P. Vandenkoornhuyse, S. Baldauf, C. Leyval, J. Straczek, and J. Young, Extensive Fungal Diversity in Plant Roots, Science, vol.295, issue.5562, p.2051, 2002.
DOI : 10.1126/science.295.5562.2051

A. Purvis and A. Hector, Getting the measure of biodiversity, Nature, vol.405, issue.6783, pp.212-219, 2000.
DOI : 10.1038/35012221

J. Taylor, D. Jacobson, S. Kroken, T. Kasuga, and D. Geiser, Phylogenetic Species Recognition and Species Concepts in Fungi, Fungal Genetics and Biology, vol.31, issue.1, pp.21-32, 2000.
DOI : 10.1006/fgbi.2000.1228

P. Vandenkoornhuyse, R. Husband, T. Daniell, I. Watson, and J. Duck, Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem, Molecular Ecology, vol.78, issue.8, pp.1555-1564, 2002.
DOI : 10.1093/nar/25.24.4876

M. Jones, I. Forn, C. Gadelha, M. Egan, and D. Bass, Discovery of novel intermediate forms redefines the fungal tree of life, Nature, vol.86, issue.7350, pp.200-203, 2011.
DOI : 10.1038/nature09984

J. Powell, M. Monaghan, O. ¨. , M. Rillig, and M. , Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories, Molecular Ecology, vol.213, issue.3, pp.655-666, 2011.
DOI : 10.1111/j.1365-294X.2010.04964.x

D. Hawksworth and A. Rossman, Where Are All the Undescribed Fungi?, Phytopathology, vol.87, issue.9, pp.888-891, 1997.
DOI : 10.1094/PHYTO.1997.87.9.888

M. Blackwell, The Fungi: 1, 2, 3 ... 5.1 million species?, American Journal of Botany, vol.98, issue.3, pp.426-438, 2011.
DOI : 10.3732/ajb.1000298

C. Woese, Interpreting the universal phylogenetic tree, Proceedings of the National Academy of Sciences, vol.97, issue.15, pp.8392-8396, 2000.
DOI : 10.1073/pnas.97.15.8392

N. Pace, Mapping the Tree of Life: Progress and Prospects, Microbiology and Molecular Biology Reviews, vol.73, issue.4, pp.565-576, 2009.
DOI : 10.1128/MMBR.00033-09

I. Choi and S. Kim, Global extent of horizontal gene transfer, Proceedings of the National Academy of Sciences, vol.104, issue.11, pp.4489-4494, 2007.
DOI : 10.1073/pnas.0611557104

E. Boon, E. Zimmerman, B. Lang, and M. Hijri, Intra-isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome, Journal of Evolutionary Biology, vol.76, issue.7, pp.1519-1527, 2010.
DOI : 10.1111/j.1420-9101.2010.02019.x

I. Sanders, M. Alt, K. Groppe, T. Boller, and A. Wiemken, Identification of ribosomal DNA polymorphisms among and within spores of the Glomales: application to studies on the genetic diversity of arbuscular mycorrhizal fungal communities, New Phytologist, vol.97, issue.3, pp.419-427, 1995.
DOI : 10.1038/363067a0

Y. Lim, R. Sturrock, I. Leal, K. Pellow, and T. Yamaguchi, Distinguishing homokaryons and heterokaryons in Phellinus sulphurascens using pairing tests and ITS polymorphisms, Antonie van Leeuwenhoek, vol.95, issue.1-2, pp.99-110, 2008.
DOI : 10.1007/s10482-007-9184-0

D. Benson, I. Karsch-mizrachi, D. Lipman, J. Ostell, and E. Sayers, GenBank, Nucleic Acids Research, vol.39, issue.Database, pp.32-37, 2011.
DOI : 10.1093/nar/gkq1079
URL : http://doi.org/10.1093/nar/gkj157

T. Kulikova, R. Akhtar, P. Aldebert, N. Althorpe, and M. Andersson, The EMBL Nucleotide Sequence Database, Nucleic Acids Research, vol.32, issue.90001, pp.16-20, 2006.
DOI : 10.1093/nar/gkh120
URL : https://hal.archives-ouvertes.fr/hal-00427196

E. Kaminuma, T. Kosuge, Y. Kodama, H. Aono, and J. Mashima, DDBJ progress report, Nucleic Acids Research, vol.39, issue.Database, pp.22-27, 2011.
DOI : 10.1093/nar/gkq1041

J. Avise, Molecular Markers, Natural History, and Evolution, 2004.
DOI : 10.1007/978-1-4615-2381-9

S. Baldauf, A Search for the Origins of Animals and Fungi: Comparing and Combining Molecular Data, The American Naturalist, vol.154, issue.S4, pp.178-188, 1999.
DOI : 10.1086/303292

S. Baldauf, A. Roger, I. Wenk-siefert, and W. Doolitle, A Kingdom-Level Phylogeny of Eukaryotes Based on Combined Protein Data, Science, vol.290, issue.5493, pp.972-977, 2000.
DOI : 10.1126/science.290.5493.972

T. Helgason, I. Watson, and J. Young, Phylogeny of the Glomerales and Diversisporales (Fungi: Glomeromycota) from actin and elongation factor 1-alpha sequences, FEMS Microbiology Letters, vol.229, issue.1, pp.127-132, 2003.
DOI : 10.1016/S0378-1097(03)00802-4

S. Baldauf and J. Palmer, Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins., Proceedings of the National Academy of Sciences, vol.90, issue.24, pp.11558-11562, 1993.
DOI : 10.1073/pnas.90.24.11558

C. Moon, C. Miles, U. Jarlfors, and C. Schardl, endophyte species from grasses indigenous to the Southern Hemisphere, Mycologia, vol.94, issue.4, pp.694-711, 2002.
DOI : 10.1080/15572536.2003.11833197

Y. Tanabe, M. Saikawa, M. Watanabe, and J. Sugiyama, Molecular phylogeny of Zygomycota based on EF-1?? and RPB1 sequences: limitations and utility of alternative markers to rDNA, Molecular Phylogenetics and Evolution, vol.30, issue.2, pp.438-449, 2004.
DOI : 10.1016/S1055-7903(03)00185-4

M. Bidartondo, Preserving Accuracy in GenBank, Science, vol.319, issue.5870, p.1616, 2008.
DOI : 10.1126/science.319.5870.1616a

P. Bridge, P. Roberts, B. Spooner, and G. Panchal, On the unreliability of published DNA sequences, New Phytologist, vol.32, issue.1, pp.43-48, 2003.
DOI : 10.1046/j.1469-8137.2003.00861.x

R. Vilgalys, Taxonomic misidentification in public DNA databases, New Phytologist, vol.295, issue.1, pp.4-5, 2003.
DOI : 10.1046/j.1469-8137.2003.00894.x

P. Bridge, B. Spooner, and P. Roberts, Reliability and use of published sequence data, New Phytologist, vol.160, issue.1, pp.15-17, 2004.
DOI : 10.1111/j.1469-8137.2004.00962.x

D. Hawksworth, ???Misidentifications??? in fungal DNA sequence databanks, New Phytologist, vol.414, issue.1, pp.13-15, 2004.
DOI : 10.1111/j.1469-8137.2004.00958.x

D. Hawksworth, Separate name for fungus's sexual stage may cause confusion, Nature, vol.457, issue.7234, p.29, 2009.
DOI : 10.1038/458029c

A. Holst-jensen, T. Vrålstad, and T. Schumacher, On reliability, New Phytologist, vol.160, issue.1, pp.11-13, 2004.
DOI : 10.1111/j.1469-8137.2004.00961.x

R. Nilsson, M. Ryberg, E. Kristiansson, K. Abarenkov, and K. Larsson, Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective, PLoS ONE, vol.2, issue.1, p.59, 2006.
DOI : 10.1371/journal.pone.0000059.s001

U. Kõljalg, K. Larsson, K. Abarenkov, R. Nilsson, and I. Alexander, UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi, New Phytologist, vol.13, issue.3, pp.1063-1068, 2005.
DOI : 10.1111/j.1469-8137.2005.01376.x

O. ¨-pik, M. Vanatoa, A. Vanatoa, E. Moora, M. Davison et al., The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota), New Phytol, vol.188, pp.223-241, 2010.

J. Cole, Q. Wang, E. Cardenas, J. Fish, and B. Chai, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Research, vol.37, issue.Database, pp.141-145, 2009.
DOI : 10.1093/nar/gkn879

E. Pruesse, C. Quast, K. Knittel, B. Fuchs, and W. Ludwig, SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Research, vol.35, issue.21, pp.7188-7196, 2007.
DOI : 10.1093/nar/gkm864

T. Desantis, P. Hugenholtz, N. Larsen, M. Rojas, and E. Brodie, Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB, Applied and Environmental Microbiology, vol.72, issue.7, pp.5069-5072, 2006.
DOI : 10.1128/AEM.03006-05

M. Larkin, G. Blackshields, N. Brown, R. Chenna, and P. Mcgettigan, Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948, 2007.
DOI : 10.1093/bioinformatics/btm404
URL : https://hal.archives-ouvertes.fr/hal-00206210

D. Bhattacharya, T. Friedl, and G. Helms, Vertical Evolution and Intragenic Spread of Lichen-Fungal Group I Introns, Journal of Molecular Evolution, vol.55, issue.1, pp.74-84, 2002.
DOI : 10.1007/s00239-001-2305-x

J. Felsenstein, Inferring phylogenies, Sinauer Associates, 2004.

D. Posada and K. Crandall, MODELTEST: testing the model of DNA substitution, Bioinformatics, vol.14, issue.9, pp.817-818, 1998.
DOI : 10.1093/bioinformatics/14.9.817

A. Bar-hen, M. Mariadassou, M. Poursat, and P. Vandenkoornhuyse, Influence Function for Robust Phylogenetic Reconstructions, Molecular Biology and Evolution, vol.25, issue.5, pp.869-873, 2008.
DOI : 10.1093/molbev/msn030
URL : https://hal.archives-ouvertes.fr/hal-00312860

P. Vandenkoornhuyse and C. Leyval, SSU rDNA Sequencing and PCR-Fingerprinting Reveal Genetic Variation within Glomus mosseae, Mycologia, vol.90, issue.5, pp.791-797, 1998.
DOI : 10.2307/3761320

T. White, T. Bruns, S. Lee, T. J. Innis, M. Gelfand et al., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics White TJ editors. PCR protocols, a guide to methods and applications, pp.315-322, 1990.

L. Calvez, T. Burgaud, G. Mahé, S. Barbier, G. Vandenkoornhuyse et al., Fungal Diversity in Deep-Sea Hydrothermal Ecosystems, Applied and Environmental Microbiology, vol.75, issue.20, pp.6415-6421, 2009.
DOI : 10.1128/AEM.00653-09
URL : https://hal.archives-ouvertes.fr/hal-00429860

D. Simmons, T. James, A. Meyer, and J. Longcore, Lobulomycetales, a new order in the Chytridiomycota, Mycological Research, vol.113, issue.4, pp.450-460, 2009.
DOI : 10.1016/j.mycres.2008.11.019

F. Lutzoni, F. Kauff, C. Cox, D. Mclaughlin, and G. Celio, Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits, American Journal of Botany, vol.91, issue.10, 2004.
DOI : 10.3732/ajb.91.10.1446

K. Abarenkov, R. Nilsson, K. Larsson, I. Alexander, and U. Eberhardt, The UNITE database for molecular identification of fungi - recent updates and future perspectives, New Phytologist, vol.51, issue.2, pp.281-285, 2010.
DOI : 10.1111/j.1469-8137.2009.03160.x

K. Abarenkov, L. Tedersoo, R. Nilsson, K. Vellak, and I. Saar, PlutoF-a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences, Evol Bioinformatics, vol.6, pp.189-196, 2010.

C. Schoch, K. Seifert, S. Huhndorf, V. Robert, and J. Spouge, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, Proceedings of the National Academy of Sciences, vol.109, issue.16, pp.6241-6246, 2012.
DOI : 10.1073/pnas.1117018109

I. Anderson and P. Parkin, Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules, Journal of Microbiological Methods, vol.68, issue.2, pp.248-253, 2007.
DOI : 10.1016/j.mimet.2006.08.005

P. Xu, Y. Han, J. Wu, H. Lv, and L. Qiu, Phylogenetic Analysis of the Sequences of rDNA Internal Transcribed Spacer (ITS) of Phytophthora sojae, Journal of Genetics and Genomics, vol.34, issue.2, pp.180-188, 2007.
DOI : 10.1016/S1673-8527(07)60019-8

D. Auria, G. Pushker, R. Rodriguez-valera, and F. , IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships, Bioinformatics, vol.22, issue.5, pp.527-531, 2006.
DOI : 10.1093/bioinformatics/btk033

D. Bass, A. Howe, N. Brown, H. Barton, and M. Demidova, Yeast forms dominate fungal diversity in the deep oceans, Proceedings of the Royal Society B: Biological Sciences, vol.28, issue.23, pp.3069-3077, 2007.
DOI : 10.1093/nar/28.23.4698

D. Hibbett, M. Binder, J. Bischoff, M. Blackwell, and P. Cannon, A higher-level phylogenetic classification of the Fungi, Mycological Research, vol.111, issue.5, pp.509-547, 2007.
DOI : 10.1016/j.mycres.2007.03.004