M. Kemler, M. Lutz, M. Göker, F. Oberwinkler, and D. Begerow, (Pucciniomycotina: Microbotryales), Systematics and Biodiversity, vol.67, issue.3, pp.297-306, 2009.
DOI : 10.1017/S0953756201004713

D. Vienne, D. Hood, M. Giraud, and T. , Phylogenetic determinants of potential host shifts in fungal pathogens, Journal of Evolutionary Biology, vol.53, issue.12, pp.2532-2573, 2009.
DOI : 10.1111/j.1420-9101.2009.01878.x

L. Gac, M. Hood, M. Fournier, E. , and G. T. , PHYLOGENETIC EVIDENCE OF HOST-SPECIFIC CRYPTIC SPECIES IN THE ANTHER SMUT FUNGUS, Evolution, vol.18, issue.1, pp.15-26, 2007.
DOI : 1010-061X(2005)018[0203:HRDITA]2.0.CO;2

L. Gac, M. Hood, M. Giraud, and T. , EVOLUTION OF REPRODUCTIVE ISOLATION WITHIN A PARASITIC FUNGAL SPECIES COMPLEX, Evolution, vol.40, issue.7, pp.1781-1788, 2007.
DOI : 10.1554/0014-3820(2003)057[0766:ICAMBF]2.0.CO;2

T. Giraud, R. Yockteng, M. Lopez-villavicencio, G. Refregier, and M. Hood, Mating System of the Anther Smut Fungus Microbotryum violaceum: Selfing under Heterothallism, Eukaryotic Cell, vol.7, issue.5, pp.765-75, 2008.
DOI : 10.1128/EC.00440-07

A. Gibson, M. Hood, and T. Giraud, SIBLING COMPETITION ARENA: SELFING AND A COMPETITION ARENA CAN COMBINE TO CONSTITUTE A BARRIER TO GENE FLOW IN SYMPATRY, Evolution, vol.55, issue.6, pp.1917-1947, 2012.
DOI : 10.1111/j.1558-5646.2011.01563.x

H. Alexander, An Experimental Field Study of Anther-Smut Disease of Silene alba Caused by Ustilago violacea: Genotypic Variation and Disease Incidence, Evolution, vol.43, issue.4, pp.835-882, 1989.
DOI : 10.2307/2409311

J. Antonovics, M. Hood, and J. Partain, The Ecology and Genetics of a Host Shift: Microbotryum as a Model System, The American Naturalist, vol.160, issue.4, pp.40-53, 2002.
DOI : 10.2307/3079268

G. Refrégier, L. Gac, M. Jabbour, F. Widmer, A. Shykoff et al., Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation, BMC Evolutionary Biology, vol.8, issue.1, p.100, 2008.
DOI : 10.1186/1471-2148-8-100

M. Hood, J. Antonovics, and B. Koskella, Shared Forces of Sex Chromosome Evolution in Haploid-Mating and Diploid-Mating Organisms: Microbotryum violaceum and Other Model Organisms, Genetics, vol.168, issue.1, pp.141-147, 2004.
DOI : 10.1534/genetics.104.029900

M. Hood, E. Petit, and G. T. , Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus, Genetics, vol.193, issue.1, pp.309-324, 2013.
DOI : 10.1534/genetics.112.146266

B. Roche, H. Alexander, and A. Maltby, Dispersal and Disease Gradients of Anther-Smut Infection of Silene Alba at Different Life Stages, Ecology, vol.76, issue.6, pp.1863-71, 1995.
DOI : 10.2307/1940719

O. Jennersten, Butterfly Visitors as Vectors of Ustilago violacea Spores between Caryophyllaceous Plants, Oikos, vol.40, issue.1, pp.125-155, 1983.
DOI : 10.2307/3544207

S. Akhter and J. Antonovics, Use of internal transcribed spacer primers and fungicide treatments to study the anther-smut disease, Microbotryum violaceum (=Ustilago violacea)

J. Kokontis and M. Ruddat, Promotion of hyphal growth in Ustilago violacea by host factors from Silene alba, Archives of Microbiology, vol.2, issue.3, pp.302-308, 1986.
DOI : 10.1007/BF00410967

J. Kokontis and M. Ruddat, Enzymatic Hydrolysis of Hyphal Growth Factors for Ustilago violacea Isolated from the Host Plant Silene alba, Botanical Gazette, vol.150, issue.4, pp.439-483, 1989.
DOI : 10.1086/337789

H. Alexander and J. Antonovics, Spread of Anther-Smut Disease (Ustilago Violacea) and Character Correlations in a Genetically Variable Experimental Population of Silene Alba, The Journal of Ecology, vol.83, issue.5, pp.783-94, 1995.
DOI : 10.2307/2261415

S. Robertson, Y. Li, C. Scutt, M. Willis, and P. Gilmartin, Spatial expression dynamics of Men-9 delineate the third floral whorl in male and female flowers of dioecious Silene latifolia, The Plant Journal, vol.12, issue.1, pp.155-68, 1997.
DOI : 10.1046/j.1365-313X.1997.12010155.x

Y. Kazama, A. Koizumi, W. Uchida, A. Ageez, and S. Kawano, Expression of the Floral B-function Gene SLM2 in Female Flowers of Silene latifolia Infected with the Smut Fungus Microbotryum violaceum, Plant and Cell Physiology, vol.46, issue.5, pp.806-817, 2005.
DOI : 10.1093/pcp/pci080

S. Billiard, M. López-villavicencio, B. Devier, M. Hood, C. Fairhead et al., Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types, Biological Reviews, vol.44, issue.2, pp.421-463, 2011.
DOI : 10.1111/j.1469-185X.2010.00153.x
URL : https://hal.archives-ouvertes.fr/hal-00609575

S. Billiard, M. López-villavicencio, M. Hood, and T. Giraud, Sex, outcrossing and mating types: unsolved questions in fungi and beyond, Journal of Evolutionary Biology, vol.5, issue.11, pp.1020-1058, 2012.
DOI : 10.1111/j.1420-9101.2012.02495.x
URL : https://hal.archives-ouvertes.fr/hal-00690911

J. Fraser and J. Heitman, Evolution of fungal sex chromosomes, Molecular Microbiology, vol.15, issue.2, pp.299-306, 2004.
DOI : 10.1046/j.1365-2958.2003.03874.x

J. Fraser, Y. Hsueh, K. Findley, J. Heitman, J. Heitman et al., Evolution of the Mating-Type Locus: The Basidiomycetes, Sex in Fungi, pp.19-34, 2007.
DOI : 10.1128/9781555815837.ch2

A. Menkis, D. Jacobson, T. Gustafsson, and H. Johannesson, The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes, PLoS Genetics, vol.19, issue.3, 2008.
DOI : 10.1371/journal.pgen.1000030.s002

M. Hood, Dimorphic mating-type chromosomes in the fungus Microbotryum violaceum, Genetics, vol.160, pp.457-61, 2002.

M. Hood and J. Antonovics, Intratetrad mating, heterozygosity, and the maintenance of deleterious alleles in Microbotryum violaceum (=Ustilago violacea), Heredity, vol.22, issue.3, pp.231-272, 2000.
DOI : 10.1086/297470

M. Hood, Repetitive DNA in the automictic fungus Microbotryum violaceum, Genetica, vol.5, issue.1, pp.1-10, 2005.
DOI : 10.1007/s10709-004-6615-y

C. Whittle, Y. Sun, and H. Johannesson, Degeneration in Codon Usage within the Region of Suppressed Recombination in the Mating-Type Chromosomes of Neurospora tetrasperma, Eukaryotic Cell, vol.10, issue.4, pp.594-603, 2011.
DOI : 10.1128/EC.00284-10

C. Whittle and H. Johannesson, Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma, Heredity, vol.155, issue.4, pp.305-319, 2011.
DOI : 10.1093/molbev/msm088

E. Fontanillas, M. Hood, H. Badouin, E. Petit, V. Barbe et al., Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi, Molecular Biology and Evolution, vol.32, issue.4, pp.928-971, 2014.
DOI : 10.1093/molbev/msu396
URL : https://hal.archives-ouvertes.fr/hal-01302682

I. Farbos, M. Oliveira, I. Negrutiu, and A. Mouras, Sex organ determination and differentiation in the dioecious plant Melandrium album ( Silene latifolia ): a cytological and histological analysis, Sexual Plant Reproduction, vol.10, issue.3, pp.155-67, 1997.
DOI : 10.1007/s004970050083

S. Grant, B. Hunkirchen, and H. Saedler, Developmental differences between male and female flowers in the dioecious plant Silene latifolia, The Plant Journal, vol.6, issue.4, pp.471-80, 1994.
DOI : 10.1046/j.1365-313X.1994.6040471.x

G. Parra, K. Bradnam, and I. Korf, CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, vol.23, issue.9, pp.1061-1068, 2007.
DOI : 10.1093/bioinformatics/btm071

T. Rouxel, J. Grandaubert, J. Hane, C. Hoede, A. Van-de-wouw et al., Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations, Nature Communications, vol.19, p.202, 2011.
DOI : 10.1105/tpc.107.052829
URL : https://hal.archives-ouvertes.fr/hal-00841751

L. Duret and N. Galtier, Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes, Annual Review of Genomics and Human Genetics, vol.10, issue.1, pp.285-311, 2009.
DOI : 10.1146/annurev-genom-082908-150001
URL : https://hal.archives-ouvertes.fr/hal-00428399

S. Duplessis, C. Cuomo, Y. Lin, A. Aerts, E. Tisserant et al., Obligate biotrophy features unraveled by the genomic analysis of rust fungi, Proceedings of the National Academy of Sciences, vol.108, issue.22, pp.9166-71, 2011.
DOI : 10.1073/pnas.1019315108
URL : https://hal.archives-ouvertes.fr/hal-01000169

R. Yockteng, S. Marthey, H. Chiapello, A. Gendrault, M. Hood et al., Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes, BMC Genomics, vol.8, issue.1, p.272, 2007.
DOI : 10.1186/1471-2164-8-272

V. Kapitonov and J. Jurka, Rolling-circle transposons in eukaryotes, Proceedings of the National Academy of Sciences, vol.98, issue.15, pp.8714-8723, 2001.
DOI : 10.1073/pnas.151269298

B. Haas, S. Kamoun, M. Zody, R. Jiang, R. Handsaker et al., Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans, Nature, vol.10, issue.7262, pp.393-401, 2009.
DOI : 10.1038/nature08358

P. Gladieux, J. Ropars, H. Badouin, A. Branca, G. Aguileta et al., Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes, Molecular Ecology, vol.7, issue.4, pp.753-73, 2014.
DOI : 10.1111/mec.12631
URL : https://hal.archives-ouvertes.fr/hal-01302695

M. Hood, M. Katawczik, and G. T. , Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum, Genetics, vol.170, issue.3, pp.1081-1090, 2005.
DOI : 10.1534/genetics.105.042564

F. Horns, E. Petit, R. Yockteng, and M. Hood, Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi, Genome Biology and Evolution, vol.4, issue.3, pp.240-247, 2012.
DOI : 10.1093/gbe/evs005

E. Cambareri, B. Jensen, E. Schabtach, and E. Selker, Repeat-induced G-C to A-T mutations in Neurospora, Science, vol.244, issue.4912, pp.1571-1576, 1989.
DOI : 10.1126/science.2544994

E. Selker, E. Cambareri, B. Jensen, and K. Haack, Rearrangement of duplicated DNA in specialized cells of Neurospora, Cell, vol.51, issue.5, pp.741-52, 1987.
DOI : 10.1016/0092-8674(87)90097-3

J. Walser and A. Furano, The mutational spectrum of non-CpG DNA varies with CpG content, Genome Research, vol.20, issue.7, pp.875-82, 2010.
DOI : 10.1101/gr.103283.109

K. Fryxell and W. Moon, CpG Mutation Rates in the Human Genome Are Highly Dependent on Local GC Content, Molecular Biology and Evolution, vol.22, issue.3, pp.650-658, 2005.
DOI : 10.1093/molbev/msi043

C. Jiang and Z. Zhao, Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome, BMC Genomics, vol.7, issue.1, p.316, 2006.
DOI : 10.1186/1471-2164-7-316

B. Morton, I. Bi, M. Mcmullen, and B. Gaut, Variation in Mutation Dynamics Across the Maize Genome as a Function of Regional and Flanking Base Composition, Genetics, vol.172, issue.1, pp.569-77, 2006.
DOI : 10.1534/genetics.105.049916

J. Amselem, M. Lebrun, and H. Quesneville, Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes, BMC Genomics, vol.16, issue.1, p.141, 2015.
DOI : 10.1186/1471-2105-7-439
URL : https://hal.archives-ouvertes.fr/hal-01142763

A. Zemach, I. Mcdaniel, P. Silva, and D. Zilberman, Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation, Science, vol.328, issue.5980, pp.916-925, 2010.
DOI : 10.1126/science.1186366

F. Nicolás, S. Torres-martínez, and R. Ruiz-vázquez, Loss and Retention of RNA Interference in Fungi and Parasites, PLoS Pathogens, vol.331, issue.1, p.1003089, 2013.
DOI : 10.1371/journal.ppat.1003089.g001

E. Petit, T. Giraud, D. De-vienne, M. Coelho, G. Aguileta et al., : INSIGHTS INTO NONRECOMBINING CHROMOSOMES, Evolution, vol.22, issue.Suppl. 1, pp.3519-3552, 2012.
DOI : 10.1111/j.1558-5646.2012.01703.x

B. Gillissen, J. Bergemann, C. Sandmann, B. Schroeer, M. Bölker et al., A two-component regulatory system for self/non-self recognition in Ustilago maydis, Cell, vol.68, issue.4, pp.647-57, 1992.
DOI : 10.1016/0092-8674(92)90141-X

B. Devier, G. Aguileta, M. Hood, and T. Giraud, Ancient Trans-specific Polymorphism at Pheromone Receptor Genes in Basidiomycetes, Genetics, vol.181, issue.1, pp.209-232, 2009.
DOI : 10.1534/genetics.108.093708

A. Votintseva and D. Filatov, Evolutionary Strata in a Small Mating-Type-Specific Region of the Smut Fungus Microbotryum violaceum, Genetics, vol.182, issue.4, pp.1391-1397, 2009.
DOI : 10.1534/genetics.109.103192

D. Bachtrog, Accumulation of Spock and Worf, Two Novel Non-LTR Retrotransposons, on the Neo-Y Chromosome of Drosophila miranda, Molecular Biology and Evolution, vol.20, issue.2
DOI : 10.1093/molbev/msg035

E. Elhaik, G. Landan, and D. Braur, Can GC Content at Third-Codon Positions Be Used as a Proxy for Isochore Composition?, Molecular Biology and Evolution, vol.26, issue.8, pp.1829-1862, 2009.
DOI : 10.1093/molbev/msp100

J. Klose, M. De-sá, and J. Kronstad, Lipid-induced filamentous growth in Ustilago maydis, Molecular Microbiology, vol.10, issue.3, pp.823-858, 2004.
DOI : 10.1111/j.1365-2958.2004.04019.x

M. Suh, A. Samuels, R. Jetter, L. Kunst, M. Pollard et al., Cuticular Lipid Composition, Surface Structure, and Gene Expression in Arabidopsis Stem Epidermis, PLANT PHYSIOLOGY, vol.139, issue.4, pp.1649-65, 2005.
DOI : 10.1104/pp.105.070805

V. Lombard, G. Ramulu, H. Drula, E. Coutinho, P. Henrissat et al., The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Research, vol.42, issue.D1, pp.490-495, 2014.
DOI : 10.1093/nar/gkt1178

B. Cantarel, P. Coutinho, C. Rancurel, T. Bernard, V. Lombard et al., The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Nucleic Acids Research, vol.37, issue.Database, pp.233-241, 2009.
DOI : 10.1093/nar/gkn663

R. Riley, A. Salamov, D. Brown, L. Nagy, D. Floudas et al., Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi, Proceedings of the National Academy of Sciences, vol.111, issue.27, pp.9923-9931, 2014.
DOI : 10.1073/pnas.1400592111

H. Prillinger, G. Deml, C. Dörfler, G. Laaser, and W. Lockau, -Typ, Botanica Acta, vol.42, issue.suppl., pp.5-17, 1991.
DOI : 10.1111/j.1438-8677.1991.tb00188.x

H. Roeijmans, H. Prillinger, C. Umile, J. Sugiyama, T. Nakase et al., Analysis of carbohydrate composition of cell walls and extracellular carbohydrates The Yeasts -A Taxonomic Study, pp.103-105, 1998.

A. Liepman, C. Nairn, W. Willats, I. Sørensen, A. Roberts et al., Functional Genomic Analysis Supports Conservation of Function Among Cellulose Synthase-Like A Gene Family Members and Suggests Diverse Roles of Mannans in Plants, PLANT PHYSIOLOGY, vol.143, issue.4, pp.1881-93, 2007.
DOI : 10.1104/pp.106.093989

N. Alexander, S. Mccormick, and T. Hohn, TRI12, a trichothecene efflux pump from Fusarium sporotrichioides : gene isolation and expression in yeast, Molecular and General Genetics MGG, vol.261, issue.6, pp.977-84, 1999.
DOI : 10.1007/s004380051046

R. Wahl, K. Wippel, S. Goos, J. Kämper, and N. Sauer, A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis, PLoS Biology, vol.22, issue.2, 2010.
DOI : 10.1371/journal.pbio.1000303.s007

R. Voegele, C. Struck, M. Hahn, and K. Mendgen, The role of haustoria in sugar supply during infection of broad bean by the rust fungus Uromyces fabae, Proceedings of the National Academy of Sciences, vol.98, issue.14, pp.8133-8141, 2001.
DOI : 10.1073/pnas.131186798

M. Moccia, C. Oger-desfeux, G. Marais, and A. Widmer, A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping, BMC Genomics, vol.10, issue.1, p.243, 2009.
DOI : 10.1186/1471-2164-10-243
URL : https://hal.archives-ouvertes.fr/hal-00428361

C. Veneault-fourrey, C. Commun, A. Kohler, E. Morin, R. Balestrini et al., Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment, Fungal Genetics and Biology, vol.72, pp.168-81, 2014.
DOI : 10.1016/j.fgb.2014.08.007
URL : https://hal.archives-ouvertes.fr/hal-01123254

J. Antoniw, C. Ritter, W. Pierpoint, and L. Loon, Comparison of Three Pathogenesis-related Proteins from Plants of Two Cultivars of Tobacco Infected with TMV, Journal of General Virology, vol.47, issue.1, pp.79-87, 1980.
DOI : 10.1099/0022-1317-47-1-79

P. Baldrian, Fungal laccases ??? occurrence and properties, FEMS Microbiology Reviews, vol.30, issue.2, pp.215-257, 2006.
DOI : 10.1111/j.1574-4976.2005.00010.x

T. Takahashi and J. Kakehi, Polyamines: ubiquitous polycations with unique roles in growth and stress responses, Annals of Botany, vol.105, issue.1, pp.1-6, 2010.
DOI : 10.1093/aob/mcp259

N. Brose, A. Betz, and H. Wegmeyer, Divergent and convergent signaling by the diacylglycerol second messenger pathway in mammals, Current Opinion in Neurobiology, vol.14, issue.3, pp.328-368, 2004.
DOI : 10.1016/j.conb.2004.05.006

W. Dong, H. Lv, G. Xia, and M. Wang, Does diacylglycerol serve as a signaling molecule in plants?, Plant Signaling & Behavior, vol.7, issue.4, pp.472-477, 2012.
DOI : 10.1016/j.chemphyslip.2007.04.003

I. Stergiopoulos and P. De-wit, Fungal Effector Proteins, Annual Review of Phytopathology, vol.47, issue.1, pp.233-63, 2009.
DOI : 10.1146/annurev.phyto.112408.132637

R. Bauer, F. Oberwinkler, and K. Vanky, Ultrastructural markers and systematics in smut fungi and allied taxa, Canadian Journal of Botany, vol.75, issue.8, pp.1273-314, 1997.
DOI : 10.1139/b97-842

G. Palmieri, C. Bianco, G. Cennamo, P. Giardina, G. Marino et al., Purification, Characterization, and Functional Role of a Novel Extracellular Protease from Pleurotus ostreatus, Applied and Environmental Microbiology, vol.67, issue.6, pp.2754-2763, 2001.
DOI : 10.1128/AEM.67.6.2754-2759.2001

G. Palmieri, G. Cennamo, V. Faraco, A. Amoresano, G. Sannia et al., Atypical laccase isoenzymes from copper supplemented Pleurotus ostreatus cultures, Enzyme and Microbial Technology, vol.33, issue.2-3, pp.220-250, 2003.
DOI : 10.1016/S0141-0229(03)00117-0

M. Whittaker, P. Kersten, D. Cullen, and J. Whittaker, Identification of Catalytic Residues in Glyoxal Oxidase by Targeted Mutagenesis, Journal of Biological Chemistry, vol.274, issue.51, pp.36226-36258, 1999.
DOI : 10.1074/jbc.274.51.36226

E. Luttrell, Tissue Replacement Diseases Caused by Fungi, Annual Review of Phytopathology, vol.19, issue.1, pp.373-89, 1981.
DOI : 10.1146/annurev.py.19.090181.002105

N. Cashion and E. Luttrell, Host-Parasite Relationships in Karnal Bunt of Wheat, Phytopathology, vol.78, issue.1, pp.75-84, 1988.
DOI : 10.1094/Phyto-78-75

C. Biémont, A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution, Genetics, vol.186, issue.4, pp.1085-93, 2010.
DOI : 10.1534/genetics.110.124180

S. Schmidt, P. Houterman, I. Schreiver, L. Ma, S. Amyotte et al., MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum, BMC Genomics, vol.14, issue.1, p.119, 2013.
DOI : 10.1128/JVI.06801-11

S. Otto, J. Pannell, C. Peichel, T. Ashman, D. Charlesworth et al., About PAR: The distinct evolutionary dynamics of the pseudoautosomal region, Trends in Genetics, vol.27, issue.9, pp.358-67, 2011.
DOI : 10.1016/j.tig.2011.05.001

H. Luo and M. Perlin, The ??-tubulin-encoding gene from the basidiomycete fungus, Ustilago violacea, has a long 5'-untranslated region, Gene, vol.137, issue.2, pp.187-94, 1993.
DOI : 10.1016/0378-1119(93)90005-N

J. Levin, M. Yassour, X. Adiconis, C. Nusbaum, D. Thompson et al., Comprehensive comparative analysis of strand-specific RNA sequencing methods, Nature Methods, vol.5, issue.9, pp.709-724, 2010.
DOI : 10.1038/nmeth.1491

D. Parkhomchuk, T. Borodina, V. Amstislavskiy, M. Banaru, L. Hallen et al., Transcriptome analysis by strand-specific sequencing of complementary DNA, Nucleic Acids Research, vol.37, issue.18, p.123, 2009.
DOI : 10.1093/nar/gkp596

M. Grabherr, B. Haas, M. Yassour, J. Levin, D. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-52, 2011.
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002

M. Borodovsky, A. Lomsadze, N. Ivanov, and R. Mills, Eukaryotic Gene Prediction Using GeneMark.hmm, Curr Protoc Bioinforma, vol.77, issue.4, pp.4-6, 2003.
DOI : 10.1002/0471250953.bi0406s01

M. Stanke, R. Steinkamp, S. Waack, and B. Morgenstern, AUGUSTUS: a web server for gene finding in eukaryotes, Nucleic Acids Research, vol.32, issue.Web Server, pp.309-321, 2004.
DOI : 10.1093/nar/gkh379

W. Majoros, M. Pertea, and S. Salzberg, TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders, Bioinformatics, vol.20, issue.16, pp.2878-2887, 2004.
DOI : 10.1093/bioinformatics/bth315

B. Haas, S. Salzberg, W. Zhu, M. Pertea, J. Allen et al., Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biology, vol.9, issue.1, p.7, 2008.
DOI : 10.1186/gb-2008-9-1-r7

E. Birney, M. Clamp, R. Durbin, and G. Genewise, GeneWise and Genomewise, Genome Research, vol.14, issue.5, pp.988-95, 2004.
DOI : 10.1101/gr.1865504

B. Haas, A. Papanicolaou, M. Yassour, M. Grabherr, P. Blood et al., De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nature Protocols, vol.500, issue.8, pp.1494-512, 2013.
DOI : 10.1038/ng.2295

B. Langmead, C. Trapnell, M. Pop, and S. Salzberg, Ultrafast and memoryefficient alignment of short DNA sequences to the human genome

B. Li and C. Dewey, RSEM, BMC Bioinformatics, vol.12, p.323, 2011.
DOI : 10.1201/b16589-5

M. Robinson, D. Mccarthy, and G. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-179, 2009.
DOI : 10.1093/bioinformatics/btp616

K. Kadota, T. Nishiyama, and K. Shimizu, A normalization strategy for comparing tag count data, Algorithms for Molecular Biology, vol.7, issue.1, p.5, 2012.
DOI : 10.1186/gb-2004-5-10-r80

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Stat Soc Ser B Methodol, vol.57, pp.289-300, 1995.

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering Transposable Element Diversification in De Novo Annotation Approaches, PLoS ONE, vol.25, issue.3, p.16526, 2011.
DOI : 10.1371/journal.pone.0016526.s021
URL : https://hal.archives-ouvertes.fr/hal-00568705

R. Edgar and E. Myers, PILER: identification and classification of genomic repeats, Bioinformatics, vol.21, issue.Suppl 1, pp.152-160, 2005.
DOI : 10.1093/bioinformatics/bti1003

H. Quesneville, C. Bergman, O. Andrieu, D. Autard, D. Nouaud et al., Combined Evidence Annotation of Transposable Elements in Genome Sequences, PLoS Computational Biology, vol.16, issue.2, pp.166-75, 2005.
DOI : 1367-4803(2000)016[1040:MAPETR]2.0.CO;2
URL : https://hal.archives-ouvertes.fr/hal-00009013

Z. Bao and S. Eddy, Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes, Genome Research, vol.12, issue.8, pp.1269-76, 2002.
DOI : 10.1101/gr.88502

J. Jurka, V. Kapitonov, A. Pavlicek, P. Klonowski, O. Kohany et al., Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and Genome Research, vol.110, issue.1-4, pp.462-469, 2005.
DOI : 10.1159/000084979

J. Hane and R. Oliver, RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences, BMC Bioinformatics, vol.9, issue.1, p.478, 2008.
DOI : 10.1186/1471-2105-9-478

M. Zytnicki and H. Quesneville, S-MART, A Software Toolbox to Aid RNA-seq Data Analysis, PLoS ONE, vol.6, issue.10, 2011.
DOI : 10.1371/journal.pone.0025988.g001

O. Emanuelsson, S. Brunak, G. Von-heijne, and H. Nielsen, Locating proteins in the cell using TargetP, SignalP and related tools, Nature Protocols, vol.22, issue.4, pp.953-71, 2007.
DOI : 10.1038/nprot.2007.131

J. Bendtsen, H. Nielsen, G. Von-heijne, and S. Brunak, Improved Prediction of Signal Peptides: SignalP 3.0, Journal of Molecular Biology, vol.340, issue.4, pp.783-95, 2004.
DOI : 10.1016/j.jmb.2004.05.028

T. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nature Methods, vol.6, issue.10, pp.785-791, 2011.
DOI : 10.1016/0005-2795(75)90109-9

A. Krogh, B. Larsson, G. Von-heijne, and E. Sonnhammer, Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-80, 2001.
DOI : 10.1006/jmbi.2000.4315

A. Pierleoni, P. Martelli, and R. Casadio, PredGPI: a GPI-anchor predictor, BMC Bioinformatics, vol.9, issue.1, p.392, 2008.
DOI : 10.1186/1471-2105-9-392

L. Käll, A. Krogh, and E. Sonnhammer, Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server, Nucleic Acids Research, vol.35, issue.Web Server, pp.429-461, 2007.
DOI : 10.1093/nar/gkm256

M. Brameier, A. Krings, and R. Maccallum, NucPred Predicting nuclear localization of proteins, Bioinformatics, vol.23, issue.9, pp.1159-60, 2007.
DOI : 10.1093/bioinformatics/btm066

C. Sigrist, L. Cerutti, E. De-castro, P. Langendijk-genevaux, V. Bulliard et al., PROSITE, a protein domain database for functional characterization and annotation, Nucleic Acids Research, vol.38, issue.Database, pp.161-167, 2010.
DOI : 10.1093/nar/gkp885

P. Horton, K. Park, T. Obayashi, N. Fujita, H. Harada et al., WoLF PSORT: protein localization predictor, Nucleic Acids Research, vol.35, issue.Web Server, pp.585-592, 2007.
DOI : 10.1093/nar/gkm259

U. Consortium, Ongoing and future developments at the Universal Protein Resource, Nucleic Acids Research, vol.39, issue.Database, pp.214-223, 2011.
DOI : 10.1093/nar/gkq1020

U. Consortium, Reorganizing the protein space at the Universal Protein Resource (UniProt), Nucleic Acids Research, vol.40, issue.D1, pp.71-76, 2012.
DOI : 10.1093/nar/gkr981

G. Lum and X. Min, FunSecKB: the Fungal Secretome KnowledgeBase, Database, vol.2011, issue.0, p.1, 2011.
DOI : 10.1093/database/bar001

L. Li, C. Stoeckert, and D. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-89, 2003.
DOI : 10.1101/gr.1224503

S. Eddy, Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011.
DOI : 10.1371/journal.pcbi.1002195.g006

A. Conesa, S. Gotz, J. Garcia-gomez, J. Terol, M. Talon et al., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, issue.18, pp.3674-3680, 2005.
DOI : 10.1093/bioinformatics/bti610

J. Huerta-cepas, S. Capella-gutierrez, L. Pryszcz, I. Denisov, D. Kormes et al., PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions, Nucleic Acids Research, vol.39, issue.Database, pp.556-60, 2011.
DOI : 10.1093/nar/gkq1109

J. Huerta-cepas and T. Gabaldón, Assigning duplication events to relative temporal scales in genome-wide studies, Bioinformatics, vol.27, issue.1, pp.38-45, 2011.
DOI : 10.1093/bioinformatics/btq609

R. Ohm, N. Feau, B. Henrissat, C. Schoch, B. Horwitz et al., Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi, PLoS Pathogens, vol.444, issue.1, p.1003037, 2012.
DOI : 10.1371/journal.ppat.1003037.s042

D. Floudas, M. Binder, R. Riley, K. Barry, R. Blanchette et al., The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes, Science, vol.336, issue.6089, pp.1715-1724, 2012.
DOI : 10.1126/science.1221748
URL : https://hal.archives-ouvertes.fr/hal-01268324

R. U. Holliday and . Maydis, Handbook of Genetics, pp.575-95, 1974.