L. Tedersoo, T. W. May, and M. E. Smith, Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages, Mycorrhiza, vol.20, pp.217-263, 2010.

G. Bonito, Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified Southern Hemisphere sister lineage, PLoS ONE, vol.8, p.52765, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268210

A. Mello, C. Murat, and P. Bonfante, Truffles: much more than a prized and local fungal delicacy, FEMS Microbiol. Lett, vol.260, pp.1-8, 2006.
DOI : 10.1111/j.1574-6968.2006.00252.x
URL : https://academic.oup.com/femsle/article-pdf/260/1/1/19120980/260-1-1.pdf

F. Le-tacon, Certainties and uncertainties about the life cycle of the Périgord black truffle Tuber melanosporum, Ann. Forest Sci, vol.73, pp.105-117, 2016.

F. Martin, Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis, Nature, vol.464, pp.1033-1038, 2010.

R. Splivallo, S. Ottonello, A. Mello, and P. Karlovsky, Truffle volatiles: from chemical ecology to aroma biosynthesis, New Phytol, vol.189, pp.688-699, 2011.
DOI : 10.1111/j.1469-8137.2010.03523.x
URL : https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1469-8137.2010.03523.x

S. Traeger, The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution, PLoS Genet, vol.9, p.1003820, 2013.

K. O'donnell, E. Cigelnik, N. S. Weber, and J. M. Trappe, Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis, Mycologia, vol.89, pp.48-65, 1997.

R. Percudani, A. Trevisi, A. Zambonelli, and S. Ottonello, Molecular phylogeny of truffles (Pezizales: Terfeziaceae, Tuberaceae) derived from nuclear rDNA sequence analysis, Mol. Phylogenet. Evol, vol.13, pp.169-180, 1999.
DOI : 10.1006/mpev.1999.0638

M. Prieto and M. Wedin, Dating the diversification of the major lineages of Ascomycota (Fungi), PLoS ONE, vol.8, p.65576, 2013.

C. R. Fitzpatrick, Assembly and ecological function of the root microbiome across angiosperm plant species, Proc. Natl Acad. Sci. USA, vol.115, pp.1157-1165, 2018.

J. A. Clutterbuck, Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes, Fungal. Genet. Biol, vol.48, pp.306-326, 2011.

B. Montanini, Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content, Genome Biol, vol.15, pp.10-1186, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01268910

J. Amselem, M. Lebrun, and H. Quesneville, Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes, BMC Genomics, vol.16, p.141, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01142763

D. Tautz and T. Domazet-lo?o, The evolutionary origin of orphan genes, Nat. Rev. Genet, vol.12, pp.692-702, 2011.

A. Kohler, Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists, Nat. Genet, vol.47, pp.410-415, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01140842

M. Peter, Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum, Nat. Commun, vol.7, p.12662, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01439098

E. A. Hobbie, N. S. Weber, and J. M. Trappe, Mycorrhizal vs saprotrophic status of fungi: the isotopic evidence, New Phytol, vol.150, pp.601-610, 2001.

B. Drigo, I. C. Anderson, G. S. Kannangara, J. W. Cairney, and D. Johnson, Rapid incorporation of carbon from ectomycorrhizal mycelial necromass into soil fungal communities, Soil Biol. Biochem, vol.49, pp.4-10, 2012.
DOI : 10.1016/j.soilbio.2012.02.003
URL : https://doi.org/10.1016/j.soilbio.2012.02.003

S. Hacquard, Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments, Environ. Microbiol, vol.15, pp.1853-1869, 2013.
DOI : 10.1111/1462-2920.12080
URL : https://hal.archives-ouvertes.fr/hal-01268103

M. Vahdatzadeh, A. Deveau, and R. Splivallo, The role of the microbiome of truffles in aroma formation: a meta-analysis approach, Appl. Environ. Microbiol, vol.81, pp.6946-6952, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01269458

L. Rhounim, A. Grégoire, S. Salama, and G. Faugeron, Clustering of multiple transgene integrations in highly-unstable Ascobolus immersus transformants, Curr. Genet, vol.26, pp.344-351, 1994.

N. Roth-bejerano, D. Livne, and V. Kagan-zur, Helianthemum-Terfezia relations in different growth media, New Phytol, vol.114, pp.235-238, 2006.

S. Gnerre, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proc. Natl Acad. Sci. USA, vol.108, pp.1513-1518, 2011.

J. Aury, High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies, BMC Genomics, vol.9, p.603, 2008.

M. Dubarry, Gmove a Tool for Eukaryotic Gene Predictions Using Various Evidences, 1000.

I. V. Grigoriev, MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Res, vol.42, pp.699-704, 2014.

L. G. Nagy, Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts, Nat. Commun, vol.5, p.4471, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01268896

F. A. Simão, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with singlecopy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015.

T. Turgeman, The role of pre-symbiotic auxin signaling in ectendomycorrhiza formation between the desert truffle Terfezia boudieri and Helianthemum sessiliflorum, Mycorrhiza, vol.26, pp.287-297, 2016.