I. Druzhinina, V. Seidl-seiboth, A. Herrera-estrella, B. Horwitz, C. Kenerley et al., Trichoderma:the genomics of opportunistic success, Nat Rev Microbiol, vol.2011, issue.10, pp.9749-759

T. Benítez, A. Rincón, M. Limón, and A. Codón, Biocontrol mechanisms of Trichoderma strains, Int Microbiol, vol.7, pp.249-260, 2004.

C. Howell, Species in the Biological Control of Plant Diseases: The History and Evolution of Current Concepts, Plant Disease, vol.87, issue.1, pp.4-10, 2003.
DOI : 10.1094/PDIS.2003.87.1.4

C. Kubicek, A. Herrera-estrella, V. Seidl-seiboth, D. Martinez, I. Druzhinina et al., Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma, Genome Biology, vol.12, issue.4, p.40, 2011.
DOI : 10.1093/bioinformatics/btm076

B. Reithner, E. Ibarra-laclette, R. Mach, and A. Herrera-estrella, Identification of Mycoparasitism-Related Genes in Trichoderma atroviride, Applied and Environmental Microbiology, vol.77, issue.13, pp.774361-4370, 2011.
DOI : 10.1128/AEM.00129-11

M. Omann, S. Lehner, E. Rodríguez, C. Brunner, K. Zeilinger et al., The seven-transmembrane receptor Gpr1 governs processes relevant for the antagonistic interaction of Trichoderma atroviride with its host, Microbiology, vol.158, issue.1, pp.107-118
DOI : 10.1099/mic.0.052035-0

V. Catalano, M. Vergara, J. Hauzenberger, B. Seiboth, S. Sarrocco et al., Use of a non-homologous end-joining-deficient strain (delta-ku70) of the biocontrol fungus Trichoderma virens to investigate the function of the laccase gene lcc1 in sclerotia degradation, Current Genetics, vol.298, issue.1, pp.13-23, 2011.
DOI : 10.1007/s00294-010-0322-2

P. Liu and Q. Yang, Identification of genes with a biocontrol function in Trichoderma harzianum mycelium using the expressed sequence tag approach, Research in Microbiology, vol.156, issue.3, pp.416-423, 2005.
DOI : 10.1016/j.resmic.2004.10.007

J. Vizcaíno, J. Redondo, M. Suárez, R. Cardoza, R. Hermosa et al., Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol, Applied Microbiology and Biotechnology, vol.6, issue.4, pp.853-862, 2007.
DOI : 10.1007/s00253-007-0885-0

M. Suárez, J. Vizcaíno, A. Llobell, and E. Monte, Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach, Current Genetics, vol.69, issue.5, pp.331-342, 2007.
DOI : 10.1007/s00294-007-0130-5

I. Samolski, A. De-luis, J. Vizcaíno, E. Monte, and M. Suárez, Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray, BMC Microbiology, vol.9, issue.1, p.217, 2009.
DOI : 10.1186/1471-2180-9-217

Z. Liu, X. Yang, D. Sun, J. Song, G. Chen et al., Expressed sequence tags-based identification of genes in a biocontrol strain Trichoderma asperellum, Molecular Biology Reports, vol.145, issue.8, pp.373673-3681, 2010.
DOI : 10.1007/s11033-010-0019-0

M. Rubio, R. Hermosa, J. Reino, I. Collado, and M. E. , Thctf1 transcription factor of Trichoderma harzianum is involved in 6-pentyl-2H-pyran-2-one production and antifungal activity, Fungal Genetics and Biology, vol.46, issue.1, pp.17-27, 2009.
DOI : 10.1016/j.fgb.2008.10.008

A. Ogoshi, Ecology and Pathogenicity of Anastomosis and Intraspecific Groups of Rhizoctonia Solani Kuhn, Annual Review of Phytopathology, vol.25, issue.1, pp.125-143, 1987.
DOI : 10.1146/annurev.py.25.090187.001013

R. Dean, J. Van-kan, Z. Pretorius, K. Hammond-kosack, A. Di-pietro et al., The Top 10 fungal pathogens in molecular plant pathology, Mol Plant Pathol, vol.2012, issue.134, pp.414-430

G. Smyth, Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, vol.3, issue.1, 2004.
DOI : 10.2202/1544-6115.1027

S. Baker, G. Perrone, N. Richardson, A. Gallo, and C. Kubicek, Phylogenomic analysis of polyketide synthase-encoding genes in Trichoderma, Microbiology, vol.158, issue.1, pp.147-154
DOI : 10.1099/mic.0.053462-0

B. Seiboth, R. Aghcheh, P. Phatale, R. Linke, L. Hartl et al., The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei, Molecular Microbiology, vol.20, issue.6, pp.1150-1164
DOI : 10.1111/j.1365-2958.2012.08083.x

M. Lorito, S. Woo, G. Harman, and M. E. , : From 'Omics to the Field, Annual Review of Phytopathology, vol.48, issue.1, pp.395-417, 2010.
DOI : 10.1146/annurev-phyto-073009-114314

V. Seidl, L. Song, E. Lindquist, S. Gruber, A. Koptchinskiy et al., Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey, BMC Genomics, vol.10, issue.1, p.567, 2009.
DOI : 10.1186/1471-2164-10-567

A. Rossmann, G. Samuels, C. Rogerson, and R. Lowen, Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes), Stud Mycol, vol.42, pp.1-83, 1999.

A. Stricker, K. Grosstessner-hain, E. Würleitner, and R. Mach, Xyr1 (Xylanase Regulator 1) Regulates both the Hydrolytic Enzyme System and D-Xylose Metabolism in Hypocrea jecorina, Eukaryotic Cell, vol.5, issue.12, pp.2128-2137, 2006.
DOI : 10.1128/EC.00211-06

N. Patron, R. Waller, A. Cozijnsen, D. Straney, D. Gardiner et al., Origin and distribution of epipolythiodioxopiperazine (ETP) gene clusters in filamentous ascomycetes, BMC Evolutionary Biology, vol.7, issue.1, p.174, 2007.
DOI : 10.1186/1471-2148-7-174

S. Wilhite, R. Lumsden, and D. Straney, in Relation to Suppression of Pythium Damping-off, Phytopathology, vol.84, issue.8, pp.816-821, 1994.
DOI : 10.1094/Phyto-84-816

R. Lumsden and J. Locke, in Soilless Mix, Phytopathology, vol.79, issue.3, pp.361-366, 1989.
DOI : 10.1094/Phyto-79-361

R. Lumsden, J. Locke, S. Adkins, J. Walter, and C. Ridout, from Alginate Prill in Soil and Soilless Media, Phytopathology, vol.82, issue.2, pp.230-235, 1992.
DOI : 10.1094/Phyto-82-230

S. Wilhite and D. Straney, Timing of gliotoxin biosynthesis in the fungal biological control agent Gliocladium virens (Trichoderma virens), Applied Microbiology and Biotechnology, vol.45, issue.4, pp.513-518, 1996.
DOI : 10.1007/s002530050721

A. Kumar and J. Paietta, The sulfur controller-2 negative regulatory gene of Neurospora crassa encodes a protein with beta-transducin repeats., Proceedings of the National Academy of Sciences, vol.92, issue.8, pp.923343-3347, 1995.
DOI : 10.1073/pnas.92.8.3343

K. Helmstaedt, A. Strittmatter, W. Lipscomb, and G. Braus, Evolution of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase-encoding genes in the yeast Saccharomyces cerevisiae, Proceedings of the National Academy of Sciences, vol.102, issue.28, pp.9784-9789, 2005.
DOI : 10.1073/pnas.0504238102

V. Seidl, C. Gamauf, I. Druzhinina, B. Seiboth, L. Hartl et al., The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome, BMC Genomics, vol.9, issue.1, p.327, 2008.
DOI : 10.1186/1471-2164-9-327

J. Reino, R. Guerrero, R. Hernández-galan, and I. Collado, Secondary metabolites from species of the biocontrol agent Trichoderma, Phytochemistry Reviews, vol.43, issue.20, pp.89-123, 2008.
DOI : 10.1007/s11101-006-9032-2

L. Serrano-carreon, Y. Hathout, M. Bensoussan, and J. Belin, Metabolism of Linoleic Acid or Mevalonate and 6-Pentyl-?-Pyrone Biosynthesis by Trichoderma Species, Appl Environ Microbiol, vol.59, pp.2945-2950, 1993.

P. Mukherjee, B. Horwitz, and C. Kenerley, Secondary metabolism in Trichoderma - a genomic perspective, Microbiology, vol.158, issue.1, pp.35-45, 2012.
DOI : 10.1099/mic.0.053629-0

R. Kulkarni, M. Thon, H. Pan, and R. Dean, Novel G-protein-coupled receptorlike proteins in the plant pathogenic fungus Magnaporthe grisea

S. Muthumeenakshi, S. Sreenivasaprasad, C. Rogers, M. Challen, and J. Whipps, Analysis of cDNA transcripts from Coniothyrium minitans reveals a diverse array of genes involved in key processes during sclerotial mycoparasitism, Fungal Genetics and Biology, vol.44, issue.12, pp.441262-1284, 2007.
DOI : 10.1016/j.fgb.2007.07.011

C. Gronover, J. Schumacher, P. Hantsch, and B. Tudzynski, controls the expression of GST-encoding genes, but is not essential for pathogenicity, Molecular Plant Pathology, vol.13, issue.3, pp.243-256, 2005.
DOI : 10.1111/j.1364-3703.2005.00278.x

S. Xiong, J. Fan, and K. Kitazato, The antiviral protein cyanovirin-N: the current state of its production and applications, Applied Microbiology and Biotechnology, vol.60, issue.4, pp.805-812, 2010.
DOI : 10.1007/s00253-010-2470-1

D. Neethling and H. Nevalainen, produce lectins, Canadian Journal of Microbiology, vol.42, issue.2, pp.141-146, 1996.
DOI : 10.1139/m96-022

J. Plett and F. Martin, Poplar root exudates contain compounds that induce the expression of MiSSP7 in Laccaria bicolor, Plant Signal Behav, vol.2012, issue.71, pp.12-15

I. Papapostolou and C. Georgiou, Superoxide radical induces sclerotial differentiation in filamentous phytopathogenic fungi: a superoxide dismutase mimetics study, Microbiology, vol.156, issue.3, pp.960-966, 2010.
DOI : 10.1099/mic.0.034579-0

K. Aliferis and S. Jabaji, Sclerotial Exudates, Journal of Agricultural and Food Chemistry, vol.58, issue.13, pp.7604-7615, 2010.
DOI : 10.1021/jf101029a

M. Ruocco, S. Lanzuise, F. Vinale, R. Marra, D. Turrà et al., : The Role of an ABC Transporter Membrane Pump in the Interaction with Different Plant-Pathogenic Fungi, Molecular Plant-Microbe Interactions, vol.22, issue.3, pp.291-301, 2009.
DOI : 10.1094/MPMI-22-3-0291

L. Basile, R. Willson, B. Sewell, and M. Benedik, Genome mining of cyanide-degrading nitrilases from filamentous fungi, Applied Microbiology and Biotechnology, vol.53, issue.Pt 6, pp.427-435, 2008.
DOI : 10.1007/s00253-008-1559-2

C. Michelsen and P. Stougaard, In5 from Greenland is highly dependent on growth medium, Canadian Journal of Microbiology, vol.58, issue.4, pp.381-390, 2011.
DOI : 10.1139/w2012-004

J. Palmer and N. Keller, Secondary metabolism in fungi: does chromosomal location matter?, Current Opinion in Microbiology, vol.13, issue.4, pp.431-436, 2010.
DOI : 10.1016/j.mib.2010.04.008

D. Martinez, R. Berka, B. Henrissat, M. Saloheimo, M. Arvas et al., Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nature Biotechnology, vol.307, issue.5, pp.553-560, 2008.
DOI : 10.1038/nbt1403

B. Metz, V. Seidl-seiboth, T. Haarmann, A. Kopchinskiy, P. Lorenz et al., Expression of Biomass-Degrading Enzymes Is a Major Event during Conidium Development in Trichoderma reesei, Eukaryotic Cell, vol.10, issue.11, pp.101527-1535, 2011.
DOI : 10.1128/EC.05014-11

C. Cuomo, U. Güldener, J. Xu, F. Trail, B. Turgeon et al., The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization, Science, vol.317, issue.5843, pp.1400-1402, 2007.
DOI : 10.1126/science.1143708

URL : https://hal.archives-ouvertes.fr/hal-00192479

T. Kasuga, G. Mannhaupt, and N. Glass, Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa, PLoS ONE, vol.57, issue.4, p.5286, 2009.
DOI : 10.1371/journal.pone.0005286.s003

J. Strauss and Y. Reyes-dominguez, Regulation of secondary metabolism by chromatin structure and epigenetic codes, Fungal Genetics and Biology, vol.48, issue.1, pp.62-69, 2011.
DOI : 10.1016/j.fgb.2010.07.009

O. Bayram and G. Braus, Coordination of secondary metabolism and development in fungi: the velvet family of regulatory proteins, FEMS Microbiol Rev, vol.2012, issue.361, pp.1-24

P. Mukherjee and C. Kenerley, Regulation of Morphogenesis and Biocontrol Properties in Trichoderma virens by a VELVET Protein, Vel1, Applied and Environmental Microbiology, vol.76, issue.7, pp.2345-2352, 2010.
DOI : 10.1128/AEM.02391-09

J. Chirgwin, A. Przybyla, R. Macdonald, and W. Rutter, Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease, Biochemistry, vol.18, issue.24, pp.5294-5299, 1979.
DOI : 10.1021/bi00591a005

L. Jourdren, A. Duclos, C. Brion, T. Portnoy, H. Mathis et al., Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments, Nucleic Acids Research, vol.38, issue.10, p.117, 2010.
DOI : 10.1093/nar/gkq110

S. Lemoine, F. Combes, N. Servant, L. Crom, and S. , Goulphar: Rapid access and expertise for standard two-color microarray normalization methods, BMC Bioinformatics, vol.7, issue.1, p.467, 2006.
DOI : 10.1186/1471-2105-7-467

URL : https://hal.archives-ouvertes.fr/inserm-00122139

K. Livak and T. Schmittgen, Analysis of relative gene expression data using real-time quantitative PCR and the 2(?Delta Delta C(T)) Method, pp.402-408, 2001.