D. L. Hawksworth and R. Lücking, Fungal Diversity Revisited: 2.2 to 3.8 Million Species, Microbiology Spectrum, vol.5, issue.4, 2017.

R. H. Nilsson, S. Anslan, M. Bahram, C. Wurzbacher, P. Baldrian et al., Mycobiome diversity: high-throughput sequencing and identification of fungi, Nature Reviews Microbiology, vol.17, issue.2, pp.95-109, 2019.

T. C. Cairns, C. Nai, and V. Meyer, How a fungus shapes biotechnology: 100 years of Aspergillus niger research, Fungal Biology and Biotechnology, vol.5, issue.1, p.13, 2018.

M. Spagnuolo, A. Yaguchi, and M. Blenner, Oleaginous yeast for biofuel and oleochemical production, Current Opinion in Biotechnology, vol.57, pp.73-81, 2019.

R. Chang, Bioactive polysaccharides from traditional Chinese medicine herbs as anticancer adjuvants, J Altern Complement Med, vol.8, issue.5, pp.559-65, 2002.

O. Rop, J. Mlcek, and T. Jurikova, Beta-glucans in higher fungi and their health effects, Nutr Rev, vol.67, issue.11, pp.624-655, 2009.

R. P. Pelley and F. M. Strickland, Plants, polysaccharides, and the treatment and prevention of neoplasia, Crit Rev Oncog, vol.11, issue.3-4, pp.189-225, 2000.

L. Nalley, F. Tsiboe, A. Durand-morat, A. Shew, and G. Thoma, Economic and Environmental Impact of Rice Blast Pathogen (Magnaporthe oryzae) Alleviation in the United States, PloS one, vol.11, issue.12, p.167295, 2016.

M. Dita, M. Barquero, D. Heck, E. Mizubuti, and C. P. Staver, Fusarium Wilt of Banana: Current Knowledge on Epidemiology and Research Needs Toward Sustainable Disease Management, Frontiers in Plant Science, vol.9, 1468.

K. P. Drees, J. M. Lorch, S. J. Puechmaille, K. L. Parise, G. Wibbelt et al., Phylogenetics of a Fungal Invasion: Origins and Widespread Dispersal of White-Nose Syndrome, vol.8, pp.1941-1958, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01872542

L. F. Grogan, J. Robert, L. Berger, L. F. Skerratt, B. C. Scheele et al., Review of the Amphibian Immune Response to Chytridiomycosis, and Future Directions, Frontiers in immunology, vol.9, p.2536, 2018.

F. Bongomin, S. Gago, O. R. Oladele, and W. D. Denning, Global and Multi-National Prevalence of Fungal Diseases-Estimate Precision, Journal of Fungi, vol.3, issue.4, p.57, 2017.

F. Bongomin, S. Gago, R. O. Oladele, and D. W. Denning, Global and Multi-National Prevalence of Fungal Diseases-Estimate Precision, Journal of fungi, vol.3, issue.4, p.57, 2017.

B. R. Jackson, K. D. Beer, T. Chiller, K. Benedict, K. J. Kwon-chung et al., Estimation of Direct Healthcare Costs of Fungal Diseases in the United States, Clininal Infectious Diseases, vol.17, issue.11, pp.1791-1797, 2019.

, Cryptococcus neoformans and Cryptococcus gattii, the etiologic agents of cryptococcosis, Cold Spring Harb Perspect Med, vol.4, p.19760, 2014.

A. H. Limper, A. Adenis, T. Le, and T. S. Harrison, Fungal infections in HIV/AIDS. The Lancet Infectious Diseases, vol.17, pp.334-377, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-01574426

N. V. Sipsas and D. P. Kontoyiannis, Invasive fungal infections in patients with cancer in the Intensive Care Unit, International journal of antimicrobial agents, vol.39, issue.6, pp.464-71, 2012.

R. Martinez, New Trends in Paracoccidioidomycosis Epidemiology, Journal of fungi, p.2017

A. A. Adenis, A. Valdes, C. Cropet, O. Z. Mccotter, G. Derado et al., Burden of HIV-associated histoplasmosis compared with tuberculosis in Latin America: a modelling study. The Lancet Infectious Diseases, vol.18, pp.1150-1159, 2018.
URL : https://hal.archives-ouvertes.fr/inserm-01868606

L. Scorzoni, P. De, A. Silva, C. M. Marcos, P. A. Assato et al., Antifungal Therapy: New Advances in the Understanding and Treatment of Mycosis, Frontiers in Microbiology, vol.8, issue.36, pp.1-23, 2017.

M. C. Fisher, N. J. Hawkins, D. Sanglard, S. J. Gurr, R. W. Bastos et al., Worldwide emergence of resistance to antifungal drugs challenges human health and food security, Science, vol.360, 2018.

, Environmental Triazole Induces Cross-Resistance to Clinical Drugs and Affects Morphophysiology and Virulence of Cryptococcus gattii and C. neoformans. Antimicrobial agents and chemotherapy, vol.62, pp.1179-1196, 2017.

M. Kneale, J. S. Bartholomew, D. W. Denning, and E. Davies, Global access to antifungal therapy and its variable cost, Journal of Antimicrobial Chemotherapy, vol.71, issue.12, pp.3599-606, 2016.

A. Casadevall, Determinants of virulence in the pathogenic fungi, Fungal biology reviews, vol.21, issue.4, pp.130-132, 2007.

T. Jones, N. A. Federspiel, H. Chibana, J. Dungan, S. Kalman et al., The diploid genome sequence of Candida albicans, Proceedings of the National Academy of Sciences of the United States of America, vol.101, issue.19, pp.7329-7363, 2004.

B. Dujon, D. Sherman, G. Fisher, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.430, pp.35-44, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00104411

G. Janbon, K. L. Ormerod, D. Paulet, I. Byrnes, . Ej et al., Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation, PLoS Genet, vol.10, p.1004261, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01204377

W. Nierman, A. Pain, M. Anderson, J. Wortman, H. Kim et al., Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus, Nature, vol.438, issue.7071, pp.1151-1157, 2005.
URL : https://hal.archives-ouvertes.fr/pasteur-02639869

O. W. Liu, C. D. Chun, E. D. Chow, C. Chen, H. D. Madhani et al., Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans, Cell, vol.135, pp.174-88, 2008.

T. Roemer, B. Jiang, J. Davison, T. Ketela, K. Veillette et al., Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery, Mol Microbiol, vol.50, pp.167-81, 2003.

T. Schwarzmüller, B. Ma, E. Hiller, F. Istel, M. Tscherner et al., Systematic Phenotyping of a Large-Scale Candida glabrata Deletion Collection Reveals Novel Antifungal Tolerance Genes, PLoS Pathog, vol.10, issue.6, p.1004211, 2014.

S. Rayner, S. Bruhn, H. Vallhov, A. Andersson, R. B. Billmyre et al., Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis, Scientific reports, vol.7, p.39742, 2017.

C. Jöchl, M. Rederstorff, J. Hertel, P. F. Stadler, I. L. Hofacker et al., Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis, Nucleic Acids Res, vol.36, issue.8, pp.2677-89, 2008.

A. Sellam, H. Hogues, C. Askew, F. Tebbji, M. Van-het-hoog et al., Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays, Genome Biol, vol.11, issue.7, p.71, 2010.

J. Yuan, Z. Wang, J. Xing, Q. Yang, and X. Chen, Genome-wide Identification and characterization of circular RNAs in the rice blast fungus Magnaporthe oryzae, Scientific Reports, vol.8, issue.1, p.6757, 2018.

N. Chacko, Y. Zhao, Y. E. Wang, L. Cai, J. J. Lin et al., The lncRNA RZE1 controls cryptococcal morphological transition, PLoS Genet, vol.11, issue.11, p.1005692, 2015.

Z. Chang, R. B. Billmyre, S. C. Lee, and J. Heitman, Broad antifungal resistance mediated by RNAi-dependent epimutation in the basal human fungal pathogen Mucor circinelloides, PLoS Genet, vol.15, issue.2, p.1007957, 2019.

S. Calo, C. Shertz-wall, S. C. Lee, R. J. Bastidas, F. E. Nicolás et al., Antifungal drug resistance evoked via RNAi-dependent epimutations, Nature, vol.513, issue.7519, pp.555-563, 2014.

X. Wang, Y. P. Hsueh, W. Li, A. Floyd, R. Skalsky et al., Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi, Genes Dev, vol.24, pp.2566-82, 2010.

G. Janbon, S. Y. Maeng, D. Ko, Y. , J. Moyrand et al., Characterizing the role of RNA silencing components in Cryptococcus neoformans, Fungal Genet Biol, vol.47, pp.1070-80, 2010.

S. Gonzalez-hilarion, D. Paulet, K. Lee, C. Hon, P. Lechat et al., Intron retention-dependent gene regulation in Cryptococcus neoformans, Scientific Reports, vol.6, p.32252, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02861773

J. E. Stajich, F. S. Dietrich, and S. W. Roy, Comparative genomic analysis of fungal genomes reveals intron-rich ancestors, Genome Biol, vol.8, p.223, 2007.

V. Pelechano, W. Wei, and L. M. Steinmetz, Extensive transcriptional heterogeneity revealed by isoform profiling, Nature, vol.497, pp.127-158, 2013.

M. Thodberg, A. Thieffry, J. Bornholdt, M. Boyd, C. Holmberg et al., Comprehensive profiling of the fission yeast transcription start site activity during stress and media response, Nucleic Acids Res, vol.47, pp.1671-91, 2019.

Y. Yue, J. Liu, and C. He, RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation, Genes Dev, vol.29, issue.13, pp.1343-55, 2015.

H. Liu, Y. Li, D. Chen, Z. Qi, Q. Wang et al., A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction in Neurospora crassa, Proceedings of the National Academy of Sciences of the United States of America, vol.114, issue.37, pp.7756-65, 2017.

J. N. Kaur and J. C. Panepinto, Morphotype-specific effector functions of Cryptococcus neoformans PUM1, Scientific Reports, vol.6, p.23638, 2016.

S. Verma and A. Idnurm, The Uve1 endonuclease Is regulated by the white collar complex to protect Cryptococcus neoformans from UV Damage, PLoS Genet, vol.9, issue.9, p.1003769, 2013.

G. Fan, Q. Sun, W. Li, W. Shi, X. Li et al., The global catalogue of microorganisms 10K type strain sequencing project: closing the genomic gaps for the validly published prokaryotic and fungi species. GigaScience, vol.7, pp.1-4, 2018.

D. Garcia-hermoso, A. Criscuolo, S. C. Lee, M. Legrand, M. Chaouat et al., Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing. mBio, vol.9, pp.573-591, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01854232

S. Vaux, A. Criscuolo, M. Desnos-ollivier, L. Diancourt, C. Tarnaud et al., Multicenter Outbreak of Infections by <em>Saprochaete clavata</em>, an Unrecognized Opportunistic Fungal Pathogen, mBio, vol.5, issue.6, pp.2309-2323, 2014.

C. A. Desjardins, C. Giamberardino, S. M. Sykes, C. Yu, J. L. Tenor et al., Population genomics and the evolution of virulence in the fungal pathogen Cryptococcus neoformans

, Genome Res, vol.27, issue.7, pp.1207-1226, 2017.

J. Rhodes, C. A. Desjardins, S. M. Sykes, M. A. Beale, M. Vanhove et al.,

, Tracing Genetic Exchange and Biogeography of Cryptococcus neoformans var. grubii at the Global Population Level

J. Ropars, C. Maufrais, D. Diogo, M. Marcet-houben, A. Perin et al., Gene flow contributes to diversification of the major fungal pathogen Candida albicans, Nature communications, vol.9, issue.1, p.2253, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01815656

F. C. Odds, M. Bougnoux, D. J. Shaw, J. M. Bain, A. D. Davidson et al., Molecular phylogenetics of Candida albicans, Eukaryot Cell, vol.6, issue.6, pp.1041-52, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02665958

F. C. Odds, Molecular phylogenetics and epidemiology of Candida albicans, Future Microbiology, vol.5, issue.1, pp.67-79, 2009.

I. V. Ene and R. J. Bennett, The cryptic sexual strategies of human fungal pathogens, Nature Reviews Microbiology, vol.12, p.239, 2014.

M. P. Hirakawa, D. A. Martinez, S. Sakthikumar, M. Z. Anderson, A. Berlin et al., Genetic and phenotypic intra-species variation in Candida albicans, Genome Res, vol.25, issue.3, pp.413-438, 2015.

M. E. Bougnoux, D. Diogo, N. François, B. Sendid, S. Veirmeire et al.,

, Multilocus sequence typing reveals intrafamilial transmission and microevolutions of Candida albicans isolates from the human digestive tract, J Clin Microbiol, vol.44, issue.5, pp.1810-1830, 2006.

C. J. Nobile, H. A. Schneider, J. E. Nett, D. C. Sheppard, S. G. Filler et al., Complementary adhesin function in C. albicans biofilm formation, Current biology : CB, vol.18, issue.14, pp.1017-1041, 2008.

A. Coste, A. Selmecki, A. Forche, D. Diogo, M. Bougnoux et al., Genotypic evolution of azole resistance mechanisms in sequential Candida albicans isolates, Eukaryot Cell, vol.6, issue.10, pp.1889-904, 2007.

A. Selmecki, A. Forche, and J. Berman, Aneuploidy and isochromosome formation in drugresistant Candida albicans, Science, vol.313, issue.5785, pp.367-70, 2006.

N. Stone, J. Rhodes, M. C. Fisher, S. Mfinanga, S. Kivuyo et al., Dynamic ploidy changes drive fluconazole resistance in human cryptococcal meningitis, The Journal of Clinical Investigation, vol.129, issue.3, pp.999-1014, 2019.

C. A. Morrow and J. A. Fraser, Ploidy variation as an adaptive mechanism in human pathogenic fungi, Seminars in Cell & Developmental Biology, vol.24, issue.4, pp.339-385, 2013.

R. J. Bennett, A. Forche, and J. Berman, Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harbor perspectives in medicine, vol.4, p.19604

S. H. Kim, S. T. Clark, A. Surendra, J. K. Copeland, P. W. Wang et al., Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation, PLoS Pathog, vol.11, issue.11, p.1005308, 2015.

G. Tso, J. A. Reales-calderon, A. Tan, X. Sem, G. Le et al., Experimental evolution of a fungal pathogen into a gut symbiont, Science, vol.362, issue.6414, p.589, 2018.

M. Chauvel, A. Nesseir, V. Cabral, S. Znaidi, S. Goyard et al., Gow NAR, van de Veerdonk FL, Brown AJP, Netea MG. Candida albicans morphogenesis and host defence: discriminating invasion from colonization, Nature reviews Microbiology, vol.7, issue.9, pp.112-134, 2011.

B. Böttcher, C. Pöllath, P. Staib, B. Hube, and S. Brunke, Candida species Rewired Hyphae Developmental Programs for Chlamydospore Formation, Frontiers in microbiology, vol.7, p.1697, 2016.

R. S. Shapiro, N. Robbins, and L. E. Cowen, Regulatory circuitry governing fungal development, drug resistance, and disease. Microbiology and molecular biology reviews : MMBR, vol.75, pp.213-67, 2011.

P. E. Sudbery, Growth of Candida albicans hyphae, Nature Reviews Microbiology, vol.9, p.737, 2011.

L. L. Hoyer, E. Cota, Q. T. Phan, C. L. Myers, Y. Fu et al., Candida albicans Agglutinin-Like Sequence (Als) Family Vignettes: A Review of Als Protein Structure and Function, Frontiers in microbiology, vol.7, 2016.

, Candida albicans invasin that binds to cadherins and induces endocytosis by host cells, PLoS Biol, vol.5, issue.3, p.64, 2007.

E. Moreno-ruiz, M. Galán-díez, W. Zhu, E. Fernández-ruiz, C. Enfert et al.,

, Candida albicans internalization by host cells is mediated by a clathrin-dependent mechanism, Cell Microbiol, vol.11, issue.8, pp.1179-89, 2009.

C. Myers, Q. T. Phan, V. Avanesian, A. S. Ibrahim, J. E. Edwards et al., Efficacy of the Anti-Candida rAls3p-N or rAls1p-N Vaccines against Disseminated and Mucosal Candidiasis, The Journal of Infectious Diseases, vol.194, issue.2, pp.256-60, 2006.

D. L. Moyes, D. Wilson, J. P. Richardson, S. Mogavero, S. X. Tang et al., Candidalysin is a fungal peptide toxin critical for mucosal infection, Nature, vol.532, issue.7597, pp.64-72, 2016.

X. Zheng, Y. Wang, and Y. Wang, Hgc1, a novel hypha-specific G1 cyclin-related protein regulates Candida albicans hyphal morphogenesis, The EMBO journal, vol.23, issue.8, pp.1845-56, 2004.

A. Bishop, R. Lane, R. Beniston, B. Chapa-y-lazo, C. Smythe et al., Hyphal growth in Candida albicans requires the phosphorylation of Sec2 by the Cdc28-Ccn1/Hgc1 kinase, The EMBO journal, vol.29, issue.17, pp.2930-2972, 2010.

S. M. Noble, S. French, L. Kohn, V. Chen, and A. D. Johnson, Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity, Nat Genet, vol.42, pp.590-598, 2010.

S. Znaidi, A. Nesseir, M. Chauvel, T. Rossignol, and C. Enfert, A comprehensive functional portrait of two heat shock factor-type transcriptional regulators involved in Candida albicans morphogenesis and virulence, PLoS Pathog, vol.9, issue.8, p.1003519, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01522813

V. Basso, S. Znaidi, V. Lagage, V. Cabral, F. Schoenherr et al., The two-component response regulator Skn7 belongs to a network of transcription factors regulating morphogenesis in Candida albicans and independently limits morphogenesisinduced ROS accumulation, Mol Microbiol, vol.106, issue.1, pp.157-82, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01570695

C. J. Nobile, E. P. Fox, J. E. Nett, T. R. Sorrells, Q. M. Mitrovich et al., A recently evolved transcriptional network controls biofilm development in Candida albicans, Cell, vol.148, issue.1-2, pp.126-164, 2012.

E. P. Fox, C. K. Bui, J. E. Nett, N. Hartooni, M. C. Mui et al., An expanded regulatory network temporally controls Candida albicans biofilm formation, Mol Microbiol, vol.96, issue.6, pp.1226-1265, 2015.

I. Bose, A. J. Reese, J. J. Ory, G. Janbon, and T. L. Doering, A yeast under cover: the capsule of Cryptococcus neoformans, Eukaryot Cell, vol.2, pp.655-63, 2003.

T. L. Doering, How Sweet it is! Cell Wall Biogenesis and Polysaccharide Capsule Formation in Cryptococcus neoformans, Ann Rev Microbiol, vol.63, issue.1, pp.223-270, 2009.

F. Moyrand, T. Fontaine, and G. Janbon, Systematic capsule gene disruption reveals the central role of galactose metabolism on Cryptococcus neoformans virulence, Mol Microbiol, vol.64, pp.771-81, 2007.

T. R. O&apos;meara and J. A. Alspaugh, The Cryptococcus neoformans capsule: a sword and a shield, Clin Microbiol Rev, vol.25, pp.387-408, 2012.

C. D. Chun, J. Brown, and H. D. Madhani, A major role for capsule-independent phagocytosis-inhibitory mechanisms in mammalian infection by Cryptococcus neoformans, Cell host & microbe, vol.9, issue.3, pp.243-51, 2011.

O. Zaragoza and K. Nielsen, Titan cells in Cryptococcus neoformans: Cells with a giant impact, Curr Opinion Microbiol, vol.16, issue.4, pp.409-422, 2013.

B. Hommel, L. Mukaremera, R. Cordero, C. Coelho, C. A. Desjardins et al., Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators, PLoS Pathog, vol.14, issue.5, p.1006982, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01854297

N. Trevijano-contador, H. C. De-oliveira, R. García-rodas, S. A. Rossi, I. Llorente et al., Cryptococcus neoformans can form titan-like cells in vitro in response to multiple signals, PLoS Pathog, vol.14, issue.5, p.1007007, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-02651826

I. M. Dambuza, T. Drake, A. Chapuis, X. Zhou, J. Correia et al., The Cryptococcus neoformans Titan cell is an inducible and regulated morphotype underlying pathogenesis, PLoS Pathog, vol.14, issue.5, p.1006978, 2018.

D. Ghez, A. Calleja, C. Protin, M. Baron, M. Ledoux et al., Early-onset invasive aspergillosis and other fungal infections in patients treated with ibrutinib, Blood, vol.131, issue.17, p.1955, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02341706

B. Pilmis, A. Puel, O. Lortholary, and F. Lanternier, New clinical phenotypes of fungal infections in special hosts, Clinical Microbiology and Infection, vol.22, issue.8, pp.681-688, 2016.

A. Duréault, C. Tcherakian, S. Poiree, E. Catherinot, F. Danion et al., Spectrum of pulmonary aspergillosis in Hyper IgE syndrome with autosomal dominant STAT3 deficiency, The Journal of Allergy and Clinical Immunology: In Practice

T. Saijo, J. Chen, S. Chen, L. B. Rosen, J. Yi et al., Anti-granulocytemacrophage colony-stimulating factor autoantibodies are a risk factor for central nervous system infection by Cryptococcus gattii in otherwise immunocompetent patients, mBio, vol.5, issue.2, pp.912-926, 2014.

S. K. Browne, P. D. Burbelo, P. Chetchotisakd, Y. Suputtamongkol, S. Kiertiburanakul et al., Adult-Onset Immunodeficiency in Thailand and Taiwan, New England Journal of Medicine, vol.367, issue.8, pp.725-759, 2012.

F. Lanternier, S. Pathan, Q. B. Vincent, L. Liu, S. Cypowyj et al., Deep Dermatophytosis and Inherited CARD9 Deficiency, New England Journal of Medicine, vol.369, issue.18, pp.1704-1718, 2013.

E. Corvilain, J. Casanova, and A. Puel, Inherited CARD9 Deficiency: Invasive Disease Caused by Ascomycete Fungi in Previously Healthy Children and Adults, Journal of Clinical Immunology, vol.38, issue.6, pp.656-93, 2018.

J. Li, D. C. Vinh, J. Casanova, and A. Puel, Inborn errors of immunity underlying fungal diseases in otherwise healthy individuals, Curr Opinion Microbiol, vol.40, pp.46-57, 2017.

C. Cunha, F. Aversa, J. F. Lacerda, A. Busca, O. Kurzai et al., Genetic PTX3 Deficiency and Aspergillosis in Stem-Cell Transplantation, New England Journal of Medicine, vol.370, issue.5, pp.421-453, 2014.

A. Rosselet, B. Müllhaupt, B. Laesser, C. P. Ziegler, C. Benden et al.,

, Polymorphisms and Invasive Mold Infections After Solid Organ Transplant, Clin Infect Dis, vol.61, issue.4, pp.619-641, 2015.

M. A. Hamon and J. Quintin, Innate immune memory in mammals, Seminars in Immunology, vol.28, issue.4, pp.351-359, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01422825

B. Milutinovi? and J. Kurtz, Immune memory in invertebrates, Seminars in Immunology, vol.28, issue.4, pp.328-370, 2016.

N. Mihai, G. , Q. J. Van-der-meer-jos, and W. M. , Trained Immunity: A Memory for Innate Host Defense, Cell Host & Microbe, vol.9, issue.5, pp.355-61, 2011.

, Environmental and Microbial Relationships, Kubicek CP, Druzhinina IS, pp.85-103, 2007.

J. Quintin, S. Saeed, J. Martens, E. J. Giamarellos-bourboulis, D. C. Ifrim et al., Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes, Cell host & microbe, vol.12, issue.2, pp.223-255, 2012.

S. Bekkering, B. A. Blok, L. Joosten, N. P. Riksen, R. Van-crevel et al., In Vitro Experimental Model of Trained Innate Immunity in Human Primary Monocytes, Clinical and vaccine immunology : CVI, vol.23, issue.12, pp.926-959, 2016.

K. Yoshida, T. Maekawa, Y. Zhu, R. , C. Chatton et al., The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory, Nature Immunology, vol.16, p.1034, 2015.

S. Saeed, J. Quintin, H. Kerstens, N. A. Rao, A. Aghajanirefah et al., Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity, Science, vol.345, issue.6204, p.1251086, 2014.

S. Cheng, J. Quintin, R. A. Cramer, K. M. Shepardson, S. Saeed et al., mTOR-and HIF-1?-mediated aerobic glycolysis as metabolic basis for trained immunity, Science, vol.345, issue.6204, p.1250684, 2014.

R. Arts, B. Novakovic, T. Horst, R. Carvalho, A. Bekkering et al., Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity, Cell metabolism, vol.24, issue.6, pp.807-826, 2016.

S. Bekkering, R. Arts, B. Novakovic, I. Kourtzelis, C. Van-der-heijden et al., Metabolic Induction of Trained Immunity through the Mevalonate Pathway, Cell, vol.172, issue.1, pp.135-181, 2018.

I. Mitroulis, K. Ruppova, B. Wang, L. Chen, M. Grzybek et al., Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity, Cell, vol.172, issue.1-2, pp.147-61, 2018.

L. M. Egerton-warburton, J. I. Querejeta, M. F. Allen, and S. L. Finkelman, Mycorrhizal Fungi?. Reference Module in Earth Systems and Environmental Sciences, 2013.

T. Spribille, V. Tuovinen, P. Resl, D. Vanderpool, H. Wolinski et al., Basidiomycete yeasts in the cortex of ascomycete macrolichens, Science, vol.353, issue.6298, p.488, 2016.

N. S. Grantham, B. J. Reich, K. Pacifici, E. B. Laber, H. L. Menninger et al., Fungi Identify the Geographic Origin of Dust Samples, PLOS ONE, vol.10, issue.4, p.122605, 2015.

M. L. Richard and H. Sokol, The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases, Nature Reviews Gastroenterology & Hepatology, vol.16, pp.331-345, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02627718

D. M. Underhill and I. D. Iliev, The mycobiota: interactions between commensal fungi and the host immune system, Nature reviews Immunology, vol.14, issue.6, pp.405-421, 2014.

I. D. Iliev, V. A. Funari, K. D. Taylor, Q. Nguyen, C. N. Reyes et al., Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis, Science, vol.336, issue.6086, pp.1314-1321, 2012.

C. Hoffmann, S. Dollive, S. Grunberg, J. Chen, H. Li et al., Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents, PloS one, vol.8, issue.6, p.66019, 2013.

P. T. Van-leeuwen, J. M. Van-der-peet, F. J. Bikker, M. A. Hoogenkamp, O. Paiva et al., Interspecies Interactions between Clostridium difficile and Candida albicans, mSphere, vol.1, issue.6, pp.187-203, 2016.

B. Briard, P. Bomme, B. E. Lechner, G. Mislin, V. Lair et al., Pseudomonas aeruginosa manipulates redox and iron homeostasis of its microbiota partner Aspergillus fumigatus via phenazines, Scientific reports, vol.5, p.8220, 2015.

B. Briard, C. Heddergott, and J. Latgé, Volatile Compounds Emitted by Pseudomonas aeruginosa stimulate growth of the fungal pathogen Aspergillus fumigatus, mBio, vol.7, issue.2, p.219, 2016.

W. Matthew, L. , L. Jose, J. , B. Agnieszka et al., Immunological consequences of intestinal fungal dysbiosis, Cell Host & Microbe, vol.19, issue.6, pp.865-73, 2016.

M. Beaudoin, P. Goyette, G. Boucher, K. S. Lo, M. A. Rivas et al., Deep Resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis, PLoS Genet, vol.9, issue.9, p.1003723, 2013.

M. A. Rivas, M. Beaudoin, A. Gardet, C. Stevens, Y. Sharma et al., Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease, Nat Genet, vol.43, issue.11, pp.1066-73, 2011.

H. S. De-vries, T. S. Plantinga, J. H. Van-krieken, R. Stienstra, A. A. Van-bodegraven et al., Genetic association analysis of the functional c.714T>G polymorphism and mucosal expression of Dectin-1 in inflammatory Bowel disease, PLOS ONE, vol.4, issue.11, p.7818, 2009.

C. Chehoud, L. G. Albenberg, C. Judge, C. Hoffmann, S. Grunberg et al., Fungal Signature in the gut microbiota of pediatric patients with inflammatory Bowel disease. inflammatory Bowel diseases, vol.21, pp.1948-56, 2015.

P. Bacher, T. Hohnstein, E. Beerbaum, M. Röcker, M. G. Blango et al., Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans, Cell, vol.176, issue.6, pp.1340-55, 2019.

F. C. Koehler, O. A. Cornely, H. Wisplinghoff, A. C. Schauss, J. Salmanton-garcia et al., Candida-reactive T cells for the diagnosis of invasive Candida infection-A prospective pilot study, Frontiers in microbiology, vol.9, p.1381, 2018.