MITF and PAX3, Nature Genetics, vol.11, issue.3, pp.283-286, 1998.
DOI : 10.1016/0888-7543(95)80076-X

G. Strain, Deafness prevalence and pigmentation and gender associations in dog breeds at risk, The Veterinary Journal, vol.167, issue.1, pp.23-32, 2004.
DOI : 10.1016/S1090-0233(03)00104-7

H. Parker, L. Kim, N. Sutter, S. Carlson, T. Lorentzen et al., Genetic Structure of the Purebred Domestic Dog, Science, vol.304, issue.5674, pp.1160-1164, 2004.
DOI : 10.1126/science.1097406

A. Brehm, La vie des animaux illustrée, Bailleres JB. Paris, vol.1868

D. Buffon, Origine des espèces Edited by: Bureau-de-lasociété-des-Publications-illustrées, Paris, vol.3, issue.1839

S. Jouquand, A. Cheron, and F. Galibert, Microsatellite analysis using a two-step procedure for fluorescence labeling of PCR products, Biotechniques, vol.26, pp.902-905, 1999.

T. Matise, M. Perlin, and A. Chakravarti, Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map, Nature Genetics, vol.21, issue.4, pp.384-390, 1994.
DOI : 10.1016/0165-4608(92)90171-4

J. Altschmied, J. Delfgaauw, B. Wilde, J. Duschl, L. Bouneau et al., Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish, Genetics, vol.161, issue.1, pp.259-67, 2002.

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-413, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

M. Arumugam, C. Wei, R. Brown, and M. Brent, Pairagon+N-SCAN_EST: a model-based gene annotation pipeline, Genome Biology, vol.7, issue.Suppl 1, pp.5-6, 2006.
DOI : 10.1186/gb-2006-7-s1-s5

J. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin et al., Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol.20, issue.7116, pp.171-179, 2006.
DOI : 10.1038/nature05230
URL : https://hal.archives-ouvertes.fr/hal-00090904

J. Bailey, Z. Gu, R. Clark, K. Reinert, R. Samonte et al., Recent Segmental Duplications in the Human Genome, Science, vol.297, issue.5583, pp.1003-1010, 2002.
DOI : 10.1126/science.1072047

J. Barrett, Genetic mapping based on radiation hybrid data, Genomics, vol.13, issue.1, pp.95-103, 1992.
DOI : 10.1016/0888-7543(92)90207-9

S. Batzoglou, D. Jaffe, K. Stanley, J. Butler, S. Gnerre et al., ARACHNE: A Whole-Genome Shotgun Assembler, Genome Research, vol.12, issue.1, pp.177-89, 2002.
DOI : 10.1101/gr.208902

S. Bjornerfeldt, M. Webster, and C. Vila, Relaxation of selective constraint on dog mitochondrial DNA following domestication, Genome Research, vol.16, issue.8, pp.990-994, 2006.
DOI : 10.1101/gr.5117706

T. Blomme, K. Vandepoele, D. Bodt, S. Simillion, C. Maere et al., Van de Peer Y. The gain and loss of genes during 600 million years of vertebrate evolution, Genome Biology, vol.7, issue.5, p.43, 2006.
DOI : 10.1186/gb-2006-7-5-r43

D. Boffelli, J. Mcauliffe, D. Ovcharenko, K. Lewis, I. Ovcharenko et al., Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science, Feb, vol.28299, issue.5611, pp.1391-1395, 2003.

D. Boffelli, M. Nobrega, and E. Rubin, Comparative genomics at the vertebrate extremes, Nature Reviews Genetics, vol.129, issue.6, pp.456-65, 2004.
DOI : 10.1016/S0378-1119(02)00592-9

G. Bourque, P. Pevzner, and G. Tesler, Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes, Genome Research, vol.14, issue.4, pp.507-523, 2004.
DOI : 10.1101/gr.1975204

M. Breen, C. Hitte, T. Lorentzen, R. Thomas, E. Cadieu et al., An integrated 4249 marker FISH/RH map of the canine genome, BMC Genomics, vol.5, issue.1, pp.65-15363096, 2004.
DOI : 10.1186/1471-2164-5-65

M. Breen, S. Jouquand, C. Renier, C. Mellersh, C. Hitte et al., Chromosomespecific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/ linkage map of the domestic dog genome to all chromosomes, Genome Res, 2001.

M. Breen, R. Thomas, M. Binns, N. Carter, and C. Langford, Reciprocal chromosome painting reveals detailed regions of conserved synteny between the karyotypes of the domestic dog (Canis familiaris) and human. Genomics, pp.145-55, 1999.

M. Brent and R. Guigo, Recent advances in gene structure prediction, Curr Opin Struct Biol, 2004.

C. B. Burge and S. Karlin, Finding the genes in genomic DNA, Current Opinion in Structural Biology, vol.8, issue.3, pp.346-354, 1998.
DOI : 10.1016/S0959-440X(98)80069-9

K. Byrne and K. Wolfe, Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser, Nucleic Acids Research, vol.34, issue.90001, pp.452-457, 2006.
DOI : 10.1093/nar/gkj041

M. Chaisson, B. Raphael, and P. Pevzner, Microinversions in mammalian evolution, Proceedings of the National Academy of Sciences, vol.103, issue.52, pp.19824-19833, 2006.
DOI : 10.1073/pnas.0603984103
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1750909

L. Clark, J. Wahl, C. Rees, and K. Murphy, From The Cover: Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog, Proceedings of the National Academy of Sciences, vol.103, issue.5, pp.1376-81, 2006.
DOI : 10.1073/pnas.0506940103

A. Coghlan, E. Eichler, S. Oliver, A. Paterson, and L. Stein, Chromosome evolution in eukaryotes: a multi-kingdom perspective, Trends in Genetics, vol.21, issue.12, pp.673-82, 2005.
DOI : 10.1016/j.tig.2005.09.009

V. Curwen, E. Eyras, T. Andrews, L. Clarke, E. Mongin et al., The Ensembl Automatic Gene Annotation System, Genome Research, vol.14, issue.5, pp.942-50, 2004.
DOI : 10.1101/gr.1858004

T. Derrien, C. Andre, F. Galibert, and C. Hitte, Analysis of the Unassembled Part of the Dog Genome Sequence: Chromosomal Localization of 115 Genes Inferred from Multispecies Comparative Genomics, Journal of Heredity, vol.98, issue.5, pp.461-468, 2007.
DOI : 10.1093/jhered/esm027

S. Djebali, F. Delaplace, and H. Crollius, Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA, Genome Biol, vol.7, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00339592

T. Domazet-loso and D. Tautz, An Evolutionary Analysis of Orphan Genes in Drosophila, Genome Research, vol.13, issue.10, pp.2213-2222, 2003.
DOI : 10.1101/gr.1311003

J. Dufayard, L. Duret, S. Penel, M. Gouy, F. Rechenmann et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-603, 2005.
DOI : 10.1093/bioinformatics/bti325
URL : https://hal.archives-ouvertes.fr/hal-00427861

S. Durinck, Y. Moreau, A. Kasprzyk, S. Davis, D. Moor et al., BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis, Bioinformatics, vol.21, issue.16, pp.3439-3479, 2005.
DOI : 10.1093/bioinformatics/bti525

. Encode-project-consortium, E. Birney, J. Stamatoyannopoulos, A. Dutta, R. Guigo et al., Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, issue.7146, pp.799-816, 2007.

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, pp.113-15318951, 2004.
DOI : 10.1186/1471-2105-5-113

E. Eichler and D. Sankoff, Structural dynamics of eukaryotic chromosome evolution. Science, Review, vol.301, issue.5634, pp.793-800, 2003.

J. Eisen, R. Coyne, M. Wu, D. Wu, M. Thiagarajan et al., Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote, Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote, pp.286-16933976, 2006.
DOI : 10.1371/journal.pbio.0040286.st017

H. Escriva, S. Bertrand, P. Germain, M. Robinson-rechavi, M. Umbhauer et al., Neofunctionalization in Vertebrates: The Example of Retinoic Acid Receptors, PLoS Genetics, vol.30, issue.7, pp.102-16839186, 2006.
DOI : 10.1371/journal.pgen.0020102.sg005
URL : https://hal.archives-ouvertes.fr/hal-00187905

T. Faraut, S. De-givry, P. Chabrier, T. Derrien, F. Galibert et al., A comparative genome approach to marker ordering, Bioinformatics, vol.23, issue.2, pp.50-56, 2007.
DOI : 10.1093/bioinformatics/btl321

G. Fischer, S. James, I. Roberts, S. Oliver, and E. Louis, Chromosomal evolution in Saccharomyces, Nature, vol.405, issue.6785, pp.451-455, 2000.

G. Fischer, E. Rocha, F. Brunet, M. Vergassola, and B. Dujon, Highly variable rates of genome rearrangements between Hemiascomycetous yeast lineages, PLoS Genetics, vol.preprint, issue.2006, pp.32-16532063, 2006.
DOI : 10.1371/journal.pgen.0020032.eor

W. Fitch, Distinguishing Homologous from Analogous Proteins, Systematic Zoology, vol.19, issue.2, pp.99-106, 1970.
DOI : 10.2307/2412448

W. Fitch, Uses for Evolutionary Trees, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.349, issue.1327, pp.93-102, 1995.
DOI : 10.1098/rstb.1995.0095

R. Fleischmann, M. Adams, O. White, R. Clayton, E. Kirkness et al., Whole-genome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, issue.5223, pp.496-512, 1995.
DOI : 10.1126/science.7542800

S. Foissac, P. Bardou, A. Moisan, M. Cros, T. Schiex et al., EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences, Nucleic Acids Research, vol.31, issue.13, pp.3742-3747, 2003.
DOI : 10.1093/nar/gkg586

J. Fondon and H. Garner, Molecular origins of rapid and continuous morphological evolution, Proceedings of the National Academy of Sciences, vol.101, issue.52, pp.18058-63, 2004.
DOI : 10.1073/pnas.0408118101

R. Franklin and R. Gosling, Molecular Configuration in Sodium Thymonucleate, Nature, vol.89, issue.4356, pp.740-741, 1953.
DOI : 10.1038/171740a0

F. Galibert, C. Andre, and C. Hitte, Dog as a mammalian genetic model, Med Sci, 2004.

N. Galtier and L. Duret, Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution, Trends in Genetics, vol.23, issue.6, pp.273-280, 2007.
DOI : 10.1016/j.tig.2007.03.011
URL : https://hal.archives-ouvertes.fr/halsde-00424420

N. Galtier, Gene conversion drives GC content evolution in mammalian histones, Trends in Genetics, vol.19, issue.2, pp.65-73, 2003.
DOI : 10.1016/S0168-9525(02)00002-1

R. Gibbs, G. Weinstock, M. Metzker, D. Muzny, E. Sodergren et al., Rat Genome Sequencing Project Consortium Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol.428, issue.6982, pp.493-521, 2004.

L. Goodstadt and C. Ponting, Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human, PLoS Computational Biology, vol.49, issue.9, pp.133-17009864, 2006.
DOI : 1434-5161(2004)049[0548:ADTPAI]2.0.CO;2

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

S. Guindon, F. Lethiec, P. Duroux, and O. Gascuel, PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference, Nucleic Acids Research, vol.33, issue.Web Server, pp.557-566, 2005.
DOI : 10.1093/nar/gki352
URL : https://hal.archives-ouvertes.fr/lirmm-00105317

R. Guyon, E. Kirkness, T. Lorentzen, C. Hitte, K. Comstock et al., Building Comparative Maps Using 1.5x Sequence Coverage: Human Chromosome 1p and the Canine Genome, Cold Spring Harbor Symposia on Quantitative Biology, vol.44, issue.0, pp.171-178, 2003.
DOI : 10.1006/geno.1999.5989

R. Guyon, S. Pearce-kelling, C. Zeiss, G. Acland, and G. Aguirre, Analysis of six candidate genes as potential modifiers of disease expression in canine XLPRA1, a model for human X-linked retinitis pigmentosa 3. Mol Vis, pp.1094-105, 2007.

R. Hardison, Comparative genomics, PLoS Biol, vol.1, issue.2, p.14624258, 2003.

C. Andre, Coat colour in dogs: identification of the merle locus in the Australian shepherd breed, BMC Vet Res Feb, vol.272, pp.9-16504149, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01068391

A. Heger and C. Ponting, Evolutionary rate analyses of orthologues and paralogues from twelve Drosophila genomes, 2007.

L. Hurst, C. Pal, and M. Lercher, The evolutionary dynamics of eukaryotic gene order, Nature Reviews Genetics, vol.5, issue.4, pp.299-310, 2004.
DOI : 10.1038/nature01107

T. Huxley, THE ORIGIN OF SPECIES, pp.541-70
DOI : 10.1017/CBO9780511693120.014

O. Jaillon, J. Aury, F. Brunet, J. Petit, N. Stange-thomann et al., Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype, Nature, vol.10, issue.7011, pp.946-57, 2004.
DOI : 10.1016/S0014-5793(00)02273-0
URL : https://hal.archives-ouvertes.fr/hal-00427605

M. Kanehisa, S. Goto, M. Hattori, K. Aoki-kinoshita, M. Itoh et al., From genomics to chemical genomics: new developments in KEGG, Nucleic Acids Research, vol.34, issue.90001, pp.354-361, 2006.
DOI : 10.1093/nar/gkj102

M. Kellis, N. Patterson, B. Birren, B. Berger, and E. Lander, Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery, Journal of Computational Biology, vol.11, issue.2-3, pp.319-55, 2004.
DOI : 10.1089/1066527041410319
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.188.2010

E. Kirkness, V. Bafna, A. Halpern, S. Levy, R. K. Rusch et al., The Dog Genome: Survey Sequencing and Comparative Analysis, Science, vol.301, issue.5641, pp.1898-903, 2003.
DOI : 10.1126/science.1086432

G. Kolesov, Z. Wunderlich, O. Laikova, M. Gelfand, and L. Mirny, How gene order is influenced by the biophysics of transcription regulation, Proceedings of the National Academy of Sciences, vol.104, issue.35, pp.13948-53, 2007.
DOI : 10.1073/pnas.0700672104

E. Koonin, Orthologs, Paralogs, and Evolutionary Genomics, Annual Review of Genetics, vol.39, issue.1, pp.309-347, 2005.
DOI : 10.1146/annurev.genet.39.073003.114725

R. Kuhn, D. Karolchik, A. Zweig, H. Trumbower, D. Thomas et al., The UCSC genome browser database: update 2007, Nucleic Acids Research, vol.35, issue.Database, pp.668-73, 2007.
DOI : 10.1093/nar/gkl928

E. Lander, L. Linton, B. Birren, C. Nusbaum, M. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.6, issue.6822, pp.860-921, 2001.
DOI : 10.1038/35057062

J. Lee and E. Sonnhammer, Genomic Gene Clustering Analysis of Pathways in Eukaryotes, Genome Research, vol.13, issue.5, pp.875-82, 2003.
DOI : 10.1101/gr.737703

J. Leonard, R. Wayne, J. Wheeler, R. Valadez, S. Guillen et al., Ancient DNA evidence for Old World origin of New World dogs. Science, pp.1613-1619, 2002.

E. Louis, Evolutionary genetics: Making the most of redundancy, Nature, vol.409, issue.7163, pp.673-677, 2007.
DOI : 10.1038/449673a

M. Lynch and J. Conery, The Evolutionary Fate and Consequences of Duplicate Genes, Science, vol.290, issue.5494, 2000.
DOI : 10.1126/science.290.5494.1151

M. Lynch and A. Force, The probability of duplicate gene preservation by subfunctionalization, Genetics, vol.154, issue.1, pp.459-73, 2000.

E. Margulies, J. Vinson, . Nisc-comparative-sequencing, . Program, W. Miller et al., An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing, Proceedings of the National Academy of Sciences, vol.102, issue.13, pp.4795-800, 2005.
DOI : 10.1073/pnas.0409882102

S. Mckay, R. Schnabel, B. Murdoch, J. Aerts, C. Gill et al., Construction of bovine wholegenome radiation hybrid and linkage maps using high-throughput genotyping, Anim Genet, 2007.

C. Mellersh, C. Hitte, M. Richman, F. Vignaux, C. Priat et al., An integrated linkage-radiation hybrid map of the canine genome, Mammalian Genome, vol.11, issue.2, pp.120-150, 2000.
DOI : 10.1007/s003350010024

M. Menotti-raymond, V. David, R. Agarwala, A. Schaffer, R. Stephens et al., Radiation hybrid mapping of 304 novel microsatellites in the domestic cat genome, Cytogenetic and Genome Research, vol.102, issue.1-4, pp.1-4272, 2003.
DOI : 10.1159/000075762

J. Meunier and L. Duret, Recombination Drives the Evolution of GC-Content in the Human Genome, Molecular Biology and Evolution, vol.21, issue.6
DOI : 10.1093/molbev/msh070
URL : https://hal.archives-ouvertes.fr/hal-00427624

E. Mignot, R. Bell, C. Rattazzi, M. Lovett, F. Grumet et al., An Immunoglobulin Switchlike Sequence Is Linked With Canine Narcolepsy, Sleep, vol.17, issue.suppl_8, pp.68-76, 1994.
DOI : 10.1093/sleep/17.suppl_8.S68

T. Mikkelsen, M. Wakefield, B. Aken, C. Amemiya, J. Chang et al., Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences, Nature, vol.22, issue.7141, pp.167-77, 2007.
DOI : 10.1038/nature05805

W. Miller, K. Makova, A. Nekrutenko, and R. Hardison, COMPARATIVE GENOMICS, Annual Review of Genomics and Human Genetics, vol.5, issue.1, pp.15-56, 2004.
DOI : 10.1146/annurev.genom.5.061903.180057

M. Genome, S. Consortium, R. Waterston, K. Lindblad-toh, E. Birney et al., Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, issue.6915, pp.520-62, 2002.

C. Muller, M. Denis, L. Gentzbittel, and T. Faraut, The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species, Nucleic Acids Research, vol.32, issue.Web Server, pp.429-463, 2004.
DOI : 10.1093/nar/gkh460

W. Murphy, D. Larkin, A. Everts-van-der-wind, G. Bourque, G. Tesler et al., Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science, pp.613-620, 2005.

J. Nadeau and B. Taylor, Lengths of chromosomal segments conserved since divergence of man and mouse., Proceedings of the National Academy of Sciences, vol.81, issue.3, pp.814-822, 1984.
DOI : 10.1073/pnas.81.3.814

M. Neff, K. Broman, C. Mellersh, K. Ray, G. Acland et al., A second-generation genetic linkage map of the domestic dog, Canis familiaris, Genetics . Feb, vol.151, issue.2, pp.803-823, 1999.

M. Nei, X. Gu, and T. Sitnikova, Evolution by the birth-and-death process in multigene families of the vertebrate immune system, Proceedings of the National Academy of Sciences, vol.94, issue.15, pp.7799-806, 1997.
DOI : 10.1073/pnas.94.15.7799

M. Nei and A. Rooney, Concerted and Birth-and-Death Evolution of Multigene Families, Annual Review of Genetics, vol.39, issue.1, pp.121-52, 2005.
DOI : 10.1146/annurev.genet.39.073003.112240

A. Novozhilov, G. Karev, and E. Koonin, Biological applications of the theory of birth-and-death processes. Brief Bioinform, Review, vol.7, issue.1, pp.70-85, 2006.

O. Brien, K. Remm, M. Sonnhammer, and E. , Inparanoid: a comprehensive database of eukaryotic orthologs, Nucleic Acids Research, vol.33, issue.Database issue, pp.476-80, 2005.
DOI : 10.1093/nar/gki107

O. Brien, S. Menotti-raymond, M. Murphy, W. Nash, W. Wienberg et al., The Promise of Comparative Genomics in Mammals, Science, vol.286, issue.5439, pp.458-62, 1999.
DOI : 10.1126/science.286.5439.458

R. Owen, On the Archetype and Homologies of the Vertebrate Skeleton, p.1848
DOI : 10.5962/bhl.title.118611

R. Page and M. Charleston, From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem, Molecular Phylogenetics and Evolution, vol.7, issue.2, pp.231-271, 1997.
DOI : 10.1006/mpev.1996.0390

X. Pan, L. Stein, and V. Brendel, SynBrowse: a synteny browser for comparative sequence analysis, Bioinformatics, vol.21, issue.17, pp.3461-3469, 2005.
DOI : 10.1093/bioinformatics/bti555

H. Parker, L. Kim, N. Sutter, S. Carlson, T. Lorentzen et al., Genetic structure of the purebred domestic dog. Science, pp.1160-1164, 2004.

E. Passarge, B. Horsthemke, and R. Farber, Incorrect use of the term synteny, Nat Genet, 1999.

P. Pevzner and G. Tesler, Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes, Genome Research, vol.13, issue.1, pp.37-45, 2003.
DOI : 10.1101/gr.757503

P. Pevzner and G. Tesler, Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution, Proceedings of the National Academy of Sciences, vol.100, issue.13, pp.7672-7679, 2003.
DOI : 10.1073/pnas.1330369100

K. Pollard, S. Salama, N. Lambert, M. Lambot, S. Coppens et al., An RNA gene expressed during cortical development evolved rapidly in humans, Nature, vol.12, issue.7108, pp.167-72, 2006.
DOI : 10.1038/nature05113

S. Potter, L. Clarke, V. Curwen, S. Keenan, E. Mongin et al., The Ensembl Analysis Pipeline, Genome Research, vol.14, issue.5, pp.934-975, 2004.
DOI : 10.1101/gr.1859804

J. Poyatos and L. Hurst, Is optimal gene order impossible? Trends Genet, Epub, vol.22, issue.8, pp.420-423, 2006.

C. Priat, Z. Jiang, C. Renier, C. Andr, and F. Galibert, Characterization of 463 Type I markers suitable for dog genome mapping, Mammalian Genome, vol.10, issue.8, pp.803-816, 1999.
DOI : 10.1007/s003359901095

K. Pruitt, T. Tatusova, and D. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res, 2007.

N. Putnam, M. Srivastava, U. Hellsten, B. Dirks, J. Chapman et al., Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization, Science, vol.317, issue.5834, pp.86-94, 2007.
DOI : 10.1126/science.1139158

P. Quignon, M. Giraud, M. Rimbault, P. Lavigne, S. Tacher et al., The dog and rat olfactory receptor repertoires, Genome Biology, vol.6, issue.10, pp.83-16207354, 2005.
DOI : 10.1186/gb-2005-6-10-r83
URL : https://hal.archives-ouvertes.fr/hal-00107100

T. Raudsepp, L. Fronicke, H. Scherthan, I. Gustavsson, and B. Chowdhary, Zoo-FISH delineates conserved chromosomal segments in horse and man, Chromosome Research, vol.24, issue.3, pp.218-243, 1996.
DOI : 10.1007/BF02254963

M. Reese and R. Guigo, EGASP: Introduction, Genome Biol, vol.7, 2006.

M. Remm, C. Storm, and E. Sonnhammer, Automatic clustering of orthologs and in-paralogs from pairwise species comparisons, Journal of Molecular Biology, vol.314, issue.5, pp.1041-52, 2001.
DOI : 10.1006/jmbi.2000.5197

M. Rhodes, R. Straw, S. Fernando, A. Evans, T. Lacey et al., A high-resolution microsatellite map of the mouse genome, Genome Res, vol.8, issue.5, pp.531-573, 1998.

P. Savolainen, Y. Zhang, J. Luo, J. Lundeberg, and T. Leitner, Genetic Evidence for an East Asian Origin of Domestic Dogs, Science, vol.298, issue.5598, pp.1610-1613, 2002.
DOI : 10.1126/science.1073906

D. Scannell, K. Byrne, J. Gordon, S. Wong, and K. Wolfe, Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts, Nature, vol.102, issue.7082, pp.341-346, 2006.
DOI : 10.1038/nature04562

H. Scherthan, D. Schweizer, and J. Loidl, Delineation of individual chromosomes of Saccharomyces cerevisiae by two-colour in situ hybridization, Trends Genet. Feb, vol.9, issue.2, pp.41-8456499, 1993.

S. Schwartz, W. Kent, A. Smit, Z. Zhang, R. Baertsch et al., Human-Mouse Alignments with BLASTZ, Genome Research, vol.13, issue.1, pp.103-7786, 2003.
DOI : 10.1101/gr.809403

M. Semon and L. Duret, Evolutionary Origin and Maintenance of Coexpressed Gene Clusters in Mammals, Molecular Biology and Evolution, vol.23, issue.9, pp.1715-1738, 2006.
DOI : 10.1093/molbev/msl034
URL : https://hal.archives-ouvertes.fr/hal-00428012

A. Siepel, G. Bejerano, J. Pedersen, A. Hinrichs, M. Hou et al., Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Research, vol.15, issue.8, pp.1034-50, 2005.
DOI : 10.1101/gr.3715005
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182216

A. Sinha and J. Meller, Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms, BMC Bioinformatics, vol.8, issue.1, pp.82-17343765, 2007.
DOI : 10.1186/1471-2105-8-82

G. Slater and E. Birney, Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics Feb, vol.156, pp.31-15713233, 2005.

E. Sonnhammer and E. Koonin, Orthology, paralogy and proposed classification for paralog subtypes, Trends in Genetics, vol.18, issue.12, pp.619-639, 2002.
DOI : 10.1016/S0168-9525(02)02793-2

H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori, and Y. Tateno, DDBJ with new system and face, Nucleic Acids Research, vol.36, issue.Database, p.17962300, 2007.
DOI : 10.1093/nar/gkm889

S. Ohno, Evolution by gene duplication, 1970.
DOI : 10.1007/978-3-642-86659-3

N. Sutter, C. Bustamante, K. Chase, M. Gray, K. Zhao et al., A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs, Science, vol.316, issue.5821, pp.112-117, 2007.
DOI : 10.1126/science.1137045

K. Tanimoto, Q. Liu, J. Bungert, and J. Engel, Effects of altered gene order or orientation of the locus control region on human ??-globin gene expression in mice, Nature, vol.95, issue.6725, pp.344-352, 1999.
DOI : 10.1038/18698

R. Tatusov, D. Natale, I. Garkavtsev, T. Tatusova, U. Shankavaram et al., The COG database: new developments in phylogenetic classification of proteins from complete genomes, Nucleic Acids Research, vol.29, issue.1, pp.22-30, 2001.
DOI : 10.1093/nar/29.1.22

G. Tesler, GRIMM: genome rearrangements web server, Bioinformatics, vol.18, issue.3, 2002.
DOI : 10.1093/bioinformatics/18.3.492

M. Van-baren and M. Brent, Iterative gene prediction and pseudogene removal improves genome annotation, Genome Research, vol.16, issue.5, pp.678-85, 2006.
DOI : 10.1101/gr.4766206

A. Varshavsky, ???Spalog??? and ???sequelog???: neutral terms for spatial and sequence similarity, Current Biology, vol.14, issue.5, pp.181-184, 2004.
DOI : 10.1016/j.cub.2004.02.014
URL : http://doi.org/10.1016/j.cub.2004.02.014

J. Venter, M. Adams, E. Myers, P. Li, R. Mural et al., The sequence of the human genome, Science. Feb, vol.16291, issue.5507, pp.1304-51, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00465088

C. Vila, P. Savolainen, J. Maldonado, I. Amorim, J. Rice et al., Multiple and Ancient Origins of the Domestic Dog, Science, vol.276, issue.5319, pp.1687-1696, 1997.
DOI : 10.1126/science.276.5319.1687

C. Vila, J. Seddon, and H. Ellegren, Genes of domestic mammals augmented by backcrossing with wild ancestors, Trends in Genetics, vol.21, issue.4, pp.214-222, 2005.
DOI : 10.1016/j.tig.2005.02.004

D. Wall, H. Fraser, and A. Hirsh, Detecting putative orthologs, Bioinformatics, vol.19, issue.13, pp.1710-1711, 2003.
DOI : 10.1093/bioinformatics/btg213

M. Wang, J. Buhler, and M. Brent, The Effects of Evolutionary Distance on TWINSCAN, an Algorithm for Pair-wise Comparative Gene Prediction, Cold Spring Harbor Symposia on Quantitative Biology, vol.8, issue.0, pp.125-155, 2003.
DOI : 10.1101/gr.703903

W. Wang and E. Kirkness, Short interspersed elements (SINEs) are a major source of canine genomic diversity, Genome Research, vol.15, issue.12, pp.1798-808, 2005.
DOI : 10.1101/gr.3765505

J. Watson and F. Crick, Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid, Nature, vol.9, issue.4356, pp.737-745, 1953.
DOI : 10.1016/0006-3002(53)90232-7

R. Wayne and E. Ostrander, Lessons learned from the dog genome, Trends in Genetics, vol.23, issue.11, p.17963975, 2007.
DOI : 10.1016/j.tig.2007.08.013

J. Weissenbach, G. Gyapay, C. Dib, A. Vignal, J. Morissette et al., A second-generation linkage map of the human genome, Nature, vol.359, issue.6398, pp.794-801, 1992.
DOI : 10.1038/359794a0

D. Wheeler, D. Church, A. Lash, D. Leipe, T. Madden et al., Database resources of the National Center for Biotechnology Information: 2002 update, Nucleic Acids Research, vol.30, issue.1, pp.13-19, 2002.
DOI : 10.1093/nar/30.1.13

M. Wilkins, A. Stokes, and H. Wilson, Molecular structure of deoxypentose nucleic acids, Nature . Apr, vol.25171, issue.4356, pp.738-778, 1953.

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, 2007.
DOI : 10.1093/molbev/msm088

Z. Yang, PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-561, 1997.
DOI : 10.1093/bioinformatics/13.5.555

D. Zheng and M. Gerstein, A computational approach for identifying pseudogenes in the EN- CODE regions, Genome Biol, vol.7, 2006.