J. R. Postgate, Chapter XVIII Viable counts and Viability, Methods in Microbiology, pp.611-628, 1969.

A. S. Kaprelyants, G. V. Mukamolova, and D. B. Kell, Estimation of dormant Micrococcus luteus cells by penicillin lysis and by resuscitation in cell-free spent culture medium at high dilution, FEMS Microbiol Lett, vol.115, p.347, 1994.

J. B. Emerson, R. I. Adams, C. Román, B. Brooks, D. A. Coil et al., Schrö dinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems, Microbiome, vol.5, p.28810907, 2017.

D. B. Roszak and R. R. Colwell, Survival strategies of bacteria in the natural environment, Microbiol Rev, vol.51, pp.365-379, 1987.

T. Nyströ-m, Nonculturable bacteria: programmed survival forms or cells at death's door?, BioEssays News Rev Mol Cell Dev Biol, vol.25, pp.204-211, 2003.

J. D. Oliver, Recent findings on the viable but nonculturable state in pathogenic bacteria, FEMS Microbiol Rev, vol.34, pp.415-425, 2010.

M. Ayrapetyan, T. C. Williams, R. Baxter, and J. D. Oliver, Viable but Nonculturable and Persister Cells Coexist Stochastically and Are Induced by Human Serum, Infect Immun, vol.83, pp.4194-4203, 2015.

L. Li, N. Mendis, H. Trigui, J. D. Oliver, and S. P. Faucher, The importance of the viable but non-culturable state in human bacterial pathogens, Front Microbiol, vol.5, p.258, 2014.

B. Divol and A. Lonvaud-funel, Evidence for viable but nonculturable yeasts in botrytis-affected wine, J Appl Microbiol, vol.99, pp.85-93, 2005.

M. Salma, S. Rousseaux, A. Grand, B. Divol, and H. Alexandre, Characterization of the Viable but Nonculturable (VBNC) State in Saccharomyces cerevisiae, PloS One, vol.8, 2013.

V. Serpaggi, F. Remize, G. Recorbet, E. Gaudot-dumas, S. Grand et al., Characterization of the "viable but nonculturable" (VBNC) state in the wine spoilage yeast Brettanomyces, Food Microbiol, vol.30, pp.438-447, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00939790

K. Brunet, A. Alanio, O. Lortholary, and B. Rammaert, Reactivation of dormant/latent fungal infection, J Infect, vol.77, pp.463-468, 2018.

S. Lewenza, J. Abboud, K. Poon, M. Kobryn, I. Humplik et al., Pseudomonas aeruginosa displays a dormancy phenotype during long-term survival in water, PloS One, vol.13, p.198384, 2018.

S. Helaine, A. M. Cheverton, K. G. Watson, L. M. Faure, S. A. Matthews et al., Internalization of Salmonella by macrophages induces formation of nonreplicating persisters, Science, vol.343, pp.204-208, 2014.

M. B. Markus, Biological concepts in recurrent Plasmodium vivax malaria, Parasitology, vol.145, pp.1765-1771, 2018.

E. Rittershaus, S. Baek, and C. M. Sassetti, The normalcy of dormancy: common themes in microbial quiescence, Cell Host Microbe, vol.13, pp.643-651, 2013.

D. Garcia-hermoso, G. Janbon, and F. Dromer, Epidemiological evidence for dormant Cryptococcus neoformans infection, J Clin Microbiol, vol.37, pp.3204-3209, 1999.

F. Dromer, O. Ronin, and B. Dupont, Isolation of Cryptococcus neoformans var. gattii from an Asian patient in France: evidence for dormant infection in healthy subjects, J Med Vet Mycol Bi-Mon Publ Int Soc Hum Anim Mycol, vol.30, pp.395-397, 1992.

K. J. Kwon-chung and J. E. Bennett, Philadelphia : Lea & Febiger; 1992

R. Rajasingham, R. M. Smith, B. J. Park, J. N. Jarvis, N. P. Govender et al., Global burden of disease of HIV-associated cryptococcal meningitis: an updated analysis, Lancet Infect Dis, vol.17, p.873, 2017.

R. D. Baker, The primary pulmonary lymph node complex of crytptococcosis, Am J Clin Pathol, vol.65, pp.83-92, 1976.

D. Goldman, S. C. Lee, and A. Casadevall, Pathogenesis of pulmonary Cryptococcus neoformans infection in the rat, Infect Immun, vol.62, pp.4755-4761, 1994.

A. Alanio, F. Vernel-pauillac, A. Sturny-leclère, and F. Dromer, Cryptococcus neoformans host adaptation: toward biological evidence of dormancy, mBio, vol.6, pp.2580-2594, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01405218

M. Latil, P. Rocheteau, L. Châ-tre, S. Sanulli, S. Mémet et al., Skeletal muscle stem cells adopt a dormant cell state post mortem and retain regenerative capacity, Nat Commun, vol.3, p.903, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-00711881

M. Gengenbacher, S. Rao, K. Pethe, and T. Dick, Nutrient-starved, non-replicating Mycobacterium tuberculosis requires respiration, ATP synthase and isocitrate lyase for maintenance of ATP homeostasis and viability, Microbiol Read Engl, vol.156, pp.81-87, 2010.

J. Sebastià, R. Cristòfol, M. Martín, E. Rodríguez-farré, and C. Sanfeliu, Evaluation of fluorescent dyes for measuring intracellular glutathione content in primary cultures of human neurons and neuroblastoma SH-SY5Y, Cytometry A, vol.51, pp.16-25, 2003.

H. Nishiuchi, Y. Tabira, and K. Yamagishi, A combination of flow cytometry and traditional screening using chemicals to isolate high glutathione-producing yeast mutants, Biosci Biotechnol Biochem, vol.76, pp.1085-1090, 2012.

K. L. Liew, J. M. Jee, I. Yap, and P. Yong, In Vitro Analysis of Metabolites Secreted during Infection of Lung Epithelial Cells by Cryptococcus neoformans, PloS One, vol.11, p.153356, 2016.

P. Albuquerque, A. M. Nicola, E. Nieves, H. C. Paes, P. R. Williamson et al., Quorum sensing-mediated, cell density-dependent regulation of growth and virulence in Cryptococcus neoformans, mBio, vol.5, pp.986-999, 2013.

R. D. Baker and R. K. Haugen, Tissue Changes and Tissue Diagnosis in Cryptococcosis: A Study of 26 Cases, Am J Clin Pathol, vol.25, p.14, 1955.

R. K. Haugen and R. D. Baker, The Pulmonary Lesions in Cryptococcosis with Special References to Subpleural Nodules, Am J Clin Pathol, vol.24, p.1381, 1954.

A. Idnurm, Y. Bahn, K. Nielsen, X. Lin, J. A. Fraser et al., Deciphering the model pathogenic fungus Cryptococcus neoformans, Nat Rev Microbiol, vol.3, pp.753-764, 2005.

D. Virgilio and C. , The essence of yeast quiescence, FEMS Microbiol Rev, vol.36, p.21658086, 2012.

N. Grahl, K. M. Shepardson, D. Chung, and R. A. Cramer, Hypoxia and fungal pathogenesis: to air or not to air?, Eukaryot Cell, vol.11, pp.560-570, 2012.

L. G. Wayne and L. G. Hayes, An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence, Infect Immun, vol.64, pp.2062-2069, 1996.

C. P. Semighini, A. F. Averette, J. R. Perfect, and J. Heitman, Deletion of Cryptococcus neoformans AIF ortholog promotes chromosome aneuploidy and fluconazole-resistance in a metacaspase-independent manner, PLoS Pathog, vol.7, 2011.

A. P. Day and J. D. Oliver, Changes in membrane fatty acid composition during entry of Vibrio vulnificus into the viable but nonculturable state, J Microbiol Seoul Korea, vol.42, pp.69-73, 2004.

J. C. Dubois, R. Pasula, J. E. Dade, and A. G. Smulian, Yeast Transcriptome and In Vivo Hypoxia Detection Reveals Histoplasma capsulatum Response to Low Oxygen Tension, Med Mycol, vol.54, pp.40-58, 2016.

J. E. Qualls and P. J. Murray, Immunometabolism within the tuberculosis granuloma: amino acids, hypoxia, and cellular respiration, Semin Immunopathol, vol.38, pp.139-152, 2016.

C. L. Sershen, S. J. Plimpton, and E. E. May, Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach, Front Cell Infect Microbiol, vol.6, 2016.

S. W. Lane, D. A. Williams, and F. M. Watt, Modulating the stem cell niche for tissue regeneration, Nat Biotechnol, vol.32, pp.795-803, 2014.

J. Mathieu, W. Zhou, Y. Xing, H. Sperber, A. Ferreccio et al., Hypoxia-inducible factors have distinct and stage-specific roles during reprogramming of human cells to pluripotency, Cell Stem Cell, vol.14, pp.592-605, 2014.

Z. Dong, J. Z. Wang, F. Yu, and M. A. Venkatachalam, Apoptosis-Resistance of Hypoxic Cells: Multiple Factors Involved and a Role for IAP-2, Am J Pathol, vol.163, issue.10, pp.63693-63693, 2003.

J. Wu, C. Parungo, G. Wu, P. M. Kang, R. J. Laham et al., PR39 inhibits apoptosis in hypoxic endothelial cells: role of inhibitor apoptosis protein-2, Circulation, vol.109, pp.1660-1667, 2004.

T. G. Graeber, C. Osmanian, T. Jacks, D. E. Housman, C. J. Koch et al., Hypoxia-mediated selection of cells with diminished apoptotic potential in solid tumours, Nature, vol.379, pp.88-91, 1996.

I. Arana, M. Orruño, D. Pé-rez-pascual, C. Seco, A. Muela et al., Inability of Escherichia coli to resuscitate from the viable but nonculturable state, FEMS Microbiol Ecol, vol.62, p.17908096, 2007.

L. Li, N. Mendis, H. Trigui, J. D. Oliver, and S. P. Faucher, The importance of the viable but non-culturable state in human bacterial pathogens, Front Microbiol, vol.5, p.258, 2014.

J. L. Oblinger and J. A. Koburger, Understanding and Teaching the Most Probable Number Technique, J Milk Food Technol, vol.38, pp.540-545, 1975.

D. Pinto, M. A. Santos, and L. Chambel, Thirty years of viable but nonculturable state research: unsolved molecular mechanisms, Crit Rev Microbiol, vol.41, pp.61-76, 2013.

C. W. Blackburn and J. D. Mccarthy, Modifications to methods for the enumeration and detection of injured Escherichia coli O157:H7 in foods, Int J Food Microbiol, vol.55, pp.285-290, 2000.

P. H. Calcott and J. R. Postgate, On substrate-accelerated death in Klebsiella aerogenes, J Gen Microbiol, vol.70, pp.115-122, 1972.

G. V. Mukamolova, A. S. Kaprelyants, D. B. Kell, and M. Young, Adoption of the transiently non-culturable state -a bacterial survival strategy?, 2003.

M. Nofal, K. Zhang, S. Han, and J. D. Rabinowitz, mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein, Mol Cell, vol.67, pp.936-946, 2017.

J. N. Steenbergen, H. A. Shuman, and A. Casadevall, Cryptococcus neoformans interactions with amoebae suggest an explanation for its virulence and intracellular pathogenic strategy in macrophages, Proc Natl Acad Sci U S A, vol.98, pp.15245-15250, 2001.

M. T. García, S. Jones, C. Pelaz, and R. D. Millar, Abu Kwaik Y. Acanthamoeba polyphaga resuscitates viable non-culturable Legionella pneumophila after disinfection, Environ Microbiol, vol.9, p.17472639, 2007.

M. Steinert, L. Emödy, R. Amann, and J. Hacker, Resuscitation of viable but nonculturable Legionella pneumophila Philadelphia JR32 by Acanthamoeba castellanii, Appl Environ Microbiol, vol.63, pp.2047-2053, 1997.

R. Schumann, T. Rieling, S. Gö-rs, A. Hammer, U. Selig et al., Viability of bacteria from different aquatic habitats. I. Environmental conditions and productivity, Aquat Microb Ecol, vol.32, pp.121-135, 2003.

J. L. Derisi, V. R. Iyer, and P. O. Brown, Exploring the metabolic and genetic control of gene expression on a genomic scale, Science, vol.278, pp.680-686, 1997.

H. Boucherie, Protein synthesis during transition and stationary phases under glucose limitation in Saccharomyces cerevisiae, J Bacteriol, vol.161, pp.385-392, 1985.

E. K. Fuge, E. L. Braun, and M. Werner-washburne, Protein synthesis in long-term stationary-phase cultures of Saccharomyces cerevisiae, J Bacteriol, vol.176, pp.5802-5813, 1994.

Q. Ju and J. R. Warner, Ribosome synthesis during the growth cycle of Saccharomyces cerevisiae, Yeast Chichester Engl, vol.10, pp.151-157, 1994.

J. Lee, S. Giordano, and J. Zhang, Autophagy, mitochondria and oxidative stress: cross-talk and redox signalling, Biochem J, vol.441, pp.523-540, 2012.

M. L. Rodrigues, E. S. Nakayasu, D. L. Oliveira, L. Nimrichter, J. D. Nosanchuk et al., Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence, Eukaryot Cell, vol.7, pp.58-67, 2008.

J. Geddes, D. Croll, M. Caza, N. Stoynov, L. J. Foster et al., Secretome profiling of Cryptococcus neoformans reveals regulation of a subset of virulence-associated proteins and potential biomarkers by protein kinase A, BMC Microbiol, vol.15, p.26453029, 2015.

S. Lev, B. Crossett, S. Y. Cha, D. Desmarini, C. Li et al., Identification of Aph1, a phosphate-regulated, secreted, and vacuolar acid phosphatase in Cryptococcus neoformans, mBio, vol.5, pp.1649-1663, 2014.

H. C. Eisenman, S. Frases, A. M. Nicola, M. L. Rodrigues, and A. Casadevall, Vesicle-associated melanization in Cryptococcus neoformans, Microbiol Read Engl, vol.155, pp.3860-3867, 2009.

M. L. Rodrigues, E. S. Nakayasu, D. L. Oliveira, L. Nimrichter, J. D. Nosanchuk et al., Extracellular vesicles produced by Cryptococcus neoformans contain protein components associated with virulence, Eukaryot Cell, vol.7, pp.58-67, 2007.

M. L. Rodrigues and J. T. Djordjevic, Unravelling secretion in Cryptococcus neoformans: more than one way to skin a cat, Mycopathologia, vol.173, p.21898146, 2012.

A. De-gassart, C. Geminard, B. Fevrier, G. Raposo, and M. Vidal, Lipid raft-associated protein sorting in exosomes, Blood, vol.102, pp.4336-4344, 2003.

C. M. Homer, D. K. Summers, A. I. Goranov, S. C. Clarke, D. L. Wiesner et al., Intracellular Action of a Secreted Peptide Required for Fungal Virulence, Cell Host Microbe, vol.19, pp.849-864, 2016.

H. Lee, Y. C. Chang, G. Nardone, and K. Kj, TUP1 disruption in Cryptococcus neoformans uncovers a peptide-mediated density-dependent growth phenomenon that mimics quorum sensing, Mol Microbiol, vol.64, p.591, 2007.

H. Lee, Y. C. Chang, A. Varma, and K. J. Kwon-chung, Regulatory diversity of TUP1 in Cryptococcus neoformans, Eukaryot Cell, vol.8, pp.1901-1908, 2009.

L. Selvan, J. E. Kaviyil, R. S. Nirujogi, B. Muthusamy, V. N. Puttamallesh et al., Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry, Clin Proteomics, vol.11, p.24484775, 2014.

L. Selvan, S. K. Sreenivasamurthy, S. Kumar, S. D. Yelamanchi, A. K. Madugundu et al., Characterization of host response to Cryptococcus neoformans through quantitative proteomic analysis of cryptococcal meningitis co-infected with HIV, Mol Biosyst, vol.11, pp.2529-2540, 2015.

M. Huang, A. S. Hebert, J. J. Coon, and C. M. Hull, Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus, PLoS Genet, vol.11, p.1005490, 2015.

D. J. Jamieson, Oxidative stress responses of the yeast Saccharomyces cerevisiae, Yeast Chichester Engl, vol.14, pp.1511-1527, 1998.

D. Virgilio, C. Loewith, and R. , The TOR signalling network from yeast to man, Int J Biochem Cell Biol, vol.38, pp.1476-1481, 2006.

J. Rohde, J. Heitman, and M. E. Cardenas, The TOR kinases link nutrient sensing to cell growth, J Biol Chem, vol.276, pp.9583-9586, 2001.

R. García-rodas, R. Cordero, N. Trevijano-contador, G. Janbon, F. Moyrand et al., Capsule growth in Cryptococcus neoformans is coordinated with cell cycle progression, mBio, vol.5, p.24939886, 2014.

D. L. Martinez, Y. Tsuchiya, and I. Gout, Coenzyme A biosynthetic machinery in mammalian cells, Biochem Soc Trans, vol.42, pp.1112-1117, 2014.

B. Srinivasan and O. Sibon, Coenzyme A, more than "just" a metabolic cofactor, Biochem Soc Trans, vol.42, pp.1075-1079, 2014.

M. Kretschmer, J. Wang, and J. W. Kronstad, Peroxisomal and mitochondrial ?-oxidation pathways influence the virulence of the pathogenic fungus Cryptococcus neoformans, Eukaryot Cell, vol.11, pp.1042-1054, 2012.

T. Itoh, H. Waki, and H. Kaneko, Changes of Lipid Composition with Growth Phase of Cryptococcus neoformans, Agric Biol Chem, vol.39, pp.2365-2371, 1975.

M. C. Lorenz, J. A. Bender, and G. R. Fink, Transcriptional response of Candida albicans upon internalization by macrophages, Eukaryot Cell, vol.3, pp.1076-1087, 2004.

G. Hu, P. Cheng, A. Sham, J. R. Perfect, and J. W. Kronstad, Metabolic adaptation in Cryptococcus neoformans during early murine pulmonary infection, Mol Microbiol, vol.69, pp.1456-1475, 2008.

L. Da-s-derengowski, H. C. Paes, P. Albuquerque, A. Tavares, L. Fernandes et al., The transcriptional response of Cryptococcus neoformans to ingestion by Acanthamoeba castellanii and macrophages provides insights into the evolutionary adaptation to the mammalian host, Eukaryot Cell, vol.12, pp.761-774, 2013.

J. Markovic, N. J. Mora, A. M. Broseta, A. Gimeno, N. De-la-concepció-n et al., The depletion of nuclear glutathione impairs cell proliferation in 3t3 fibroblasts, PloS One, vol.4, p.6413, 2009.

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, p.1006982, 2018.
URL : https://hal.archives-ouvertes.fr/pasteur-01854297

Z. Zou, F. Tong, N. J. Faergeman, C. Børsting, P. N. Black et al., Vectorial acylation in Saccharomyces cerevisiae. Fat1p and fatty acyl-CoA synthetase are interacting components of a fatty acid import complex, J Biol Chem, vol.278, pp.16414-16422, 2003.

G. F. Ferreira, L. De-matos-baltazar, J. Santos, A. S. Monteiro, L. A. De-oliveira-fraga et al., The role of oxidative and nitrosative bursts caused by azoles and amphotericin B against the fungal pathogen Cryptococcus gattii, J Antimicrob Chemother, vol.68, pp.1801-1811, 2013.

M. Kahm, G. Hasenbrink, H. Lichtenberg-fraté, J. Ludwig, and M. Kschischo, grofit: Fitting Biological Growth Curves withR, J Stat Softw, vol.33, 2010.

A. Alanio, M. Desnos-ollivier, and F. Dromer, Dynamics of Cryptococcus neoformans-macrophage interactions reveal that fungal background influences outcome during cryptococcal meningoencephalitis in humans, mBio, vol.2, pp.158-169, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-01405254

A. Casadevall, M. Deshaw, M. Fan, F. Dromer, T. R. Kozel et al., Molecular and idiotypic analysis of antibodies to Cryptococcus neoformans glucuronoxylomannan, Infect Immun, vol.62, pp.3864-3872, 1994.

K. Nielsen, G. M. Cox, A. P. Litvintseva, E. Mylonakis, S. D. Malliaris et al., Cryptococcus neoformans {alpha} strains preferentially disseminate to the central nervous system during coinfection, Infect Immun, vol.73, pp.4922-4933, 2005.

B. R. Bochner, P. Gadzinski, and E. Panomitros, Phenotype microarrays for high-throughput phenotypic testing and assay of gene function, Genome Res, vol.11, pp.1246-1255, 2001.

F. Moyrand, I. Lafontaine, T. Fontaine, and G. Janbon, UGE1 and UGE2 regulate the UDP-glucose/UDPgalactose equilibrium in Cryptococcus neoformans, Eukaryot Cell, vol.7, pp.2069-2077, 2008.

J. Vandesompele, D. Preter, K. Pattyn, F. Poppe, B. Van-roy et al., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

, Genome Biol, vol.3, p.34, 2002.

M. W. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Res, vol.29, 2001.

X. Wu, E. Xiong, W. Wang, M. Scali, and M. Cresti, Universal sample preparation method integrating trichloroacetic acid/acetone precipitation with phenol extraction for crop proteomic analysis, Nat Protoc, vol.9, pp.362-374, 2014.

J. Cox, N. Neuhauser, A. Michalski, R. A. Scheltema, J. V. Olsen et al., Andromeda: a peptide search engine integrated into the MaxQuant environment, J Proteome Res, vol.10, pp.1794-1805, 2011.

J. Cox and M. Mann, MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification, Nat Biotechnol, vol.26, pp.1367-1372, 2008.

S. Tyanova, T. Temu, and J. Cox, The MaxQuant computational platform for mass spectrometry-based shotgun proteomics, Nat Protoc, vol.11, pp.2301-2319, 2016.

J. Cox, M. Y. Hein, C. A. Luber, I. Paron, N. Nagaraj et al., Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction

, Mol Cell Proteomics MCP, vol.13, pp.2513-2526, 2014.

T. H. Bø, B. Dysvik, and I. Jonassen, LSimpute: accurate estimation of missing values in microarray data with least squares methods, Nucleic Acids Res, vol.32, 2004.

J. C. Gower, Some distance properties of latent root and vector methods used in multivariate analysis, Biometrika, pp.325-363, 1966.

M. E. Ritchie, B. Phipson, . Wu, Y. Hu, C. W. Law et al., limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, vol.43, 2015.

Y. Benjamini and Y. Hochberg, Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, J R Stat Soc Ser B Methodol, vol.57, pp.289-300, 1995.

S. Priebe, C. Kreisel, F. Horn, R. Guthke, and J. Linde, FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species, Bioinforma Oxf Engl, vol.31, pp.445-446, 2014.

P. Bardou, J. Mariette, F. Escudié, C. Djemiel, and C. Klopp, jvenn: an interactive Venn diagram viewer, BMC Bioinformatics, vol.15, p.25176396, 2014.

D. Szklarczyk, A. Franceschini, S. Wyder, K. Forslund, D. Heller et al., STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-52, 2014.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. journal, vol.17, pp.10-12, 2011.

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNAseq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

Y. Liao, G. K. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinforma Oxf Engl, vol.30, pp.923-930, 2014.

P. Ewels, M. Magnusson, S. Lundin, and M. Käller, MultiQC: summarize analysis results for multiple tools and samples in a single report, Bioinformatics, vol.32, pp.3047-3048, 2016.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

E. Y. Basenko, J. A. Pulman, A. Shanmugasundram, O. S. Harb, K. Crouch et al., FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes, J Fungi Basel Switz, vol.4, 2018.

A. Marchler-bauer, Y. Bo, L. Han, J. He, C. J. Lanczycki et al., CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017.

H. Nielsen, Predicting Secretory Proteins with SignalP, Methods Mol Biol Clifton NJ, vol.1611, pp.59-73, 2017.