D. Carvalho, M. Loreto, and E. , Methods for detection of horizontal transfer of transposable elements in complete genomes, Genetics and Molecular Biology, vol.35, issue.4, pp.1078-84, 2012.
DOI : 10.1590/S1415-47572012000600024

D. Fitzpatrick, Horizontal gene transfer in fungi, FEMS Microbiology Letters, vol.329, issue.1, pp.1-8, 2012.
DOI : 10.1111/j.1574-6968.2011.02465.x

T. Richards, Genome Evolution: Horizontal Movements in the Fungi, Current Biology, vol.21, issue.4, pp.166-174, 2011.
DOI : 10.1016/j.cub.2011.01.028

C. Hall, S. Brachat, and F. Dietrich, Contribution of Horizontal Gene Transfer to the Evolution of Saccharomyces cerevisiae, Eukaryotic Cell, vol.4, issue.6, pp.1102-1117, 2005.
DOI : 10.1128/EC.4.6.1102-1115.2005

S. Garcia-vallve, A. Romeu, and J. Palau, Horizontal Gene Transfer of Glycosyl Hydrolases of the Rumen Fungi, Molecular Biology and Evolution, vol.17, issue.3, pp.352-61, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026315

D. Lawrence, S. Kroken, B. Pryor, and A. Arnold, Interkingdom Gene Transfer of a Hybrid NPS/PKS from Bacteria to Filamentous Ascomycota, PLoS ONE, vol.17, issue.4, p.28231, 2011.
DOI : 10.1371/journal.pone.0028231.s010

M. Novo, F. Bigey, E. Beyne, V. Galeote, F. Gavory et al., Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118, Proceedings of the National Academy of Sciences, vol.106, issue.38, pp.16333-16341, 2009.
DOI : 10.1073/pnas.0904673106

T. Friesen, E. Stukenbrock, Z. Liu, S. Meinhardt, H. Ling et al., Emergence of a new disease as a result of interspecific virulence gene transfer, Nature Genetics, vol.263, issue.8, pp.953-959, 2006.
DOI : 10.1007/s00122-005-2064-y

L. Ma, H. Van-der-does, K. Borkovich, J. Coleman, M. Daboussi et al., Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, vol.22, issue.7287, pp.367-73, 2010.
DOI : 10.1038/nature08850

URL : https://hal.archives-ouvertes.fr/hal-00574227

T. Richards, D. Soanes, P. Foster, G. Leonard, C. Thomton et al., Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi, THE PLANT CELL ONLINE, vol.21, issue.7, pp.1897-911, 2009.
DOI : 10.1105/tpc.109.065805

V. Jaramillo, W. Vargas, S. Sukno, and M. Thon, Horizontal Transfer of a Subtilisin Gene from Plants into an Ancestor of the Plant Pathogenic Fungal Genus Colletotrichum, PLoS ONE, vol.111, issue.3, p.59078, 2013.
DOI : 10.1371/journal.pone.0059078.s001

N. Nikolaidis, N. Doran, and D. Cosgrove, Plant Expansins in Bacteria and Fungi: Evolution by Horizontal Gene Transfer and Independent Domain Fusion, Molecular Biology and Evolution, vol.31, issue.2, pp.376-86, 2013.
DOI : 10.1093/molbev/mst206

J. Slot and D. Hibbett, Horizontal Transfer of a Nitrate Assimilation Gene Cluster and Ecological Transitions in Fungi: A Phylogenetic Study, PLoS ONE, vol.300, issue.(Pt 1), p.1097, 2007.
DOI : 10.1371/journal.pone.0001097.s005

J. Macmilan, Occurrence of Gibberellins in Vascular Plants, Fungi, and Bacteria, Journal of Plant Growth Regulation, vol.20, issue.4, pp.387-442, 2002.
DOI : 10.1007/s003440010038

R. Cao, Y. Zhang, F. Mann, C. Huang, D. Mukkamala et al., Diterpene cyclases and the nature of the isoprene fold, Proteins: Structure, Function, and Bioinformatics, vol.456, issue.Web Server issu, pp.2417-2449, 2010.
DOI : 10.1002/prot.22751

M. Smanski, R. Peterson, S. Huang, and B. Shen, Bacterial diterpene synthases: new opportunities for mechanistic enzymology and engineered biosynthesis, Current Opinion in Chemical Biology, vol.16, issue.1-2, pp.132-173, 2012.
DOI : 10.1016/j.cbpa.2012.03.002

K. Aya, Y. Hiwatashi, M. Kojima, H. Sakakibara, M. Ueguchi-tanaka et al., The Gibberellin perception system evolved to regulate a pre-existing GAMYB-mediated system during land plant evolution, Nature Communications, vol.50, p.544, 2011.
DOI : 10.1038/ncomms1552

K. Hayashi, K. Horie, Y. Hiwatashi, H. Kawaide, S. Yamaguchi et al., Endogenous Diterpenes Derived from ent-Kaurene, a Common Gibberellin Precursor, Regulate Protonema Differentiation of the Moss Physcomitrella patens, PLANT PHYSIOLOGY, vol.153, issue.3, pp.1085-97, 2010.
DOI : 10.1104/pp.110.157909

S. Yamagushi, Gibberellin Metabolism and its Regulation, Annual Review of Plant Biology, vol.59, issue.1, pp.225-51, 2008.
DOI : 10.1146/annurev.arplant.59.032607.092804

C. Keeling and J. Bohlman, Diterpene resin acids in conifers, Phytochemistry, vol.67, issue.22, pp.2415-2438, 2006.
DOI : 10.1016/j.phytochem.2006.08.019

J. Bohlmann, G. Meyer-gauen, and R. Croteau, Plant terpenoid synthases: Molecular biology and phylogenetic analysis, Proceedings of the National Academy of Sciences, vol.95, issue.8, pp.4126-4159, 1998.
DOI : 10.1073/pnas.95.8.4126

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC22453

S. Withers and J. Keasling, Biosynthesis and engineering of isoprenoid small molecules, Applied Microbiology and Biotechnology, vol.40, issue.Pt 2, pp.980-90, 2007.
DOI : 10.1007/s00253-006-0593-1

S. Rensing, D. Lang, A. Zimmer, A. Terry, A. Salamov et al., The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants, Science, vol.319, issue.5859, pp.64-73, 2008.
DOI : 10.1126/science.1150646

F. Chen, D. Tholl, J. Bohlmann, and E. Pichersky, The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom, The Plant Journal, vol.71, issue.1, pp.212-241, 2011.
DOI : 10.1111/j.1365-313X.2011.04520.x

G. Li, T. Köllner, Y. Yin, Y. Jiang, H. Chen et al., Nonseed plant Selaginella moellendorffii has both seed plant and microbial types of terpene synthases, Proceedings of the National Academy of Sciences, vol.109, issue.36, pp.14711-14716, 2012.
DOI : 10.1073/pnas.1204300109

P. Hedden, A. Phillips, M. Rojas, E. Carrera, and B. Tudzynski, Gibberellin Biosynthesis in Plants and Fungi: A Case of Convergent Evolution?, Journal of Plant Growth Regulation, vol.20, issue.4, pp.319-350, 2002.
DOI : 10.1007/s003440010037

C. Bömke and B. Tudzynski, Diversity, regulation, and evolution of the gibberellin biosynthetic pathway in fungi compared to plants and bacteria, Phytochemistry, vol.70, issue.15-16, pp.1876-93, 2009.
DOI : 10.1016/j.phytochem.2009.05.020

J. Mondego, M. Carazzolle, G. Costa, E. Formighieri, L. Parizzi et al., A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao, BMC Genomics, vol.9, issue.1, p.548, 2008.
DOI : 10.1186/1471-2164-9-548

P. Zerbe, B. Hamberger, M. Yuen, A. Chiang, H. Sandhu et al., Gene Discovery of Modular Diterpene Metabolism in Nonmodel Systems, PLANT PHYSIOLOGY, vol.162, issue.2, pp.1073-91, 2013.
DOI : 10.1104/pp.113.218347

T. Toyomasu, H. Kawaide, A. Ishizaki, S. Shinoda, M. Otsuka et al., : Functional Analysis of a Bifunctional Diterpene Cyclase, Bioscience, Biotechnology, and Biochemistry, vol.48, issue.8, pp.660-664, 2000.
DOI : 10.1104/pp.118.4.1517

J. Taylor and M. Berbee, Dating divergences in the Fungal Tree of Life: review and new analyses, Mycologia, vol.98, issue.6, pp.838-887, 2006.
DOI : 10.1080/15572536.2006.11832614

R. Lücking, D. Pfister, E. Plave, and H. Lumbsch, Fungi evolved right on track, Mycologia, vol.101, issue.6, pp.810-832, 2009.
DOI : 10.3852/09-016

M. Sanderson, Molecular data from 27 proteins do not support a Precambrian origin of land plants, American Journal of Botany, vol.90, issue.6, pp.954-960, 2003.
DOI : 10.3732/ajb.90.6.954

A. Willis, B. Rodrigues, and P. Harris, The Ecology of Arbuscular Mycorrhizal Fungi, Critical Reviews in Plant Sciences, vol.5, issue.628, pp.1-20, 2013.
DOI : 10.1016/S1360-1385(03)00184-5

E. Kemen and J. Jones, Obligate biotroph parasitism: can we link genomes to lifestyles?, Trends in Plant Science, vol.17, issue.8, pp.448-547, 2012.
DOI : 10.1016/j.tplants.2012.04.005

M. Bidartondo, D. Read, J. Trappe, V. Merckx, R. Ligrone et al., The dawn of symbiosis between plants and fungi, Biology Letters, vol.24, issue.3, pp.574-581, 2013.
DOI : 10.1016/j.ympev.2004.12.006

J. Crouzet, T. Trombik, A. Fraysse, and M. Boutry, Organization and function of the plant pleiotropic drug resistance ABC transporter family, FEBS Letters, vol.39, issue.4, pp.1123-1153, 2005.
DOI : 10.1016/j.febslet.2005.12.043

H. Chu, E. Wegel, and A. Osbourn, From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants, The Plant Journal, vol.372, issue.1, pp.66-79, 2011.
DOI : 10.1111/j.1365-313X.2011.04503.x

S. Swaminathan, D. Morrone, Q. Wang, B. Fulton, and R. Peters, CYP76M7 Is an ent-Cassadiene C11??-Hydroxylase Defining a Second Multifunctional Diterpenoid Biosynthetic Gene Cluster in Rice, The Plant Cell, vol.21, issue.10, pp.3315-3340, 2009.
DOI : 10.1105/tpc.108.063677

M. Mizutani and D. Ohta, Diversification of P450 Genes During Land Plant Evolution, Annual Review of Plant Biology, vol.61, issue.1, pp.291-315, 2010.
DOI : 10.1146/annurev-arplant-042809-112305

D. Nelson, M. Schuler, S. Paquette, D. Werck-reichhart, and S. Bak, Comparative Genomics of Rice and Arabidopsis. Analysis of 727 Cytochrome P450 Genes and Pseudogenes from a Monocot and a Dicot, PLANT PHYSIOLOGY, vol.135, issue.2, pp.756-72, 2004.
DOI : 10.1104/pp.104.039826

A. Gacek and J. Strauss, The chromatin code of fungal secondary metabolite gene clusters, Applied Microbiology and Biotechnology, vol.15, issue.Suppl 1, pp.1389-404, 2012.
DOI : 10.1007/s00253-012-4208-8

J. Slot and A. Rokas, Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi, Proceedings of the National Academy of Sciences, vol.107, issue.22, pp.10136-10177, 2010.
DOI : 10.1073/pnas.0914418107

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890473

L. Cota, L. Maffia, E. Mizubuti, and P. Macedo, Biological control by Clonostachys rosea as a key component in the integrated management of strawberry gray mold, Biological Control, vol.50, issue.3, pp.222-252, 2009.
DOI : 10.1016/j.biocontrol.2009.04.017

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

R. Nicoletti, D. Stephano, and M. , Penicillium restrictum as an antagonist of plant pathogenic fungi, Dyn Biochem Process Biotech Mol Biol, vol.6, pp.61-70, 2012.

B. Tudzynski, Biosynthesis of gibberellins in Gibberella fujikoroi: biomolecular aspects, Appl Microbiol Biotechnol, vol.52, pp.198-310, 1999.

B. Tudzynski, Gibberellin biosynthesis in fungi: genes, enzymes, evolution, and impact on biotechnology, Applied Microbiology and Biotechnology, vol.95, issue.Suppl 2, pp.597-611, 2005.
DOI : 10.1007/s00253-004-1805-1

C. Schardl, C. Young, U. Hesse, S. Amyotte, K. Andreeva et al., Plant-Symbiotic Fungi as Chemical Engineers: Multi-Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci, PLoS Genetics, vol.41, issue.2, 2013.
DOI : 10.1371/journal.pgen.1003323.s012

P. Zhang, P. Zhou, and J. Yu, MD3, FEMS Microbiology Letters, vol.293, issue.2, pp.155-164, 2009.
DOI : 10.1111/j.1574-6968.2009.01481.x

A. Lopes and M. Pupo, Biosynthesis of aphidicolin proceeds via the mevalonate pathway in the endophytic fungus Nigrospora sphaerica, Journal of the Brazilian Chemical Society, vol.22, issue.1, pp.80-85, 2011.
DOI : 10.1590/S0103-50532011000100010

D. Souza, J. Vieira, I. Rodrigues-filho, E. Braz-filho, and R. , Terpenoids from Endophytic Fungi, Molecules, vol.16, issue.12, pp.10604-10622, 2011.
DOI : 10.3390/molecules161210604

W. Pongcharoen, V. Rukachaisirikul, S. Pongpaichit, N. Rungjindamai, and J. Sakayajoj, PSU-D44, Journal of Natural Products, vol.69, issue.5, pp.856-864, 2006.
DOI : 10.1021/np0600649

E. Tsavkelova, C. Bömke, A. Netrusov, J. Weiner, and B. Tudzynski, Production of gibberellic acids by an orchid-associated Fusarium proliferatum strain, Fungal Genetics and Biology, vol.45, issue.10, pp.1393-403, 2008.
DOI : 10.1016/j.fgb.2008.07.011

K. Bromann, M. Toivari, K. Viljanen, A. Vuoristo, L. Ruohonen et al., Identification and Characterization of a Novel Diterpene Gene Cluster in Aspergillus nidulans, PLoS ONE, vol.32, issue.4, p.35450, 2012.
DOI : 10.1371/journal.pone.0035450.s007

T. Roncal, S. Cordobes, O. Sterner, and U. Ugalde, Conidiation in Penicillium cyclopium Is Induced by Conidiogenone, an Endogenous Diterpene, Eukaryotic Cell, vol.1, issue.5, pp.823-832, 2002.
DOI : 10.1128/EC.1.5.823-829.2002

E. Parker and D. Scott, Indole-diterpene biosynthesis in ascomycetous fungi Handbook of industrial mycology, pp.405-431, 2004.

S. Saikia, M. Nicholson, C. Young, E. Parker, and B. Scott, The genetic basis for indole-diterpene chemical diversity in filamentous fungi, Mycological Research, vol.112, issue.2, pp.184-99, 2008.
DOI : 10.1016/j.mycres.2007.06.015

S. Zhang, B. Monahan, J. Tkacz, and B. Scott, Indole-Diterpene Gene Cluster from Aspergillus flavus, Applied and Environmental Microbiology, vol.70, issue.11, pp.6875-83, 2004.
DOI : 10.1128/AEM.70.11.6875-6883.2004

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC525135

T. Toyomasu, K. Nakaminami, T. Mie, K. Watanabe, H. Ito et al., Cloning of a Gene Cluster Responsible for the Biosynthesis of Diterpene Aphidicolin, a Specific Inhibitor of DNA Polymerase ??, Bioscience, Biotechnology, and Biochemistry, vol.68, issue.1, pp.146-52, 2004.
DOI : 10.1271/bbb.68.146

T. Toyomasu, M. Tsukahara, A. Kaneko, R. Niida, W. Litsuhashi et al., Fusicoccins are biosynthesized by an unusual chimera diterpene synthase in fungi, Proceedings of the National Academy of Sciences, vol.104, issue.9, pp.3084-3092, 2007.
DOI : 10.1073/pnas.0608426104

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1805559

C. Boemke, M. Rojas, P. Hedden, and B. Tudzynski, Loss of Gibberellin Production in Fusarium verticillioides (Gibberella fujikuroi MP-A) Is Due to a Deletion in the Gibberellic Acid Gene Cluster, Applied and Environmental Microbiology, vol.74, issue.24, pp.7790-801, 2008.
DOI : 10.1128/AEM.01819-08

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

F. Plewniak, L. Bianchetti, Y. Brelivet, A. Carles, F. Chalmel et al., PipeAlign: a new toolkit for protein family analysis, Nucleic Acids Research, vol.31, issue.13, pp.3829-3861, 2003.
DOI : 10.1093/nar/gkg518

URL : http://doi.org/10.1093/nar/gkg518

G. Beck, D. Coman, E. Herren, M. Ruiz-sola, M. Rodriguez-conception et al., Characterization of the GGPP synthase gene family in Arabidopsis thaliana, Plant Molecular Biology, vol.35, issue.3, pp.393-416, 2013.
DOI : 10.1007/s11103-013-0070-z

V. Solovyev, P. Kosarev, I. Seledsov, and D. Vorobyev, Automatic annotation of eukaryotic genes, pseudogenes and promoters, Genome Biology, vol.7, issue.Suppl 1, p.10, 2006.
DOI : 10.1186/gb-2006-7-s1-s10

F. Corpet, Multiple sequence alignment with hierarchical clustering, Nucleic Acids Research, vol.16, issue.22, pp.10881-90, 1998.
DOI : 10.1093/nar/16.22.10881

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-52, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

D. Darriba, G. Taboada, R. Doallo, and D. Posada, ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, issue.8, pp.1164-1169, 2011.
DOI : 10.1093/bioinformatics/btr088

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-225, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00705187