K. J. Affeldt, M. Brodhagen, and N. P. Keller, Aspergillus oxylipin signaling and quorum sensing pathways depend on G protein-coupled receptors, Toxins, vol.4, issue.9, pp.695-717, 2012.

M. T. Agler, J. Ruhe, S. Kroll, C. Morhenn, S. T. Kim et al., , 2016.

, Microbial hub taxa link host and abiotic factors to plant microbiome variation, PLoS biology, vol.14, issue.1, p.1002352

J. F. Alberts, W. C. Gelderblom, A. Botha, and W. H. Van-zyl, Degradation of aflatoxin B1 by fungal laccase enzymes, International Journal of Food Microbiology, vol.135, issue.1, pp.47-52, 2009.

S. Amand, M. Vallet, L. Guedon, G. Genta-jouve, F. Wien et al., A reactive eremophilane and its antibacterial 2 (1 H)-naphthalenone rearrangement product, witnesses of a microbial chemical warfare, Organic Letters, vol.19, issue.15, pp.4038-4041, 2017.

Ö. Bayram and G. H. Braus, Coordination of secondarymetabolism and development in fungi: the velvet familyof regulatory proteins, FEMS microbiology reviews, vol.36, issue.1, pp.1-24, 2012.

E. Blée, Impact of phyto-oxylipins in plant defense, Trends in plant science, vol.7, issue.7, pp.315-322, 2002.

M. Brodhagen and N. P. Keller, Signalling pathways connecting mycotoxin production and sporulation, Molecular Plant Pathology, vol.7, issue.4, pp.285-301, 2006.

F. Brodhun and I. Feussner, Oxylipins in fungi, The FEBS journal, vol.278, issue.7, pp.1047-1063, 2011.

F. Brodhun, A. Cristobal-sarramian, S. Zabel, J. Newie, M. Hamberg et al., An iron 13S-lipoxygenase with an ?-linolenic acid specific hydroperoxidase activity from Fusarium oxysporum, PLOS one, vol.8, issue.5, p.64919, 2013.

D. Bulgarelli, M. Rott, K. Schlaeppi, E. V. Van-themaat, N. Ahmadinejad et al.,

J. Peplies, Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, vol.488, issue.7409, p.91, 2012.

D. Bulgarelli, K. Schlaeppi, S. Spaepen, E. V. Van-themaat, and P. Schulze-lefert, , 2013.

, Structure and functions of the bacterial microbiota of plants. Annual review of plant biology, vol.64, pp.807-838

G. B. Burow, T. C. Nesbitt, J. Dunlap, and N. P. Keller, Seed lipoxygenase products modulate Aspergillus mycotoxin biosynthesis, Molecular Plant-Microbe Interactions, vol.10, issue.3, pp.380-387, 1997.

H. Forootanfar, M. A. Faramarzi, A. R. Shahverdi, and M. T. Yazdi, Purification and biochemical characterization of extracellular laccase from the ascomycete Paraconiothyrium variabile, Bioresource Technology, vol.102, issue.2, pp.1808-1814, 2011.

M. L. Friesen, S. S. Porter, S. C. Stark, E. J. Von-wettberg, J. L. Sachs et al., Microbially mediated plant functional traits. Annual review of ecology, evolution, and systematics, p.42, 2011.

C. D. Funk, Prostaglandins and leukotrienes: advances in eicosanoid biology, science, vol.294, issue.5548, pp.1871-1875, 2001.

X. Gao, W. B. Shim, C. Göbel, S. Kunze, I. Feussner et al., with mycotoxin fumonisin. Molecular plant-microbe interactions, vol.20, issue.8, pp.922-933, 2007.

X. Gao and M. V. Kolomiets, Host-derived lipids and oxylipins are crucial signals in modulating mycotoxin production by fungi, Toxin Reviews, vol.28, issue.2-3, pp.79-88, 2009.

F. K. Gao, C. C. Dai, and X. Z. Liu, Mechanisms of fungal endophytes in plant protection against pathogens, African Journal of Microbiology Research, vol.4, issue.13, pp.1346-1351, 2010.

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.221-224, 2009.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

R. L. Hamill, C. E. Higgens, H. E. Boaz, and M. Gorman, The structure op beauvericin, a new depsipeptide antibiotic toxic to Artemia salina, Tetrahedron Letters, vol.10, issue.49, pp.4255-4258, 1969.

P. R. Hardoim, L. S. Van-overbeek, G. Berg, A. M. Pirttilä, S. Compant et al., The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes, Microbiology and Molecular Biology Reviews, vol.79, issue.3, pp.293-320, 2015.

J. Hellemans, G. Mortier, A. De-paepe, F. Speleman, and J. Vandesompele, qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data, Genome biology, vol.8, issue.2, p.19, 2007.

M. Herrmann, R. Zocher, and A. Haese, Enniatin production by fusarium strains and its effect on potato tuber tissue, Applied and Environmental Microbiology, vol.62, issue.2, pp.393-398, 1996.

R. Heshof, S. Jylhä, T. Haarmann, A. L. Jørgensen, T. K. Dalsgaard et al., A novel class of fungal lipoxygenases, Applied microbiology and biotechnology, vol.98, issue.3, pp.1261-1270, 2014.

L. Hörnsten, C. Su, A. E. Osbourn, U. Hellman, and E. H. Oliw, Cloning of the manganese lipoxygenase gene reveals homology with the lipoxygenase gene family, European journal of biochemistry, vol.269, issue.11, pp.2690-2697, 2002.

A. Joubert, B. Calmes, R. Berruyer, M. Pihet, J. P. Bouchara et al., Laser nephelometry applied in an automated microplate system to study filamentous fungus growth, Biotechniques, vol.48, issue.5, pp.399-404, 2010.

S. Kaul, T. Sharma, and M. Dhar, Omics" tools for better understanding the plantendophyte interactions, Frontiers in plant science, vol.7, p.955, 2016.

L. L. Kiiskinen, L. Viikari, and K. Kruus, Purification and characterisation of a novel laccase from the ascomycete Melanocarpus albomyces, Applied Microbiology and Biotechnology, vol.59, issue.2-3, pp.198-204, 2002.

H. Kühn, R. Wiesner, J. Rathmann, and T. Schewe, Formation of ketodienoic fatty acids by the pure pea lipoxygenase-1, Eicosanoids, vol.4, issue.1, pp.9-14, 1991.

A. Langenfeld, S. Prado, B. Nay, C. Cruaud, S. Lacoste et al., , 2013.

, Geographic locality greatly influences fungal endophyte communities in Cephalotaxus harringtonia, Fungal biology, vol.117, issue.2, pp.124-136

S. L. Lebeis, The potential for give and take in plant-microbiome relationships. Frontiers in plant science, vol.5, p.287, 2014.

M. S. López-berges, J. Capilla, D. Turrà, L. Schafferer, S. Matthijs et al.,

A. Di-pietro, HapX-mediated iron homeostasis is essential for rhizosphere competence and virulence of the soilborne pathogen Fusarium oxysporum, The Plant Cell, p.112, 2012.

M. S. López-berges, C. Hera, M. Sulyok, K. Schäfer, J. Capilla et al., The velvet complex governs mycotoxin production and virulence of F usarium oxysporum on plant and mammalian hosts, Molecular microbiology, vol.87, issue.1, pp.49-65, 2013.

A. Logrieco, A. Moretti, G. Castella, M. Kostecki, P. Golinski et al., Beauvericin Production by FusariumSpecies, Applied and Environmental Microbiology, vol.64, issue.8, 1998.

D. S. Lundberg, S. L. Lebeis, S. H. Paredes, S. Yourstone, J. Gehring et al., Defining the core Arabidopsis thaliana root microbiome, Nature, vol.488, issue.7409, p.86, 2012.

T. Mcdonald, T. Devi, K. Shimizu, S. Sim, and N. Keller, Signaling events connecting mycotoxin biosynthesis and sporulation in Aspergillus and Fusarium spp, JSM Mycotoxins, issue.Suppl3, pp.139-147, 2003.

G. Meca, T. Zhou, X. Z. Li, and J. Manes, Beauvericin degradation during bread and beer making, Food control, vol.34, issue.1, pp.1-8, 2013.

C. B. Michielse and M. Rep, Pathogen profile update: Fusarium oxysporum, Molecular plant pathology, vol.10, issue.3, pp.311-324, 2009.

A. Moretti, A. Belisario, A. Tafuri, A. Ritieni, L. Corazza et al., Production of beauvericin by different races of Fusarium oxysporum f. sp. melonis, the Fusarium wilt agent of muskmelon, Mycotoxins in Plant Disease, pp.661-666, 2002.

T. Netzker, J. Fischer, J. Weber, D. J. Mattern, C. C. König et al., Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters, Frontiers in microbiology, vol.6, p.299, 2015.

E. M. Niehaus, L. Studt, K. W. Von-bargen, W. Kummer, H. U. Humpf et al.,

B. Tudzynski, Sound of silence: the beauvericin cluster in Fusarium fujikuroi is controlled by cluster-specific and global regulators mediated by H3K27 modification, Environmental microbiology, vol.18, issue.11, pp.4282-4302, 2016.

K. O'donnell, C. Gueidan, S. Sink, P. R. Johnston, P. W. Crous et al., A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex, Fungal Genetics and Biology, vol.46, issue.12, pp.936-948, 2009.

S. Oide, W. Moeder, S. Krasnoff, D. Gibson, H. Haas et al., , 2006.

, NPS6, encoding a nonribosomal peptide synthetase involved in siderophore-mediated iron metabolism, is a conserved virulence determinant of plant pathogenic ascomycetes, The plant cell, vol.18, issue.10, pp.2836-2853

C. Paciolla, N. Dipierro, G. Mule, A. Logrieco, and S. Dipierro, The mycotoxins beauvericin and T-2 induce cell death and alteration to the ascorbate metabolism in tomato protoplasts, Physiological and Molecular Plant Pathology, vol.65, issue.1, pp.49-56, 2004.

L. P. Partida-martinez and M. Heil, The microbe-free plant: fact or artifact, Frontiers in plant science, vol.2, p.100, 2011.

R. N. Patkar, P. I. Benke, Z. Qu, Y. Y. Chen, F. Yang et al., A fungal monooxygenase-derived jasmonate attenuates host innate immunity, Nature chemical biology, vol.11, issue.9, p.733, 2015.

J. Peñuelas and J. Terradas, The foliar microbiome, Trends in plant science, vol.19, issue.5, pp.278-280, 2014.

O. Petrini, Fungal endophytes of tree leaves, Microbial ecology of leaves, pp.179-197, 1991.

R. Peyraud, U. Dubiella, A. Barbacci, S. Genin, S. Raffaele et al., Advances on plant-pathogen interactions from molecular toward systems biology perspectives, The Plant Journal, vol.90, issue.4, pp.720-737, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01607459

H. Rho, M. Hsieh, S. L. Kandel, J. Cantillo, S. L. Doty et al., Do endophytes promote growth of host plants under stress? A meta-analysis on plant stress mitigation by endophytes, Microbial ecology, vol.75, issue.2, pp.407-418, 2018.

M. Riemann, K. Haga, T. Shimizu, K. Okada, S. Ando et al., , 2013.

, Identification of rice Allene Oxide Cyclase mutants and the function of jasmonate for defence against Magnaporthe oryzae, The Plant Journal, vol.74, issue.2, pp.226-238

R. J. Rodriguez, J. Henson, E. Van-volkenburgh, M. Hoy, L. Wright et al., Stress tolerance in plants via habitat-adapted symbiosis, The ISME journal, vol.2, issue.4, p.404, 2008.

M. Sagakuchi, A. Moretti, E. Endo, Y. Matsuda, H. Toyoda et al., An approach to the use of plant sensitivity for simple detection of mycotoxins, Proceedings of First Asian Conference of Plant Pathology, pp.262-279, 2000.

M. Scarpari, M. Punelli, V. Scala, M. Zaccaria, C. Nobili et al., , 2014.

, Lipids in Aspergillus flavus-maize interaction, Frontiers in Microbiology, vol.5, p.74

J. C. Schultz and H. M. Appel, Cross-kingdom cross-talk: hormones shared by plants and their insect herbivores, Ecology, vol.85, issue.1, pp.70-77, 2004.

C. Su and E. H. Oliw, Manganese lipoxygenase purification and characterization, Journal of Biological Chemistry, vol.273, issue.21, pp.13072-13079, 1998.

L. F. Thatcher, J. M. Manners, and K. Kazan, Fusarium oxysporum hijacks COI1-mediated jasmonate signaling to promote disease development in Arabidopsis, The Plant Journal, vol.58, issue.6, pp.927-939, 2009.

Y. Tian, S. Amand, D. Buisson, C. Kunz, F. Hachette et al., The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host-plant metabolome for its own benefit, Phytochemistry, vol.108, pp.95-101, 2014.

D. I. Tsitsigiannis, T. M. Kowieski, R. Zarnowski, and N. P. Keller, Three putative oxylipin biosynthetic genes integrate sexual and asexual development in Aspergillus nidulans, Microbiology, issue.6, pp.1809-1821, 2005.

D. I. Tsitsigiannis and N. P. Keller, Oxylipins act as determinants of natural product biosynthesis and seed colonization in Aspergillus nidulans, Molecular microbiology, vol.59, issue.3, pp.882-892, 2006.

D. I. Tsitsigiannis and N. P. Keller, Oxylipins as developmental and host-fungal communication signals, Trends in microbiology, vol.15, issue.3, pp.109-118, 2007.

M. Vallet, Q. P. Vanbellingen, T. Fu, J. P. Le-caer, S. Della-negra et al., An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis, Journal of natural products, vol.80, issue.11, pp.2863-2873, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01998984

P. Vandenkoornhuyse, A. Quaiser, M. Duhamel, L. Van, A. Dufresne et al., The importance of the microbiome of the plant holobiont, New Phytologist, vol.206, issue.4, pp.1196-1206, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01115639

Q. Wang and L. Xu, Beauvericin, a bioactive compound produced by fungi: a short review, Molecules, vol.17, issue.3, pp.2367-2377, 2012.

C. Wasternack and I. Feussner, The oxylipin pathways: biochemistry and function. Annual review of plant biology, vol.69, pp.363-386, 2018.

A. Wennman and E. H. Oliw, Secretion of two novel enzymes, manganese 9S-lipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii, Journal of lipid research, p.33787, 2012.

A. Wennman, A. Magnuson, M. Hamberg, and E. H. Oliw, Manganese lipoxygenase of Fusarium oxysporum and the structural basis for biosynthesis of distinct 11-hydroperoxy stereoisomers, Journal of lipid research, p.60178, 2015.

D. Wilson, Fungal endophytes which invade insect galls: insect pathogens, benign saprophytes, or fungal inquilines?, Oecologia, vol.103, issue.2, pp.255-260, 1995.

D. J. Winter, rentrez: An R package for the NCBI eUtils API (No. e3179v1), 2017.

Y. Xu, R. Orozco, E. K. Wijeratne, A. L. Gunatilaka, S. P. Stock et al., , 2008.

, Biosynthesis of the cyclooligomer depsipeptide beauvericin, a virulence factor of the entomopathogenic fungus Beauveria bassiana, Chemistry & biology, vol.15, issue.9, pp.898-907

L. Zhang, K. Yan, Y. Zhang, R. Huang, J. Bian et al., High-throughput synergy screening identifies microbial metabolites as combination agents for the treatment of fungal infections, Proceedings of the National Academy of Sciences, vol.104, issue.11, pp.4606-4611, 2007.

H. Abdelkafi and B. Nay, Natural products from Cephalotaxus sp.: chemical diversity and synthetic aspects, Natural product reports, vol.29, issue.8, pp.845-869, 2012.

K. J. Affeldt, M. Brodhagen, and N. P. Keller, Aspergillus oxylipin signaling and quorum sensing pathways depend on G protein-coupled receptors, Toxins, vol.4, issue.9, pp.695-717, 2012.

M. T. Agler, J. Ruhe, S. Kroll, C. Morhenn, S. T. Kim et al., , 2016.

, Microbial hub taxa link host and abiotic factors to plant microbiome variation, PLoS biology, vol.14, issue.1, p.1002352

J. U. Ahlholm, M. Helander, S. Lehtimäki, P. Wäli, and K. Saikkonen, Vertically transmitted fungal endophytes: different responses of host-parasite systems to environmental conditions, Oikos, vol.99, issue.1, pp.173-183, 2002.

J. F. Alberts, W. C. Gelderblom, A. Botha, and W. H. Van-zyl, Degradation of aflatoxin B1 by fungal laccase enzymes, International Journal of Food Microbiology, vol.135, issue.1, pp.47-52, 2009.

R. I. Amann, W. Ludwig, and K. H. Schleifer, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiological reviews, vol.59, issue.1, pp.143-169, 1995.

A. Andreou, F. Brodhun, and I. Feussner, Biosynthesis of oxylipins in non-mammals, Progress in lipid research, vol.48, issue.3, pp.148-170, 2009.

S. Angersbach, B. Hipler, S. Brand, and C. Ruckert, Monitoring of microbial growth curves by laser nephelometry, vol.7, p.35, 2005.

G. M. Armstrong, Formae speciales and races of Fusarium oxysporum causing wilt disease. Fusarium: disease, biology, and taxonomy, pp.391-399, 1981.

C. L. Armstrong, W. L. Petersen, W. G. Buchholz, B. A. Bowen, and S. L. Sulc, Factors affecting PEG-mediated stable transformation of maize protoplasts, Plant Cell Reports, vol.9, issue.6, pp.335-339, 1990.

A. E. Arnold and E. A. Herre, Canopy cover and leaf age affect colonization by tropical fungal endophytes: ecological pattern and process in Theobroma cacao (Malvaceae), Mycologia, vol.95, issue.3, pp.388-398, 2003.

A. E. Arnold, L. C. Mejía, D. Kyllo, E. I. Rojas, Z. Maynard et al., , 2003.

, Fungal endophytes limit pathogen damage in a tropical tree, Proceedings of the National Academy of Sciences, vol.100, issue.26, pp.15649-15654

A. E. Arnold, Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers, Fungal biology reviews, vol.21, issue.2-3, pp.51-66, 2007.

D. K. Asch and J. A. Kinsey, Relationship of vector insert size to homologous integration during transformation of Neurospora crassa with the cloned am (GDH) gene. Molecular and General Genetics MGG, vol.221, pp.37-43, 1990.

E. T. Aschehoug, R. M. Callaway, G. Newcombe, N. Tharayil, and S. Chen, Fungal endophyte increases the allelopathic effects of an invasive forb, Oecologia, vol.175, issue.1, pp.285-291, 2014.

Y. Aylon and M. Kupiec, New insights into the mechanism of homologous recombination in yeast, Mutation Research/Reviews in Mutation Research, vol.566, issue.3, pp.231-248, 2004.

C. W. Bacon and J. F. White, Physiological adaptations in the evolution of endophytism in the Clavicipitaceae, Microbial endophytes, pp.251-276, 2000.

C. W. Bacon, A. E. Glenn, and I. E. Yates, Fusarium verticillioides: managing the endophytic association with maize for reduced fumonisins accumulation, Toxin Reviews, vol.27, issue.3-4, pp.411-446, 2008.

H. Bae, D. P. Roberts, H. S. Lim, M. D. Strem, S. C. Park et al., , 2011.

, Endophytic Trichoderma isolates from tropical environments delay disease onset and induce resistance against Phytophthora capsici in hot pepper using multiple mechanisms, Molecular PlantMicrobe Interactions, vol.24, issue.3, pp.336-351

H. Baltruschat, J. Fodor, B. D. Harrach, E. Niemczyk, B. Barna et al., Salt tolerance of barley induced by the root endophyte Piriformospora indica is associated with a strong increase in antioxidants, New Phytologist, vol.180, issue.2, pp.501-510, 2008.

F. Baneyx, Recombinant protein expression in Escherichia coli, Current opinion in biotechnology, vol.10, issue.5, pp.411-421, 1999.

F. Baneyx and M. Mujacic, Recombinant protein folding and misfolding in Escherichia coli, Nature biotechnology, vol.22, issue.11, p.1399, 2004.

L. Barelli, S. Moonjely, S. W. Behie, and M. J. Bidochka, Fungi with multifunctional lifestyles: endophytic insect pathogenic fungi, Plant molecular biology, vol.90, issue.6, pp.657-664, 2016.

C. N. Bastos, Mycoparasitic nature of the antagonism between Trichoderma viride and Crinipellis perniciosa, Fitopatologia Brasileira, 1996.

Ö. Bayram, S. Krappmann, M. Ni, J. W. Bok, K. Helmstaedt et al., VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism, Science, vol.320, issue.5882, pp.1504-1506, 2008.

Ö. Bayram and G. H. Braus, Coordination of secondarymetabolism and development in fungi: the velvet familyof regulatory proteins, FEMS microbiology reviews, vol.36, issue.1, pp.1-24, 2012.

M. Becker, Y. Becker, K. Green, and B. Scott, The endophytic symbiont Epichloë festucae establishes an epiphyllous net on the surface of Lolium perenne leaves by development of an expressorium, an appressorium-like leaf exit structure, New Phytologist, vol.211, issue.1, pp.240-254, 2016.

E. Blée, Impact of phyto-oxylipins in plant defense, Trends in plant science, vol.7, issue.7, pp.315-322, 2002.

M. Bocar, A. Jossang, and B. Bodo, New Alkaloids from Cephalotaxus f ortunei, Journal of natural products, vol.66, issue.1, pp.152-154, 2003.

J. W. Bok and N. P. Keller, LaeA, a regulator of secondary metabolism in Aspergillus spp, Eukaryotic cell, vol.3, issue.2, pp.527-535, 2004.

A. A. Brakhage, Regulation of fungal secondary metabolism, Nature Reviews Microbiology, vol.11, issue.1, p.21, 2013.

G. Brader, S. Compant, K. Vescio, B. Mitter, F. Trognitz et al., Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes, Annual review of phytopathology, vol.55, pp.61-83, 2017.

A. R. Brash, Lipoxygenases: occurrence, functions, catalysis, and acquisition of substrate, Journal of Biological Chemistry, vol.274, issue.34, pp.23679-23682, 1999.

M. Brodhagen and N. P. Keller, Signalling pathways connecting mycotoxin production and sporulation, Molecular Plant Pathology, vol.7, issue.4, pp.285-301, 2006.

F. Brodhun and I. Feussner, Oxylipins in fungi, The FEBS journal, vol.278, issue.7, pp.1047-1063, 2011.

D. Bulgarelli, M. Rott, K. Schlaeppi, E. V. Van-themaat, N. Ahmadinejad et al., Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, vol.488, issue.7409, p.91, 2012.

D. Bulgarelli, K. Schlaeppi, S. Spaepen, E. V. Van-themaat, and P. Schulze-lefert, , 2013.

, Structure and functions of the bacterial microbiota of plants. Annual review of plant biology, vol.64, pp.807-838

L. A. Calhoun, J. A. Findlay, J. D. Miller, and N. J. Whitney, Metabolites toxic to spruce budworm from balsam fir needle endophytes, Mycological Research, vol.96, issue.4, pp.281-286, 1992.

M. M. Carrio, J. L. Corchero, and A. Villaverde, Dynamics of in vivo protein aggregation: building inclusion bodies in recombinant bacteria, FEMS microbiology letters, vol.169, issue.1, pp.9-15, 1998.

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Molecular biology and evolution, vol.17, issue.4, pp.540-552, 2000.

B. N. Chakraborty and M. Kapoor, Transformation of filamentous fungi by electroporation, Nucleic acids research, vol.18, issue.22, p.6737, 1990.

D. Carroll, Genome engineering with zinc-finger nucleases, Genetics, vol.188, issue.4, pp.773-782, 2011.

S. P. Champe, P. Rao, and A. Chang, An endogenous inducer of sexual development in Aspergillus nidulans, Microbiology, vol.133, issue.5, pp.1383-1387, 1987.

A. Chauvin, D. Caldelari, J. L. Wolfender, and E. E. Farmer, Four 13-lipoxygenases contribute to rapid jasmonate synthesis in wounded Arabidopsis thaliana leaves: a role for lipoxygenase 6 in responses to long-distance wound signals, New Phytologist, vol.197, issue.2, pp.566-575, 2013.

S. A. Christensen and M. V. Kolomiets, The lipid language of plant-fungal interactions, Fungal Genetics and Biology, vol.48, issue.1, pp.4-14, 2011.

K. Clay, Fungal endophytes of grasses: a defensive mutualism between plants and fungi, Ecology, vol.69, issue.1, pp.10-16, 1988.

K. Clay and C. Schardl, Evolutionary origins and ecological consequences of endophyte symbiosis with grasses. the american naturalist, vol.160, pp.99-127, 2002.

G. Coffa and A. R. Brash, A single active site residue directs oxygenation stereospecificity in lipoxygenases: stereocontrol is linked to the position of oxygenation, Proceedings of the National Academy of Sciences, vol.101, issue.44, pp.15579-15584, 2004.

H. V. Colot, G. Park, G. E. Turner, C. Ringelberg, C. M. Crew et al., A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors, Proceedings of the National Academy of Sciences, vol.103, issue.27, pp.10352-10357, 2006.

A. Combès, I. Ndoye, C. Bance, J. Bruzaud, C. Djediat et al., Chemical communication between the endophytic fungus Paraconiothyrium variabile and the phytopathogen Fusarium oxysporum, PLoS One, vol.7, issue.10, p.47313, 2012.

R. A. Creelman and J. E. Mullet, Jasmonic acid distribution and action in plants: regulation during development and response to biotic and abiotic stress, Proceedings of the National Academy of Sciences, vol.92, issue.10, pp.4114-4119, 1995.

M. Cristea, Å. Engström, C. Su, L. Hörnsten, and E. H. Oliw, Expression of manganese lipoxygenase in Pichia pastoris and site-directed mutagenesis of putative metal ligands, Archives of biochemistry and biophysics, vol.434, issue.1, pp.201-211, 2005.

T. T. Cushnie and A. J. Lamb, Antimicrobial activity of flavonoids, International journal of antimicrobial agents, vol.26, issue.5, pp.343-356, 2005.

U. Damm, G. J. Verkley, P. W. Crous, P. H. Fourie, A. Haegi et al., Novel Paraconiothyrium species on stone fruit trees and other woody hosts, Persoonia: Molecular Phylogeny and Evolution of Fungi, vol.20, p.9, 2008.

R. Dean, J. A. Van-kan, Z. A. Pretorius, K. E. Hammond-kosack, A. Di-pietro et al.,

G. D. Foster, The Top 10 fungal pathogens in molecular plant pathology, Molecular plant pathology, vol.13, issue.4, pp.414-430, 2012.

A. De-bary, The phenomenon of symbiosis, Karl J. Trubner, 1879.

R. J. Deckert, L. H. Melville, and R. L. Peterson, Structural features of a Lophodermium endophyte during the cryptic life-cycle phase in the foliage of Pinus strobus, Mycological Research, issue.8, pp.991-997, 2001.

A. Decottignies, Alternative end-joining mechanisms: a historical perspective, Frontiers in genetics, vol.4, p.48, 2013.

D. Souza, R. S. Okura, V. K. Armanhi, J. S. Jorrín, B. Lozano et al., Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome, Scientific reports, vol.6, p.28774, 2016.

T. Ding, M. W. Palmer, and U. Melcher, Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria, BMC microbiology, vol.13, issue.1, p.1, 2013.

Z. Ding, M. Li, F. Sun, P. Xi, L. Sun et al., Mitogen-activated protein kinases are associated with the regulation of physiological traits and virulence in Fusarium oxysporum f. sp. cubense, PloS one, vol.10, issue.4, p.122634, 2015.

P. N. Dodds and J. P. Rathjen, Plant immunity: towards an integrated view of plantpathogen interactions, Nature Reviews Genetics, vol.11, issue.8, p.539, 2010.

T. Donald, R. O. Shoshannah, S. T. Deyrup, and J. B. Gloer, A protective endophyte of maize: Acremonium zeae antibiotics inhibitory to Aspergillus flavus and Fusarium verticillioides, Mycological Research, vol.109, issue.5, pp.610-618, 2005.

M. T. Drott, B. P. Lazzaro, D. L. Brown, I. Carbone, and M. G. Milgroom, Balancing selection for aflatoxin in Aspergillus flavus is maintained through interference competition with, and fungivory by insects, Proc. R. Soc. B, vol.284, 1869.

J. Duvick and T. A. Rood, U.S. Patent, vol.798, issue.5, 1998.

J. Edwards, C. Johnson, C. Santos-medellín, E. Lurie, N. K. Podishetty et al., Structure, variation, and assembly of the root-associated microbiomes of rice, Proceedings of the National Academy of Sciences, vol.112, issue.8, pp.911-920, 2015.

N. Eleftheriadis, S. Thee, J. Te-biesebeek, P. Van-der-wouden, B. J. Baas et al., Identification of 6-benzyloxysalicylates as a novel class of inhibitors of 15-lipoxygenase-1, European journal of medicinal chemistry, vol.94, pp.265-275, 2015.

C. Enfert, Selection of multiple disruption events in Aspergillus fumigatus using the orotidine-5?-decarboxylase gene, pyrG, as a unique transformation marker, Current genetics, vol.30, issue.1, pp.76-82, 1996.

A. Erlacher, M. Cardinale, R. Grosch, M. Grube, and G. Berg, The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome, Frontiers in microbiology, vol.5, p.175, 2014.

M. Ernst, K. W. Mendgen, and S. G. Wirsel, Endophytic fungal mutualists: seed-borne Stagonospora spp. enhance reed biomass production in axenic microcosms, Molecular Plant-Microbe Interactions, vol.16, issue.7, pp.580-587, 2003.

L. Evanno, A. Jossang, J. Nguyen-pouplin, D. Delaroche, P. Herson et al., Further studies of the norditerpene (+)-harringtonolide isolated from Cephalotaxus harringtonia var. drupacea: absolute configuration, cytotoxic and antifungal activities, Planta medica, vol.74, issue.08, pp.870-872, 2008.

M. Ferrer, T. N. Chernikova, K. N. Timmis, and P. N. Golyshin, Expression of a temperature-sensitive esterase in a novel chaperone-based Escherichia coli strain, Applied and environmental microbiology, vol.70, issue.8, pp.4499-4504, 2004.

P. H. Fesel and A. Zuccaro, Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis, Current opinion in microbiology, vol.32, pp.103-112, 2016.

I. Feussner and C. Wasternack, The lipoxygenase pathway. Annual review of plant biology, vol.53, pp.275-297, 2002.

R. Finking and M. A. Marahiel, Biosynthesis of nonribosomal peptides, Annu. Rev. Microbiol, vol.58, pp.453-488, 2004.

M. Fouillaud, M. Venkatachalam, M. Llorente, H. Magalon, P. Cuet et al., Biodiversity of Pigmented Fungi Isolated from Marine Environment in La Réunion Island, Indian Ocean: New Resources for Colored Metabolites, Journal of Fungi, vol.3, issue.3, p.36, 2017.

G. J. Fischer and N. P. Keller, Production of cross-kingdom oxylipins by pathogenic fungi: An update on their role in development and pathogenicity, Journal of Microbiology, vol.54, issue.3, pp.254-264, 2016.

S. Freeman, M. Pham, and R. J. Rodriguez, Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A+ T-rich DNA, and nuclear DNA analyses, Experimental Mycology, vol.17, issue.4, pp.309-322, 1993.

R. Freudl, Signal peptides for recombinant protein secretion in bacterial expression systems, Microbial cell factories, vol.17, issue.1, p.52, 2018.

M. L. Friesen, S. S. Porter, S. C. Stark, E. J. Von-wettberg, J. L. Sachs et al., Microbially mediated plant functional traits. Annual review of ecology, evolution, and systematics, p.42, 2011.

C. D. Funk, Prostaglandins and leukotrienes: advances in eicosanoid biology, science, vol.294, issue.5548, pp.1871-1875, 2001.

X. Gao, W. B. Shim, C. Göbel, S. Kunze, I. Feussner et al., Disruption of a maize 9-lipoxygenase results in increased resistance to fungal pathogens and reduced levels of contamination with mycotoxin fumonisin, Molecular plant-microbe interactions, vol.20, issue.8, pp.922-933, 2007.

X. Gao, M. Brodhagen, T. Isakeit, S. H. Brown, C. Göbel et al., Inactivation of the lipoxygenase ZmLOX3 increases susceptibility of maize to Aspergillus spp, Molecular plant-microbe interactions, vol.22, issue.2, pp.222-231, 2009.

A. García, S. A. Rhoden, C. J. Rubin-filho, C. V. Nakamura, and J. A. Pamphile, Diversity of foliar endophytic fungi from the medicinal plant Sapindus saponaria L. and their localization by scanning electron microscopy, Biological research, vol.45, issue.2, pp.139-148, 2012.

J. F. Grove and M. Pople, The insecticidal activity of beauvericin and the enniatin complex, Mycopathologia, vol.70, issue.2, pp.103-105, 1980.

A. L. Gunatilaka, Natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence, Journal of Natural Products, vol.69, issue.3, pp.509-526, 2006.

S. Hacquard, B. Kracher, K. Hiruma, P. C. Münch, R. Garrido-oter et al., Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi, Nature communications, vol.7, p.11362, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01412262

W. Hamada, P. Reignault, G. Bompeix, and M. Boccara, Transformation of Botrytis cinerea with the hygromycin B resistance gene, hph, Current genetics, vol.26, issue.3, pp.251-255, 1994.

M. Hamberg, C. Su, and E. Oliw, Manganese lipoxygenase discovery of a bis-allylic hydroperoxide as product and intermediate in a lipoxygenase reaction, Journal of Biological Chemistry, vol.273, issue.21, pp.13080-13088, 1998.

R. L. Hamill, C. E. Higgens, H. E. Boaz, and M. Gorman, The structure op beauvericin, a new depsipeptide antibiotic toxic to Artemia salina, Tetrahedron Letters, vol.10, issue.49, pp.4255-4258, 1969.

K. Hamonts, P. Trivedi, A. Garg, C. Janitz, J. Grinyer et al., , 2018.

, Field study reveals core plant microbiota and relative importance of their drivers, Environmental microbiology, vol.20, issue.1, pp.124-140

K. Hartman, M. G. Van-der-heijden, R. A. Wittwer, S. Banerjee, J. C. Walser et al., Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming, vol.6, p.14, 2018.

P. J. Hastings, Mechanism and control of recombination in fungi. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.284, pp.97-110, 1992.

Z. He, C. Proudfoot, C. B. Whitelaw, and S. G. Lillico, Comparison of CRISPR/Cas9 and TALENs on editing an integrated EGFP gene in the genome of HEK293FT cells, Springerplus, vol.5, issue.1, p.814, 2016.

O. Heinisch, E. Kowalski, B. Tauscher, and H. Ludwig, Staining for soybean lipoxygenase activity in electrophoretic gels, Lipid/Fett, vol.98, issue.5, pp.183-184, 1996.

U. Hentschel, M. Steinert, and J. Hacker, Common molecular mechanisms of symbiosis and pathogenesis, Trends in microbiology, vol.8, issue.5, pp.226-231, 2000.

M. Herrmann, R. Zocher, and A. Haese, Enniatin production by fusarium strains and its effect on potato tuber tissue, Applied and Environmental Microbiology, vol.62, issue.2, pp.393-398, 1996.

E. A. Herre, L. C. Mejía, D. A. Kyllo, E. Rojas, Z. Maynard et al., Ecological implications of anti-pathogen effects of tropical fungal endophytes and mycorrhizae, Ecology, vol.88, issue.3, pp.550-558, 2007.

R. W. Herzog, H. Daniell, N. K. Singh, and P. A. Lemke, A comparative study on the transformation of Aspergillus nidulans by microprojectile bombardment of conidia and a more conventional procedure using protoplasts treated with polyethyleneglycol, Applied microbiology and biotechnology, vol.45, issue.3, pp.333-337, 1996.

R. Heshof, S. Jylhä, T. Haarmann, A. L. Jørgensen, T. K. Dalsgaard et al., A novel class of fungal lipoxygenases, Applied microbiology and biotechnology, vol.98, issue.3, pp.1261-1270, 2014.

W. S. Horn, M. S. Simmonds, R. E. Schwartz, and W. M. Blaney, Phomopsichalasin, a novel antimicrobial agent from an endophytic Phomopsis sp, Tetrahedron, vol.51, issue.14, pp.3969-3978, 1995.

E. Hornung, M. Walther, H. Kühn, and I. Feussner, Conversion of cucumber linoleate 13lipoxygenase to a 9-lipoxygenating species by site-directed mutagenesis, Proceedings of the National Academy of Sciences, vol.96, issue.7, pp.4192-4197, 1999.

Y. L. Huang, N. B. Zimmerman, and A. E. Arnold, Observations on the Early Establishment of Foliar Endophytic Fungi in Leaf Discs and Living Leaves of a Model Woody Angiosperm, Populus trichocarpa (Salicaceae), Journal of fungi, vol.4, issue.2, 2018.

A. Idnurm, A. S. Urquhart, D. R. Vummadi, S. Chang, A. P. Wouw et al., Spontaneous and CRISPR/Cas9-induced mutation of the osmosensor histidine kinase of the canola pathogen Leptosphaeria maculans, Fungal biology and biotechnology, vol.4, issue.1, p.12, 2017.

S. Jersh, C. Scherer, G. Huth, and E. Schlosser, Proanthocyanidins as basis for quiescence of Botrytis cinerea in immature strawberry, Journal of Plant pathology, vol.22, pp.67-70, 1989.

D. Jiang, W. Zhu, Y. Wang, C. Sun, K. Q. Zhang et al., Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies, Biotechnology advances, issue.8, pp.1562-1574, 2013.

S. M. Kang, A. L. Khan, M. Hamayun, J. Hussain, G. J. Joo et al., , 2012.

, Gibberellin-producing Promicromonospora sp. SE188 improves Solanum lycopersicum plant growth and influences endogenous plant hormones, Journal of Microbiology, vol.50, issue.6, pp.902-909

S. Kaul, T. Sharma, and M. Dhar, Omics" tools for better understanding the plantendophyte interactions, Frontiers in plant science, vol.7, p.955, 2016.

H. C. Kistler and U. K. Benny, Genetic transformation of the fungal plant wilt pathogen, Fusarium oxysporum, Current Genetics, vol.13, issue.2, pp.145-149, 1988.

M. Kostylev, A. E. Otwell, R. E. Richardson, and Y. Suzuki, Cloning should be simple: Escherichia coli DH5?-mediated assembly of multiple DNA fragments with short end homologies, PLoS One, vol.10, issue.9, p.137466, 2015.

K. Kouri, C. Studenik, and R. Lemmens-gruber, Channel forming activity of beauvericin on mammalian cells, BIOPHYSICAL JOURNAL, vol.82, pp.554-554, 2002.

R. Pike and . Bethesda,

S. Krappmann, Gene targeting in filamentous fungi: the benefits of impaired repair, Fungal biology reviews, vol.21, issue.1, pp.25-29, 2007.

M. Krings, T. N. Taylor, H. Hass, H. Kerp, N. Dotzler et al., Fungal endophytes in a 400-million-yr-old land plant: infection pathways, spatial distribution, and host responses, New Phytologist, vol.174, issue.3, pp.648-657, 2007.

H. Kühn, R. Wiesner, J. Rathmann, and T. Schewe, Formation of ketodienoic fatty acids by the pure pea lipoxygenase-1, Eicosanoids, vol.4, issue.1, pp.9-14, 1991.

C. Kunz, E. Vandelle, S. Rolland, B. Poinssot, C. Bruel et al., Characterization of a new, nonpathogenic mutant of Botrytis cinerea with impaired plant colonization capacity, New phytologist, vol.170, issue.3, pp.537-550, 2006.

D. M. Kupfer, S. D. Drabenstot, K. L. Buchanan, H. Lai, H. Zhu et al., Introns and splicing elements of five diverse fungi, Eukaryotic cell, vol.3, issue.5, pp.1088-1100, 2004.

S. Kusari and M. Spiteller, Are we ready for industrial production of bioactive plant secondary metabolites utilizing endophytes?, Natural product reports, vol.28, issue.7, pp.1203-1207, 2011.

S. Kusari, S. Zuhlke, and M. Spiteller, Effect of artificial reconstitution of the interaction between the plant Camptotheca acuminata and the fungal endophyte Fusarium solani on camptothecin biosynthesis, Journal of natural products, vol.74, issue.4, pp.764-775

S. Kusari, C. Hertweck, and M. Spiteller, Chemical ecology of endophytic fungi: origins of secondary metabolites, Chemistry & biology, vol.19, issue.7, pp.792-798, 2012.

A. Langenfeld, S. Prado, B. Nay, C. Cruaud, S. Lacoste et al., Geographic locality greatly influences fungal endophyte communities in Cephalotaxus harringtonia, Fungal biology, vol.117, issue.2, pp.124-136, 2013.

S. L. Lebeis, The potential for give and take in plant-microbiome relationships. Frontiers in plant science, vol.5, p.287, 2014.

R. Lemmens-gruber, B. Rachoy, E. Steininger, K. Kouri, P. Saleh et al., The effect of the Fusarium metabolite beauvericin on electromechanical andphysiological properties in isolated smooth and heart muscle preparations of guinea pigs, Mycopathologia, vol.149, issue.1, pp.5-12, 2000.

J. Y. Li, J. K. Harper, D. M. Grant, B. O. Tombe, B. Bashyal et al., Ambuic acid, a highly functionalized cyclohexenone with antifungal activity from Pestalotiopsis spp. and Monochaetia sp, Phytochemistry, vol.56, issue.5, pp.463-468, 2001.

D. C. Li, Z. W. Lui, and J. Lu, Purification and characterization of lipoxygenase from the thermophilic fungus Thermomyces lanuginosus, Mycological Research, vol.105, issue.2, pp.190-194, 2001.

H. Li, C. Qing, Y. Zhang, and Z. Zhao, Screening for endophytic fungi with antitumour and antifungal activities from Chinese medicinal plants, World Journal of Microbiology and Biotechnology, vol.21, issue.8-9, pp.1515-1519, 2005.

D. Li, Y. Tang, J. Lin, and W. Cai, Methods for genetic transformation of filamentous fungi. Microbial cell factories, vol.16, p.168, 2017.

E. K. Ligoxigakis, I. A. Papaioannou, E. A. Markakis, and M. A. Typas, First report of leaf spot of Phoenix theophrasti caused by Paraconiothyrium variabile in Greece, Plant disease, vol.97, issue.9, pp.1250-1250, 2013.

R. Liu, L. Chen, Y. Jiang, Z. Zhou, and G. Zou, Efficient genome editing in filamentous fungus Trichoderma reesei using the CRISPR/Cas9 system, Cell Discovery, vol.1, p.15007, 2015.

V. C. Liuzzi, V. Mirabelli, M. T. Cimmarusti, M. Haidukowski, J. F. Leslie et al., Enniatin and Beauvericin Biosynthesis in Fusarium Species: Production Profiles and Structural Determinant Prediction, Toxins, vol.9, issue.2, p.45, 2017.

J. L. Lockwood, Exploitation competition. The fungal community: its organization and role in the ecosystem, pp.243-263, 1992.

A. Logrieco, A. Moretti, G. Castella, M. Kostecki, P. Golinski et al., Beauvericin Production by FusariumSpecies, Applied and Environmental Microbiology, vol.64, issue.8, pp.3084-3088, 1998.

M. S. López-berges, K. Schäfer, C. Hera, and A. Di-pietro, Combinatorial function of velvet and AreA in transcriptional regulation of nitrate utilization and secondary metabolism, Fungal Genetics and Biology, vol.62, pp.78-84, 2014.

J. C. Lord, S. Anderson, and D. W. Stanley, Eicosanoids mediate Manduca sexta cellular response to the fungal pathogen Beauveria bassiana: a role for the lipoxygenase pathway, Archives of Insect Biochemistry and Physiology, vol.51, issue.1, pp.46-54, 2002.

D. S. Lundberg, S. L. Lebeis, S. H. Paredes, S. Yourstone, J. Gehring et al., Occurrence of peptide and clavine ergot alkaloids in tall fescue grass, Science, vol.488, issue.7409, pp.487-489, 1986.

L. J. Ma, D. M. Geiser, R. H. Proctor, A. P. Rooney, K. O'donnell et al., Fusarium pathogenomics. Annual review of microbiology, vol.67, pp.399-416, 2013.

K. S. Makarova, N. V. Grishin, S. A. Shabalina, Y. I. Wolf, and E. V. Koonin, A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action, Biology direct, vol.1, issue.1, p.7, 2006.

K. Mandyam and A. Jumpponen, Seeking the elusive function of the root-colonising dark septate endophytic fungi, Studies in Mycology, vol.53, pp.173-189, 2005.

J. Mathieu and M. Erfia, Contans, du nouveau: Résultats récents sur ce champignon anti-sclérotinia. Phytoma-La Défense des végétaux, pp.14-17, 2008.

J. Martín-garcía, E. Espiga, V. Pando, and J. J. Diez, Factors influencing endophytic communities in poplar plantations, Silva Fennica, vol.45, issue.2, pp.169-180, 2011.

G. Meca, T. Zhou, X. Z. Li, and J. Manes, Beauvericin degradation during bread and beer making, Food control, vol.34, issue.1, pp.1-8, 2013.

J. Merhej, M. Urban, M. Dufresne, K. E. Hammond-kosack, F. Richard-forget et al., The velvet gene, FgVe1, affects fungal development and positively regulates trichothecene biosynthesis and pathogenicity in Fusarium graminearum, Molecular plant pathology, vol.13, issue.4, pp.363-374, 2012.

V. Meyer, Genetic engineering of filamentous fungi-progress, obstacles and future trends, Biotechnology advances, vol.26, issue.2, pp.177-185, 2008.

C. B. Michielse, P. J. Hooykaas, C. A. Van-den-hondel, and A. F. Ram, Agrobacteriummediated transformation as a tool for functional genomics in fungi, Current genetics, vol.48, issue.1, pp.1-17, 2005.

C. B. Michielse and M. Rep, Pathogen profile update: Fusarium oxysporum, Molecular plant pathology, vol.10, issue.3, pp.311-324, 2009.

W. Minor, J. Steczko, J. T. Bolin, Z. Otwinowski, and B. Axelrod, Crystallographic determination of the active site iron and its ligands in soybean lipoxygenase L-1, Biochemistry, vol.32, issue.25, pp.6320-6323, 1993.

E. Mönke and W. Schäfer, Transient and stable gene expression in the fungal maize pathogen Cochliobolus heterostrophus after transformation with the ?-glucuronidase (GUS) gene. Molecular and General Genetics MGG, pp.73-80, 1993.

H. Mooibroek, A. G. Kuipers, J. H. Sietsma, P. J. Punt, and J. G. Wessels, Introduction of hygromycin B resistance into Schizophyllum commune: preferential methylation of donor DNA, Molecular and General Genetics MGG, vol.222, issue.1, pp.41-48, 1990.

A. Moretti, G. Mule, A. Ritieni, and A. Logrieco, Further data on the production of beauvericin, enniatins and fusaproliferin and toxicity to Artemia salina by Fusarium species of Gibberella fujikuroi species complex, International journal of food microbiology, vol.118, issue.2, pp.158-163, 2007.

A. Mosblech, I. Feussner, and I. Heilmann, Oxylipins: structurally diverse metabolites from fatty acid oxidation, Plant Physiology and Biochemistry, vol.47, issue.6, pp.511-517, 2009.

K. Myung, N. C. Zitomer, M. Duvall, A. E. Glenn, R. T. Riley et al., The conserved global regulator VeA is necessary for symptom production and mycotoxin synthesis in maize seedlings by Fusarium verticillioides, Plant pathology, issue.1, pp.152-160, 2012.

T. Nilsson, Studies on wood degradation and cellulolytic activity of microfungi, 1973.

T. Netzker, J. Fischer, J. Weber, D. J. Mattern, C. C. König et al., , 2015.

M. E. Newcomer and A. R. Brash, The structural basis for specificity in lipoxygenase catalysis, Protein Science, vol.24, issue.3, pp.298-309, 2015.

J. Newie, P. Neumann, M. Werner, R. A. Mata, R. Ficner et al., Lipoxygenase 2 from Cyanothece sp. controls dioxygen insertion by steric shielding and substrate fixation, Scientific reports, vol.7, issue.1, p.2069, 2017.

E. M. Niehaus, L. Studt, K. W. Von-bargen, W. Kummer, H. U. Humpf et al., Sound of silence: the beauvericin cluster in Fusarium fujikuroi is controlled by cluster-specific and global regulators mediated by H3K27 modification, Environmental microbiology, vol.18, issue.11, pp.4282-4302, 2016.

C. S. Nødvig, J. B. Nielsen, M. E. Kogle, and U. H. Mortensen, A CRISPR-Cas9 system for genetic engineering of filamentous fungi, PLoS One, vol.10, issue.7, p.133085, 2015.

C. S. Nødvig, J. B. Hoof, M. E. Kogle, Z. D. Jarczynska, J. Lehmbeck et al., Efficient oligo nucleotide mediated CRISPR-Cas9 gene editing in Aspergilli, Fungal Genetics and Biology, vol.115, pp.78-89, 2018.

M. C. Noverr, G. B. Toews, and G. B. Huffnagle, Production of prostaglandins and leukotrienes by pathogenic fungi, Infection and immunity, vol.70, issue.1, pp.400-402, 2002.

M. C. Noverr, J. R. Erb-downward, and G. B. Huffnagle, Production of eicosanoids and other oxylipins by pathogenic eukaryotic microbes, Clinical microbiology reviews, vol.16, issue.3, pp.517-533, 2003.

S. Oide, W. Moeder, S. Krasnoff, D. Gibson, H. Haas et al., , 2006.

E. H. Oliw, Plant and fungal lipoxygenases, Prostaglandins & other lipid mediators, vol.68, pp.313-323, 2002.

D. G. Panaccione, W. T. Beaulieu, and D. Cook, Bioactive alkaloids in vertically transmitted fungal endophytes, Functional Ecology, vol.28, issue.2, pp.299-314, 2014.

R. N. Patkar, P. I. Benke, Z. Qu, Y. Y. Chen, F. Yang et al., A fungal monooxygenase-derived jasmonate attenuates host innate immunity, Nature chemical biology, vol.11, issue.9, p.733, 2015.

J. Peñuelas and J. Terradas, The foliar microbiome, Trends in plant science, vol.19, issue.5, pp.278-280, 2014.

M. Pérez-gilabert, I. Sánchez-felipe, and F. García-carmona, Purification and partial characterization of lipoxygenase from desert truffle (Terfezia claveryi Chatin) ascocarps, Journal of agricultural and food chemistry, vol.53, issue.9, pp.3666-3671, 2005.

G. L. Peskett, Studies on the growth of yeast: a nephelometric method of counting yeast suspensions, Biochemical Journal, vol.21, issue.3, p.460, 1927.

O. Petrini, Fungal endophytes of tree leaves, Microbial ecology of leaves, pp.179-197, 1991.

C. M. Pieterse, C. Zamioudis, R. L. Berendsen, D. M. Weller, S. C. Van-wees et al., Induced systemic resistance by beneficial microbes. Annual review of phytopathology, p.52, 2014.

C. H. Pohl and J. L. Kock, Oxidized fatty acids as inter-kingdom signaling molecules, Molecules, vol.19, issue.1, pp.1273-1285, 2014.

A. Porras-alfaro and P. Bayman, Hidden fungi, emergent properties: endophytes and microbiomes. Annual review of phytopathology, vol.49, pp.291-315, 2011.

H. Porta and M. Rocha-sosa, Plant lipoxygenases. Physiological and molecular features, Plant physiology, vol.130, issue.1, pp.15-21, 2002.

I. Promputtha, S. Lumyong, V. Dhanasekaran, E. H. Mckenzie, K. D. Hyde et al., A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence, Microbial Ecology, vol.53, issue.4, pp.579-590, 2007.

C. Ravel, C. Courty, A. Coudret, and G. Charmet, Beneficial effects of Neotyphodium lolii on the growth and the water status in perennial ryegrass cultivated under nitrogen deficiency or drought stress, Agronomie, vol.17, issue.3, pp.173-181, 1997.
URL : https://hal.archives-ouvertes.fr/hal-00885835

B. G. Rector, M. Czarnoleski, A. Skoracka, and M. Lembicz, Change in abundance of three phytophagous mite species (Acari: Eriophyidae, Tetranychidae) on quackgrass in the presence of choke disease, Experimental and Applied Acarology, vol.70, issue.1, pp.35-43, 2016.

R. S. Redman, K. B. Sheehan, R. G. Stout, R. J. Rodriguez, and J. M. Henson, , 2002.

, Thermotolerance generated by plant/fungal symbiosis, Science, vol.298, issue.5598, pp.1581-1581

R. S. Redman, Y. O. Kim, C. J. Woodward, C. Greer, L. Espino et al., Increased fitness of rice plants to abiotic stress via habitat adapted symbiosis: a strategy for mitigating impacts of climate change, PLOS one, vol.6, issue.7, p.14823, 2011.

M. Reverberi, F. Punelli, M. Scarpari, E. Camera, S. Zjalic et al., , 2010.

, Lipoperoxidation affects ochratoxin A biosynthesis in Aspergillus ochraceus and its interaction with wheat seeds, Applied microbiology and biotechnology, vol.85, issue.6, pp.1935-1946

M. G. Richey, E. T. Marek, C. L. Schardl, and D. A. Smith, Transformation of filamentous fungi with plasmid DNA by electroporation, Phytopathology, vol.79, issue.8, pp.844-847, 1989.

M. Riemann, K. Haga, T. Shimizu, K. Okada, S. Ando et al., Identification of rice Allene Oxide Cyclase mutants and the function of jasmonate for defence against Magnaporthe oryzae, The Plant Journal, vol.74, issue.2, pp.226-238, 2013.

R. J. Rodriguez, J. Henson, E. Van-volkenburgh, M. Hoy, L. Wright et al., Stress tolerance in plants via habitat-adapted symbiosis, The ISME journal, vol.2, issue.4, p.404, 2008.

R. J. Rodriguez, J. F. White, A. E. Arnold, and A. R. Redman, Fungal endophytes: diversity and functional roles, New phytologist, vol.182, issue.2, pp.314-330, 2009.

C. W. Rogers, M. P. Challen, J. R. Green, and J. M. Whipps, Use of REMI and Agrobacterium-mediated transformation to identify pathogenicity mutants of the biocontrol fungus, Coniothyrium minitans, FEMS Microbiology Letters, issue.2, pp.207-214, 2004.

M. Rohlfs and B. Obmann, Species-specific responses of dew fly larvae to mycotoxins, Mycotoxin research, vol.25, issue.2, pp.103-112, 2009.

G. L. Rosano and E. A. Ceccarelli, Recombinant protein expression in Escherichia coli: advances and challenges, Frontiers in microbiology, vol.5, p.172, 2014.

E. Rosenberg, G. Sharon, and I. Zilber-rosenberg, The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework, Environmental microbiology, vol.11, issue.12, pp.2959-2962, 2009.

K. Saikkonen, S. H. Faeth, M. Helander, and T. J. Sullivan, Fungal endophytes: a continuum of interactions with host plants, Annual Review of Ecology and Systematics, vol.29, issue.1, pp.319-343, 1998.

K. Saikkonen, P. E. Gundel, and M. Helander, Chemical ecology mediated by fungal endophytes in grasses, Journal of chemical ecology, vol.39, issue.7, pp.962-968, 2013.

F. Sainsbury and G. P. Lomonossoff, Transient expressions of synthetic biology in plants, Current opinion in plant biology, vol.19, pp.1-7, 2014.

Ö. Sarikaya-bayram, J. M. Palmer, N. Keller, G. H. Braus, and Ö. Bayram, One Juliet and four Romeos: VeA and its methyltransferases, Frontiers in microbiology, vol.6, p.1, 2015.

M. Saunders, A. E. Glenn, and L. M. Kohn, Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes, Evolutionary Applications, vol.3, issue.5-6, pp.525-537, 2010.

V. Scala, P. Giorni, M. Cirlini, M. Ludovici, I. Visentin et al., , 2014.

, LDS1-produced oxylipins are negative regulators of growth, conidiation and fumonisin synthesis in the fungal maize pathogen Fusarium verticillioides, Frontiers in microbiology, vol.5, p.669

M. Scarpari, M. Punelli, V. Scala, M. Zaccaria, C. Nobili et al., Lipids in Aspergillus flavus-maize interaction, Frontiers in Microbiology, vol.5, p.74, 2014.

M. A. Selosse, A. Bessis, and M. J. Pozo, Microbial priming of plant and animal immunity: symbionts as developmental signals, Trends in microbiology, vol.22, issue.11, pp.607-613, 2014.

M. A. Selosse and C. L. Schardl, Fungal endophytes of grasses: hybrids rescued by vertical transmission? An evolutionary perspective, New Phytologist, vol.173, issue.3, pp.452-458, 2007.

C. L. Schoch, G. H. Sung, F. López-giráldez, J. P. Townsend, J. Miadlikowska et al.,

C. Gueidan, The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits, Systematic biology, vol.58, issue.2, pp.224-239, 2009.

B. Schulz, A. K. Römmert, U. Dammann, H. J. Aust, and D. Strack, The endophyte-host interaction: a balanced antagonism, Mycological Research, vol.103, issue.10, pp.1275-1283, 1999.

B. Schulz, C. Boyle, S. Draeger, A. K. Römmert, and K. Krohn, Endophytic fungi: a source of novel biologically active secondary metabolites, Mycological Research, vol.106, issue.9, pp.996-1004, 2002.

J. C. Schultz and H. M. Appel, Cross-kingdom cross-talk: hormones shared by plants and their insect herbivores, Ecology, vol.85, issue.1, pp.70-77, 2004.

B. Schulz and C. Boyle, The endophytic continuum, Mycological research, vol.109, issue.6, pp.661-686, 2005.

K. J. Sheridan, S. K. Dolan, and S. Doyle, Endogenous cross-talk of fungal metabolites, Frontiers in microbiology, vol.5, p.732, 2015.

T. N. Sieber, Endophytic fungi in forest trees: are they mutualists?, Fungal Biology Reviews, vol.21, issue.2-3, pp.75-89, 2007.

E. Skrzypczak-jankun, R. A. Bross, R. T. Carroll, W. R. Dunham, and M. O. Funk, Threedimensional structure of a purple lipoxygenase, Journal of the American Chemical Society, vol.123, issue.44, pp.10814-10820, 2001.

D. L. Sloane, R. Leung, C. S. Craik, and E. Sigal, A primary determinant for lipoxygenase positional specificity, Nature, vol.354, issue.6349, p.149, 1991.

V. Solovyev, P. Kosarev, I. Seledsov, and D. Vorobyev, Automatic annotation of eukaryotic genes, pseudogenes and promoters, Genome biology, vol.7, issue.1, p.10, 2006.

H. P. Sørensen and K. K. Mortensen, Advanced genetic strategies for recombinant protein expression in Escherichia coli, Journal of biotechnology, vol.115, issue.2, pp.113-128, 2005.

M. J. Spiering, D. H. Greer, and J. A. Schmid, Effects of the fungal endophyte, Neotyphodium lolii, on net photosynthesis and growth rates of perennial ryegrass (Lolium perenne) are independent of in planta endophyte concentration, Annals of botany, vol.98, issue.2, pp.379-387, 2006.

P. Spiteller, Chemical ecology of fungi, Natural product reports, vol.32, issue.7, pp.971-993, 2015.

C. Staben, B. Jensen, M. Singer, J. Pollock, M. Schechtman et al., Use of a bacterial hygromycin B resistance gene as a dominant selectable marker in Neurospora crassa transformation, Fungal Genetics Reports, vol.36, issue.1, p.79, 1989.

G. A. Strobel, E. Dirkse, J. Sears, and C. Markworth, Volatile antimicrobials from Muscodor albus, a novel endophytic fungus, Microbiology, vol.147, issue.11, pp.2943-2950, 2001.

G. Strobel and B. Daisy, Bioprospecting for microbial endophytes and their natural products, Microbiology and molecular biology reviews, vol.67, issue.4, pp.491-502, 2003.

F. W. Studier, Protein production by auto-induction in high-density shaking cultures. Protein expression and purification, vol.41, pp.207-234, 2005.

L. Studt, P. Wiemann, K. Kleigrewe, H. U. Humpf, and B. Tudzynski, Biosynthesis of fusarubins accounts for pigmentation of Fusarium fujikuroi perithecia, Applied and environmental microbiology, p.823, 2012.

C. Su and E. H. Oliw, Manganese lipoxygenase purification and characterization, Journal of Biological Chemistry, vol.273, issue.21, pp.13072-13079, 1998.

C. Sun, J. M. Johnson, D. Cai, I. Sherameti, R. Oelmüller et al., Piriformospora indica confers drought tolerance in Chinese cabbage leaves by stimulating antioxidant enzymes, the expression of drought-related genes and the plastid-localized CAS protein, Journal of plant physiology, vol.167, issue.12, pp.1009-1017, 2010.

M. S. Torres, A. P. Singh, N. Vorsa, T. Gianfagna, and J. F. White, Were endophytes pre-adapted for defensive mutualism, 6th International Symposium on Fungal Endophytes of Grasses, pp.63-67, 2007.

D. I. Tsitsigiannis, R. Zarnowski, and N. P. Keller, The lipid body protein, PpoA, coordinates sexual and asexual sporulation in Aspergillus nidulans, Journal of Biological Chemistry, vol.279, issue.12, pp.11344-11353, 2004.

D. I. Tsitsigiannis and N. P. Keller, Oxylipins as developmental and host-fungal communication signals, Trends in microbiology, vol.15, issue.3, pp.109-118, 2007.

B. Tudzynski, Nitrogen regulation of fungal secondary metabolism in fungi, Frontiers in microbiology, vol.5, 2014.

U. 'ren, J. M. Lutzoni, F. Miadlikowska, J. Laetsch, A. D. Arnold et al., Host and geographic structure of endophytic and endolichenic fungi at a continental scale, American Journal of Botany, vol.99, issue.5, pp.898-914, 2012.

J. Vadassery, C. Ritter, Y. Venus, I. Camehl, A. Varma et al., The role of auxins and cytokinins in the mutualistic interaction between Arabidopsis and Piriformospora indica, Molecular Plant-Microbe Interactions, vol.21, issue.10, pp.1371-1383, 2008.

M. G. Van-der-heijden and M. Hartmann, Networking in the plant microbiome, PLoS Biology, vol.14, issue.2, p.1002378, 2016.

J. A. Vorholt, Microbial life in the phyllosphere, Nature Reviews Microbiology, vol.10, issue.12, p.828, 2012.

T. Vu, R. Hauschild, and R. A. Sikora, Fusarium oxysporum endophytes induced systemic resistance against Radopholus similis on banana, Nematology, vol.8, issue.6, pp.847-852, 2006.

P. R. Wäli, M. Helander, O. Nissinen, and K. Saikkonen, Susceptibility of endophyteinfected grasses to winter pathogens (snow molds), Botany, vol.84, issue.7, pp.1043-1051, 2006.

Q. Wang and L. Xu, Beauvericin, a bioactive compound produced by fungi: a short review, Molecules, vol.17, issue.3, pp.2367-2377, 2012.

C. Wasternack and B. Hause, Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany, Annals of botany, vol.111, issue.6, pp.1021-1058, 2013.

C. Wasternack and I. Feussner, The oxylipin pathways: biochemistry and function. Annual review of plant biology, vol.69, pp.363-386, 2018.

R. J. Weld, K. M. Plummer, M. A. Carpenter, and H. J. Ridgway, Approaches to functional genomics in filamentous fungi, Cell research, vol.16, issue.1, p.31, 2006.

A. Wennman and E. H. Oliw, Secretion of two novel enzymes, manganese 9Slipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii, Journal of lipid research, vol.54, issue.3, pp.762-775, 2012.

A. Wennman, E. H. Oliw, S. Karkehabadi, and Y. Chen, Crystal structure of manganese lipoxygenase of the rice blast fungus Magnaporthe oryzae, Journal of Biological Chemistry, p.115, 2016.

D. Wilson, Fungal endophytes which invade insect galls: insect pathogens, benign saprophytes, or fungal inquilines?, Oecologia, vol.103, issue.2, pp.255-260, 1995.

D. J. Winter, rentrez: An R package for the NCBI eUtils API (No. e3179v1). PeerJ Preprints, 2017.

Y. Xu, R. Orozco, E. K. Wijeratne, A. L. Gunatilaka, S. P. Stock et al., , 2008.

, Biosynthesis of the cyclooligomer depsipeptide beauvericin, a virulence factor of the entomopathogenic fungus Beauveria bassiana, Chemistry & biology, vol.15, issue.9, pp.898-907

W. Zhang and R. Wu, Efficient regeneration of transgenic plants from rice protoplasts and correctly regulated expression of the foreign gene in the plants, Theoretical and Applied Genetics, vol.76, issue.6, pp.835-840, 1988.

Y. Zhang, U. Werling, and W. Edelmann, SLiCE: a novel bacterial cell extract-based DNA cloning method, Nucleic acids research, vol.40, issue.8, pp.55-55, 2012.

A. Zienkiewicz, J. D. Rejón, J. De-dios-alché, M. I. Rodríguez-garcía, and A. J. Castro, A protocol for protein extraction from lipid-rich plant tissues suitable for electrophoresis, pp.85-91, 2014.

, Un infini merci à Maxime pour m'avoir écoutée, soutenue, redonné confiance

, Au cours de leur interaction, on détecte des quantités moindres de beauvéricine, une mycotoxine synthétisée par F. oxysporum. En parallèle, on observe une augmentation de la synthèse de deux oxylipines, l'acide 13hydroperoxyoctadécadiénoïque (13-HPODE) et l'acide 13-oxo-octadécadiénoïque (13-oxo-ODE), dans la zone de confrontation. L'objectif de ce travail était de comprendre les mécanismes conduisant à la diminution de la beauvéricine au cours de l'interaction et d'explorer le rôle des oxylipines dans la régulation de cette dernière. Dans mon travail de thèse, je montre la présence de deux gènes lox chez P. variabile (pvlox1 et pvlox2) codant tous deux pour des manganèse lipoxygénases, potentiellement à l'origine des acides 13-HPODE et 13-oxo-ODE. Pvlox2 est spécifiquement induit pendant l'interaction, et ces résultats sont corroborés par une synthèse accrue de 13-HPODE chez P. variabile. Par ailleurs, l'interaction avec l'endophyte, ainsi que l'ajout de l'oxylipine 13-HPODE, régulent positivement la voie de biosynthèse de la beauvéricine, comme l'indiquent les teneurs plus élevées en mycotoxines observées chez F. oxysporum. Enfin, nous avons montré que la beauvéricine inhibait la croissance de l'endophyte, mais que ce dernier était capable de dégrader la mycotoxine, Les champignons endophytes sont des microorganismes non-pathogènes impliqués dans des associations mutualistes avec les plantes. Les endophytes foliaires, en particulier, représentent un groupe très divers, mais leurs interactions avec la plante hôte et ses micro-organismes associés sont peu connues

, In preliminary work, exploring the leaf microbial diversity of the conifer Cephalotaxus harringtonia, our team isolated the fungal strain Paraconiothyrium variabile (Ascomycota), an antagonist of the phytopathogen Fusarium oxysporum. During their interaction, decreased amounts of the F. oxysporum mycotoxin beauvericin, and higher amounts of the two oxylipins, 13-hydroperoxyoctadecadienoic acid (13-HPODE) and 13-oxooctadecadienoic acid (13-oxo-ODE), were observed in the confrontation zone. The objective of the present work was to understand the mechanisms leading to beauvericin decrease during the interaction and to explore the role of oxylipins in beauvericin regulation. In my thesis work I show the presence of two lox genes in P. variabile (pvlox1 and pvlox2) coding both for manganese lipoxygenases, potentially at the origin of 13-HPODE and 13-oxo-ODE. Pvlox2 is specifically induced during the interaction, which lead to an increased synthesis of 13-HPODE in P. variabile. The endophyte itself, as well as the oxylipin 13-HPODE, up-regulated the beauvericin biosynthesis gene beas, which was paralleled by higher mycotoxin content in the mycelium of F. oxysporum. Finally, we showed that beauvericin inhibited the endophyte's growth, ABSTRACT Endophytic fungi are non-pathogenic microorganisms involved in mutualistic associations with their host. Foliar endophytes, in particular, represent a very diverse group but little is known about their interactions with the host and its associated micro-organisms