P. Lerouge, Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal, Nature, vol.344, pp.781-784, 1990.
URL : https://hal.archives-ouvertes.fr/hal-02713445

J. Dénarié, F. Debellé, and J. Promé, Rhizobium lipo-chitooligosaccharide nodulation factors: signaling molecules mediating recognition and morphogenesis, Annu. Rev. Biochem, vol.65, pp.503-535, 1996.

J. Sun, Activation of symbiosis signaling by arbuscular mycorrhizal fungi in legumes and rice, Plant Cell, vol.27, pp.823-838, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02119231

F. Maillet, Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza, Nature, vol.469, pp.58-63, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02649013

M. Venkateshwaran, J. D. Volkening, M. R. Sussman, and J. Ané, Symbiosis and the social network of higher plants, Curr. Opin. Plant Biol, vol.16, pp.118-127, 2013.

C. Zipfel and G. E. Oldroyd, Plant signalling in symbiosis and immunity, Nature, vol.543, pp.328-336, 2017.

F. Feng, A combination of chitooligosaccharide and lipochitooligosaccharide recognition promotes arbuscular mycorrhizal associations in Medicago truncatula, Nat. Commun, vol.10, p.5047, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02351401

S. Kelly, S. Radutoiu, and J. Stougaard, Legume LysM receptors mediate symbiotic and pathogenic signalling, Curr. Opin. Plant Biol, vol.39, pp.152-158, 2017.

K. R. Cope, The ectomycorrhizal fungus Laccaria bicolor produces lipochitooligosaccharides and uses the common symbiosis pathway to colonize Populus roots, Plant Cell, vol.31, pp.2386-2410, 2019.

K. Garcia, P. Delaux, K. R. Cope, and J. Ané, Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses, N. Phytol, vol.208, pp.79-87, 2015.

G. Despras, A. Alix, D. Urban, B. Vauzeilles, and J. Beau, From chitin to bioactive chitooligosaccharides and conjugates: access to lipochitooligosaccharides and the TMG-chitotriomycin, Angew. Chem. Int. Ed. Engl, vol.53, pp.11912-11916, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01076451

A. Genre, Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca 2+ spiking in Medicago truncatula roots and their production is enhanced by strigolactone, N. Phytol, vol.198, pp.190-202, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02651472

L. Buendia, A. Girardin, T. Wang, L. Cottret, and B. Lefebvre, LysM receptorlike kinase and LysM receptor-like protein families: an update on phylogeny and functional characterization, Front. Plant Sci, vol.9, p.1531, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02621378

S. Brunke and B. Hube, Two unlike cousins: Candida albicans and C. glabrata infection strategies, Cell. Microbiol, vol.15, pp.701-708, 2013.

C. J. Gimeno, P. O. Ljungdahl, C. A. Styles, and G. R. Fink, Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS, Cell, vol.68, pp.1077-1090, 1992.

C. Gibelin-viala, The Medicago truncatula LysM receptor-like kinase LYK9 plays a dual role in immunity and the arbuscular mycorrhizal symbiosis, N. Phytol, vol.223, pp.1516-1529, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02366095

E. Limpens, A. Van-zeijl, and R. Geurts, Lipochitooligosaccharides modulate plant host immunity to enable endosymbioses, Annu. Rev. Phytopathol, vol.53, pp.311-334, 2015.

Y. Liang, Nonlegumes respond to rhizobial nod factors by suppressing the innate immune response, Science, vol.341, pp.1384-1387, 2013.

Y. Liang, Lipochitooligosaccharide recognition: an ancient story, J. Physiol, vol.204, pp.289-296, 2014.

C. Gutjahr, Rice perception of symbiotic arbuscular mycorrhizal fungi requires the karrikin receptor complex, Science, vol.350, pp.1521-1524, 2015.

J. Choi, The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice, Nat. Commun, vol.11, p.2114, 2020.

X. Zhang, The receptor kinase CERK1 has dual functions in symbiosis and immunity signalling, Plant J, vol.81, pp.258-267, 2015.

M. A. Djordjevic, Lipo-chitin oligosaccharides, plant symbiosis signalling molecules that modulate mammalian angiogenesis in vitro, PLoS One, vol.9, p.112635, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01110904

A. Mehmood, Fungal Quorum-Sensing Molecules and Inhibitors with Potential Antifungal Activity: A Review. Molecules, vol.24, p.1950, 2019.

S. Horowitz-brown, R. Zarnowski, W. C. Sharpee, and N. P. Keller, Morphological transitions governed by density dependence and lipoxygenase activity in Aspergillus flavus, Appl. Environ. Microbiol, vol.74, pp.5674-5685, 2008.

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, pp.695-717, 2012.

C. Csank and K. Haynes, Candida glabrata displays pseudohyphal growth, FEMS Microbiol. Lett, vol.189, pp.115-120, 2000.

S. A. Lachke, S. Joly, K. Daniels, and D. R. Soll, Phenotypic switching and filamentation in Candida glabrata, Microbiology, vol.148, pp.2661-2674, 2002.

S. Tati, Candida glabrata binding to Candida albicans hyphae enables its development in oropharyngeal candidiasis, PLoS Pathog, vol.12, pp.1-21, 2016.

J. W. Spatafora, The fungal tree of life: from molecular systematics to genome-scale phylogenies, Microbiol. Spectr, vol.5, 2017.

M. Gardes and T. D. Bruns, ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts, Mol. Ecol, vol.2, pp.113-118, 1993.

W. G. Weisburg, S. M. Barns, D. A. Pelletier, and D. J. Lane, 16S ribosomal DNA amplification for phylogenetic study, J. Bacteriol, vol.173, pp.697-703, 1991.

A. Botha, An isolation procedure for arachidonic acid producing Mortierella species, Antonie Van. Leeuwenhoek, vol.75, pp.253-256, 1999.

P. Jargeat, J. Chaumeton, O. Navaud, A. Vizzini, and H. Gryta, The Paxillus involutus (Boletales, Paxillaceae) complex in Europe: Genetic diversity and morphological description of the new species Paxillus cuprinus, typification of P. involutus s.s., and synthesis of species boundaries, Fungal Biol, vol.118, pp.12-31, 2014.

J. F. Castro, Identification and heterologous expression of the chaxamycin biosynthesis gene cluster from Streptomyces leeuwenhoekii, Appl. Environ. Microbiol, vol.81, pp.5820-5831, 2015.

K. V. Solomon, Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes, Science, vol.351, pp.1192-1195, 2016.

C. H. Haitjema, A parts list for fungal cellulosomes revealed by comparative genomics, Nat. Microbiol, vol.2, p.17087, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608502

Y. Hoffman, Isolation and characterization of a novel chytrid species (phylum Blastocladiomycota), parasitic on the green alga Haematococcus, Mycol. Res, vol.112, pp.70-81, 2008.

L. W. Doner and G. Bécard, Solubilization of gellan gels by chelation of cations, Biotechnol. Tech, vol.5, pp.25-28, 1991.

C. Kurtzman, J. W. Fell, and T. Boekhout, The Yeasts: A Taxonomic Study, 2011.

J. E. Longcore, Morphology and zoospore ultrastructure of Entophlyctis luteolus sp. nov. (Chytridiales): Implications for chytrid taxonomy, Mycologia, vol.87, pp.25-33, 1995.

D. H. Marx and W. C. Bryan, Growth and ectomycorrhizal development of loblolly pine seedlings in fumigated soil infested with the fungal symbiont Pisolithus tinctorius, Forest Sci, vol.21, pp.245-254, 1975.

C. J. Johnson, J. F. Kernien, A. R. Hoyer, and J. E. Nett, Mechanisms involved in the triggering of neutrophil extracellular traps (NETs) by Candida glabrata during planktonic and biofilm growth, Sci. Rep, vol.7, p.13065, 2017.

B. T. Pfannenstiel, Revitalization of a forward genetic screen identifies three new regulators of fungal secondary metabolism in the genus Aspergillus, mBio, vol.8, 2017.

M. J. Powell, Handbook of the Protists, pp.1523-1558, 2017.

D. R. Simmons, Phylogeny of Powellomycetaceae fam. nov. and description of Geranomyces variabilis gen. et comb. nov, Mycologia, vol.103, pp.1411-1420, 2011.

L. M. Schloegel, Novel, panzootic and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade, Mol. Ecol, vol.21, pp.5162-5177, 2012.

L. L. Singleton, J. D. Mihail, and C. M. Rush, Methods for Research on Soilborne Phytopathogenic Fungi, 1992.

G. Bécard and J. A. Fortin, Early events of vesicular-arbuscular mycorrhiza formation on Ri T-DNA transformed roots, N. Phytol, vol.108, pp.211-218, 1988.

N. P. Price, Broad-host-range Rhizobium species strain NGR234 secretes a family of carbamoylated, and fucosylated, nodulation signals that are O-acetylated or sulphated, Mol. Microbiol, vol.6, pp.3575-3584, 1992.
URL : https://hal.archives-ouvertes.fr/hal-02706335

A. Andriankaja, AP2-ERF transcription factors mediate Nod factor-dependent Mt ENOD11 activation in root hairs via a novel cisregulatory motif, Plant Cell, vol.19, pp.2866-2885, 2007.

J. L. Brookman and D. W. Denning, Molecular genetics in Aspergillus fumigatus, Curr. Opin. Microbiol, vol.3, pp.468-474, 2000.

W. C. Nierman, Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus, Nature, vol.438, pp.1151-1156, 2005.
URL : https://hal.archives-ouvertes.fr/pasteur-02639869

N. L. Bray, H. Pimentel, P. Melsted, and L. Pachter, Erratum: near-optimal probabilistic RNA-seq quantification, Nat. Biotechnol, vol.34, p.888, 2016.

H. Pimentel, N. L. Bray, S. Puente, P. Melsted, and L. Pachter, Differential analysis of RNA-seq incorporating quantification uncertainty, Nat. Methods, vol.14, pp.687-690, 2017.

J. E. Stajich, FungiDB: an integrated functional genomics database for fungi, Nucleic Acids Res, vol.40, pp.675-681, 2012.

M. Kanehisa and Y. Sato, KEGG Mapper for inferring cellular functions from protein sequences, Protein Sci, vol.29, pp.28-35, 2020.

M. M. Weerasekera, Culture media profoundly affect Candida albicans and Candida tropicalis growth, adhesion and biofilm development, Mem. Inst. Oswaldo Cruz, vol.111, pp.697-702, 2016.

I. R. Gonçalves, Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi, BMC Evol. Biol, vol.16, 2016.

R. Liu, C. Xu, Q. Zhang, S. Wang, and W. Fang, Evolution of the chitin synthase gene family correlates with fungal morphogenesis and adaptation to ecological niches, Sci. Rep, vol.7, p.44527, 2017.

L. Ma, Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication, PLoS Genet, vol.5, p.1000549, 2009.

J. R. Pacheco-arjona and J. H. Ramirez-prado, Large-scale phylogenetic classification of fungal chitin synthases and identification of a putative cellwall metabolism gene cluster in Aspergillus genomes, PLoS ONE, vol.9, p.104920, 2014.

I. Mouyna, What are the functions of chitin deacetylases in Aspergillus fumigatus? Front, Cell. Infect. Microbiol, vol.10, p.28, 2020.

E. Larriba, Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia, Fungal Genet. Biol, vol.65, pp.69-80, 2014.

S. Petrasch, Infection strategies deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a function of tomato fruit ripening stage, Front. Plant Sci, vol.10, p.223, 2019.

M. C. Chibucos, An integrated genomic and transcriptomic survey of mucormycosis-causing fungi, Nat. Commun, vol.7, p.12218, 2016.

J. Abramyan and J. E. Stajich, Species-specific chitin-binding module 18 expansion in the amphibian pathogen Batrachochytrium dendrobatidis, vol.3, pp.150-162, 2012.

R. De-jonge and B. P. Thomma, Fungal LysM effectors: extinguishers of host immunity?, Trends Microbiol, vol.17, pp.151-157, 2009.

H. Nordberg, The genome portal of the Department of Energy Joint Genome Institute: 2014 updates, Nucleic Acids Res, vol.42, pp.26-31, 2014.

E. W. Sayers, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, vol.48, pp.9-16, 2020.