G. Barron, Nematophagous destroying fungi. Guelph: Lancester press, pp.1-140

M. Linford, STIMULATED ACTIVITY OF NATURAL ENEMIES OF NEMATODES, Science, vol.85, issue.2196, pp.123-127, 1937.
DOI : 10.1126/science.85.2196.123

D. Ahren, M. Tholander, C. Fekete, B. Rajashekar, E. Friman et al., Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum, Microbiology, vol.151, issue.3, pp.789-803, 2005.
DOI : 10.1099/mic.0.27485-0

C. Fekete, M. Tholander, B. Rajashekar, D. Ahren, E. Friman et al., Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans, Environmental Microbiology, vol.57, issue.2, pp.364-75, 2008.
DOI : 10.1105/tpc.003426

T. Meerupati, K. Andersson, E. Friman, D. Kumar, A. Tunlid et al., Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi, PLoS Genetics, vol.3, issue.Suppl 1, p.24244185, 2013.
DOI : 10.1371/journal.pgen.1003909.s018

K. Andersson, D. Kumar, J. Bentzer, E. Friman, D. Ahren et al., Interspecific and host-related gene expression patterns in nematode-trapping fungi, BMC Genomics, vol.15, issue.1, pp.968-25384908, 2014.
DOI : 10.1038/nmeth.1701

URL : http://doi.org/10.1186/1471-2164-15-968

K. Liu, W. Zhang, Y. Lai, M. Xiang, X. Wang et al., Drechslerella stenobrocha genome illustrates the mechanism of constricting rings and the origin of nematode predation in fungi, BMC Genomics, vol.15, issue.1, pp.114-24507587, 2014.
DOI : 10.1038/nmeth.1226

J. Yang, L. Wang, J. X. Feng, Y. Li, X. Zou et al., Genomic and Proteomic Analyses of the Fungus Arthrobotrys oligospora Provide Insights into Nematode-Trap Formation, PLoS Pathogens, vol.187, issue.9, pp.1002179-21909256, 2011.
DOI : 10.1371/journal.ppat.1002179.s016

Y. Lai, K. Liu, X. Zhang, K. Li, N. Wang et al., Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis, Genome Biology and Evolution, vol.6, issue.11
DOI : 10.1093/gbe/evu241

J. Dijksterhuis, M. Veenhuis, and W. Harder, Ultrastructural study of adhesion and initial stages of infection of nematodes by conidia of Drechmeria coniospora, Mycological Research, vol.94, issue.1, pp.1-8, 1990.
DOI : 10.1016/S0953-7562(09)81257-4

V. Rouger, G. Bordet, C. Couillault, S. Monneret, S. Mailfert et al., Independent Synchronized Control and Visualization of Interactions between Living Cells and Organisms, Biophysical Journal, vol.106, issue.10, pp.2096-104, 2014.
DOI : 10.1016/j.bpj.2014.03.044

D. Gernandt and J. Stone, Phylogenetic Analysis of Nuclear Ribosomal DNA Places the Nematode Parasite, Drechmeria coniospora, in Clavicipitaceae, Mycologia, vol.91, issue.6, pp.993-1000, 1999.
DOI : 10.2307/3761630

C. Quandt, R. Kepler, W. Gams, J. Araujo, S. Ban et al., Phylogenetic-based nomenclatural proposals for <I>Ophiocordycipitaceae</I> (<I>Hypocreales</I>) with new combinations in <I>Tolypocladium</I>, IMA Fungus, vol.5, issue.1, pp.121-155, 2014.
DOI : 10.5598/imafungus.2014.05.01.12

H. Jansson, A. Jeyaprakash, and B. Zuckerman, Differential adhesion and infection of nematodes by the endoparasitic fungus Meria coniospora (Deuteromycetes), Appl Envir Microbiol, vol.49, pp.552-557, 1985.

G. Coles, M. Dicklow, and B. Zuckerman, Protein changes associated with the infection of the nematode Caenorhabditis elegans by the nematophagous fungus Drechmeria coniospora, International Journal for Parasitology, vol.19, issue.7, pp.733-739, 1989.
DOI : 10.1016/0020-7519(89)90059-3

B. Fuchs and E. Mylonakis, Using non-mammalian hosts to study fungal virulence and host defense, Current Opinion in Microbiology, vol.9, issue.4, pp.346-51, 2006.
DOI : 10.1016/j.mib.2006.06.004

J. Ewbank and O. C. Zugasti, C. elegans: model host and tool for antimicrobial drug discovery, Disease Models & Mechanisms, vol.4, issue.3, pp.300-304, 2011.
DOI : 10.1242/dmm.006684

URL : https://hal.archives-ouvertes.fr/hal-01261848

L. Clark and J. Hodgkin, Commensals, probiotics and pathogens in the Caenorhabditis elegans model. Cellular microbiology, pp.27-38, 2014.

L. Cohen and E. Troemel, Microbial pathogenesis and host defense in the nematode C. elegans, Current Opinion in Microbiology, vol.23, pp.94-10103, 2014.
DOI : 10.1016/j.mib.2014.11.009

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4324121

S. Labed and N. Pujol, Caenorhabditis elegans Antifungal Defense Mechanisms, International Journal of Clinical Reviews, vol.5, issue.4, pp.110-117, 2011.
DOI : 10.5275/ijcr.2012.04.07

J. Ewbank and N. Pujol, Local and long-range activation of innate immunity by infection and damage in C. elegans, Current Opinion in Immunology, vol.38, pp.1-7, 2016.
DOI : 10.1016/j.coi.2015.09.005

URL : https://hal.archives-ouvertes.fr/hal-01438525

D. Kim and J. Ewbank, Signaling in the Immune Response, 2015.

M. Felix and F. Duveau, Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae, BMC Biology, vol.10, issue.1, p.59, 2012.
DOI : 10.1534/genetics.106.058651

URL : https://hal.archives-ouvertes.fr/inserm-00723270

O. Zugasti, N. Bose, B. Squiban, J. Belougne, C. Kurz et al., Activation of a G protein???coupled receptor by its endogenous ligand triggers the innate immune response of Caenorhabditis elegans, Nature Immunology, vol.351, issue.9, pp.833-841, 2014.
DOI : 10.1021/ja210202y

URL : https://hal.archives-ouvertes.fr/hal-01134518

B. Squiban, J. Belougne, J. Ewbank, and O. Zugasti, Quantitative and automated high-throughput genomewide RNAi screens in C. elegans, J Vis Exp, vol.60, p.3448, 2012.
DOI : 10.3791/3448

URL : https://hal.archives-ouvertes.fr/hal-00685587

S. Labed, S. Omi, M. Gut, J. Ewbank, and N. Pujol, The Pseudokinase NIPI-4 Is a Novel Regulator of Antimicrobial Peptide Gene Expression, PLoS ONE, vol.175, issue.3, pp.33887-22470487, 2012.
DOI : 10.1371/journal.pone.0033887.s002

K. Dierking, J. Polanowska, S. Omi, I. Engelmann, M. Gut et al., Unusual Regulation of a STAT Protein by an SLC6 Family Transporter in C.??elegans Epidermal Innate Immunity, Cell Host & Microbe, vol.9, issue.5, pp.425-460, 2011.
DOI : 10.1016/j.chom.2011.04.011

URL : https://hal.archives-ouvertes.fr/hal-00611411

O. Zugasti and J. Ewbank, Neuroimmune regulation of antimicrobial peptide expression by a noncanonical TGF-?? signaling pathway in Caenorhabditis elegans epidermis, Nature Immunology, vol.269, issue.3, pp.249-56, 2009.
DOI : 10.1016/S0378-1119(00)00579-5

URL : https://hal.archives-ouvertes.fr/hal-00408369

K. Nomura, S. Debroy, Y. Lee, N. Pumplin, J. Jones et al., A Bacterial Virulence Protein Suppresses Host Innate Immunity to Cause Plant Disease, Science, vol.313, issue.5784, pp.220-223, 2006.
DOI : 10.1126/science.1129523

N. Elde and H. Malik, The evolutionary conundrum of pathogen mimicry, Nature Reviews Microbiology, vol.201, issue.11, pp.787-97, 2009.
DOI : 10.1038/nrmicro2222

O. Kepp, L. Senovilla, L. Galluzzi, T. Panaretakis, A. Tesniere et al., Viral subversion of immunogenic cell death, Cell Cycle, vol.8, issue.6, pp.860-869, 2009.
DOI : 10.4161/cc.8.6.7939

S. Shames, S. Auweter, and B. Finlay, Co-evolution and exploitation of host cell signaling pathways by bacterial pathogens, The International Journal of Biochemistry & Cell Biology, vol.41, issue.2, pp.380-389, 2008.
DOI : 10.1016/j.biocel.2008.08.013

N. Pujol, O. Zugasti, D. Wong, C. Couillault, C. Kurz et al., Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides, ):e1000105. Epub, p.18636113, 2008.
DOI : 10.1371/journal.ppat.1000105.s010

D. Zerbino and E. Birney, Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5
DOI : 10.1101/gr.074492.107

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2336801

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin et al., SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing, Journal of Computational Biology, vol.19, issue.5, pp.455-77, 2012.
DOI : 10.1089/cmb.2012.0021

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342519

R. Luo, B. Liu, Y. Xie, Z. Li, W. Huang et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, GigaScience, vol.1, issue.1, p.23587118, 2012.
DOI : 10.1186/2047-217X-1-18

URL : http://doi.org/10.1186/2047-217x-1-18

J. Simpson, K. Wong, S. Jackman, J. Schein, S. Jones et al., ABySS: A parallel assembler for short read sequence data, Genome Research, vol.19, issue.6, pp.1117-1140, 2009.
DOI : 10.1101/gr.089532.108

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694472

M. Boetzer, C. Henkel, H. Jansen, D. Butler, and W. Pirovano, Scaffolding pre-assembled contigs using SSPACE, Bioinformatics, vol.27, issue.4, pp.578-587, 2010.
DOI : 10.1093/bioinformatics/btq683

M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne et al., Circos: An information aesthetic for comparative genomics, Genome Research, vol.19, issue.9, pp.1639-1684, 2009.
DOI : 10.1101/gr.092759.109

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752132

Q. Gao, J. K. Ying, S. Zhang, Y. Xiao, G. Shang et al., Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum):e1001264, PLoS Genet. Epub, vol.7, issue.1, p.21253567, 2011.

X. Hu, Y. Zhang, G. Xiao, P. Zheng, Y. Xia et al., Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus, Chinese Science Bulletin, vol.10, issue.23, pp.2846-54, 2013.
DOI : 10.1007/s11434-013-5929-5

A. Price, N. Jones, and P. Pevzner, De novo identification of repeat families in large genomes, Bioinformatics, vol.21, issue.Suppl 1, pp.351-359, 2005.
DOI : 10.1093/bioinformatics/bti1018

T. Lowe and S. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997.
DOI : 10.1093/nar/25.5.0955

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-1005, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

M. Stanke, M. Diekhans, R. Baertsch, and D. Haussler, Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, vol.24, issue.5, pp.637-681, 2008.
DOI : 10.1093/bioinformatics/btn013

F. Simao, R. Waterhouse, P. Ioannidis, E. Kriventseva, and E. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, issue.19, pp.3210-3212, 2015.
DOI : 10.1093/bioinformatics/btv351

K. Katoh and D. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Molecular Biology and Evolution, vol.30, issue.4, pp.772-80, 2013.
DOI : 10.1093/molbev/mst010

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=

R. Lin, C. Liu, B. Shen, M. Bai, J. Ling et al., Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales, BMC Microbiology, vol.15, issue.1, p.5, 2015.
DOI : 10.1093/bioinformatics/btr088

E. Zdobnov and R. Apweiler, InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, vol.17, issue.9, pp.847-855, 2001.
DOI : 10.1093/bioinformatics/17.9.847

D. Lipman, A. Souvorov, E. Koonin, A. Panchenko, and T. Tatusova, The relationship of protein conservation and sequence length, BMC Evolutionary Biology, vol.2, issue.1, pp.20-12410938, 2002.
DOI : 10.1186/1471-2148-2-20

L. Li, C. Stoeckert, and D. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9
DOI : 10.1101/gr.1224503

G. Xiao, S. Ying, P. Zheng, Z. Wang, S. Zhang et al., Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana, Scientific Reports, vol.18, pp.483-22761991, 2012.
DOI : 10.1038/srep00483

W. Li, A. Cowley, M. Uludag, T. Gur, H. Mcwilliam et al., The EMBL-EBI bioinformatics web and programmatic tools framework, Nucleic Acids Research, vol.43, issue.W1, p.8, 2015.
DOI : 10.1093/nar/gkv279

URL : http://doi.org/10.1093/nar/gkv279

E. Sonnhammer and R. Durbin, A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis, Gene, vol.167, issue.1-2, pp.1-10, 1995.
DOI : 10.1016/0378-1119(95)00714-8

A. Bateman, L. Coin, R. Durbin, R. Finn, V. Hollich et al., The Pfam protein families database, Nucleic Acids Research, vol.32, issue.90001, pp.138-179, 2004.
DOI : 10.1093/nar/gkh121

URL : https://hal.archives-ouvertes.fr/hal-01294685

J. Habicht, C. Woehle, and S. Gould, Tetrahymena Expresses More than a Hundred Proteins with Lipidbinding MORN Motifs that can Differ in their Subcellular Localisations, J Eukaryot Microbiol, p.8, 2015.

J. Li and K. Zhang, Independent Expansion of Zincin Metalloproteinases in Onygenales Fungi May Be Associated with Their Pathogenicity, PLoS ONE, vol.60, issue.2, pp.90225-24587291, 2014.
DOI : 10.1371/journal.pone.0090225.s009

J. Li, L. Yu, Y. Tian, and K. Zhang, Molecular Evolution of the Deuterolysin (M35) Family Genes in Coccidioides, PLoS ONE, vol.39, issue.3, pp.31536-22363666, 2012.
DOI : 10.1371/journal.pone.0031536.s009

W. Dyrka, M. Lamacchia, P. Durrens, B. Kobe, A. Daskalov et al., Diversity and Variability of NOD-Like Receptors in Fungi, Genome Biology and Evolution, vol.6, issue.12, pp.3137-58, 2014.
DOI : 10.1093/gbe/evu251

URL : https://hal.archives-ouvertes.fr/hal-01083450

H. Fang and J. Gough, dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more, Nucleic Acids Research, vol.41, issue.D1, pp.536-580, 2013.
DOI : 10.1093/nar/gks1080

URL : http://doi.org/10.1093/nar/gks1080

N. Khaldi, F. Seifuddin, G. Turner, D. Haft, W. Nierman et al., SMURF: Genomic mapping of fungal secondary metabolite clusters, Fungal Genetics and Biology, vol.47, issue.9, pp.736-777, 2010.
DOI : 10.1016/j.fgb.2010.06.003

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916752

D. Scharf, T. Heinekamp, and A. Brakhage, Human and Plant Fungal Pathogens: The Role of Secondary Metabolites, PLoS Pathogens, vol.132, issue.1, pp.1003859-24497825, 2014.
DOI : 10.1371/journal.ppat.1003859.g001

C. Quandt, K. Bushley, and J. Spatafora, The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics, BMC Genomics, vol.56, issue.Web Server issu, p.553, 2015.
DOI : 10.1186/s12864-015-1777-9

R. Winnenburg, M. Urban, A. Beacham, T. Baldwin, S. Holland et al., PHI-base update: additions to the pathogen host interaction database, Nucleic Acids Research, vol.36, issue.Database, pp.572-578, 2007.
DOI : 10.1093/nar/gkm858

URL : http://doi.org/10.1093/nar/gkm858

B. Shen, X. J. Dai, L. Huang, Y. Mao, Z. Lin et al., Development of a high-efficiency gene knockout system for Pochonia chlamydosporia, Microbiological Research, vol.170, pp.18-26, 2015.
DOI : 10.1016/j.micres.2014.10.001

X. Hu, G. Xiao, P. Zheng, Y. Shang, Y. Su et al., Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation, Proceedings of the National Academy of Sciences, vol.4, issue.11, pp.16796-801, 2014.
DOI : 10.1093/sysbio/syq010

C. Xue, Y. Hsueh, and J. Heitman, Magnificent seven: roles of G protein-coupled receptors in extracellular sensing in fungi, FEMS Microbiology Reviews, vol.32, issue.6, pp.1010-1042, 2008.
DOI : 10.1111/j.1574-6976.2008.00131.x

R. Kulkarni, H. Kelkar, and R. Dean, An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins, Trends in Biochemical Sciences, vol.28, issue.3, pp.118-139, 2003.
DOI : 10.1016/S0968-0004(03)00025-2

M. Stringer, R. Dean, T. Sewall, and W. Timberlake, Rodletless, a new Aspergillus developmental mutant induced by directed gene inactivation., Genes & Development, vol.5, issue.7, pp.1161-71, 1991.
DOI : 10.1101/gad.5.7.1161

T. Linder and C. Gustafsson, Molecular phylogenetics of ascomycotal adhesins???A novel family of putative cell-surface adhesive proteins in fission yeasts, Fungal Genetics and Biology, vol.45, issue.4, pp.485-97, 2007.
DOI : 10.1016/j.fgb.2007.08.002

S. Ohtaki, H. Maeda, T. Takahashi, Y. Yamagata, F. Hasegawa et al., Novel hydrophobic surface binding protein, HsbA, produced by Aspergillus oryzae Applied and environmental microbiology, pp.2407-1307, 2006.
DOI : 10.1128/aem.72.4.2407-2413.2006

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449009

J. Yang, X. Zhao, L. Liang, Z. Xia, L. Lei et al., Overexpression of a cuticle-degrading protease Ver112 increases the nematicidal activity of Paecilomyces lilacinus, Applied Microbiology and Biotechnology, vol.78, issue.6, pp.1895-903, 2010.
DOI : 10.1007/s00253-010-3012-6

I. Engelmann, A. Griffon, L. Tichit, F. Montanana-sanchis, G. Wang et al., A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans, PLoS ONE, vol.104, issue.5, pp.19055-21602919, 2011.
DOI : 10.1371/journal.pone.0019055.s022

URL : https://hal.archives-ouvertes.fr/hal-01261853

P. Teixeira, D. Thomazella, R. Vidal, P. Prado, O. Reis et al., The Fungal Pathogen Moniliophthora perniciosa Has Genes Similar to Plant PR-1 That Are Highly Expressed during Its Interaction with Cacao, PLoS ONE, vol.7, issue.9, p.23029323, 2012.
DOI : 10.1371/journal.pone.0045929.s005

Y. Sakamoto, K. Nakade, and N. Konno, Endo-??-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family, Applied and Environmental Microbiology, vol.77, issue.23, pp.8350-8354, 2011.
DOI : 10.1128/AEM.05581-11

P. Punt and C. Van-den-hondel, [39] Transformation of filamentous fungi based on hygromycin b and phleomycin resistance markers, Methods Enzymol. Epub, vol.216, pp.447-57, 1992.
DOI : 10.1016/0076-6879(92)16041-H

C. Michielse, R. Van-wijk, L. Reijnen, B. Cornelissen, and M. Rep, Insight into the molecular requirements for pathogenicity of Fusarium oxysporum f. sp. lycopersici through large-scale insertional mutagenesis, Genome Biology, vol.10, issue.1, 2009.
DOI : 10.1186/gb-2009-10-1-r4

A. Fleissner, S. Sarkar, D. Jacobson, M. Roca, N. Read et al., The so Locus Is Required for Vegetative Cell Fusion and Postfertilization Events in Neurospora crassa, Eukaryotic Cell, vol.4, issue.5, pp.920-3005, 2005.
DOI : 10.1128/EC.4.5.920-930.2005

P. Rosales, R. , D. Pietro, and A. , Vegetative Hyphal Fusion Is Not Essential for Plant Infection by Fusarium oxysporum, Eukaryotic Cell, vol.7, issue.1, pp.162-71, 2007.
DOI : 10.1128/EC.00258-07

Y. Duverger, J. Belougne, S. Scaglione, D. Brandli, C. Beclin et al., A semi-automated high-throughput approach to the generation of transposon insertion mutants in the nematode Caenorhabditis elegans, Nucleic Acids Research, vol.35, issue.2, pp.11-17164286, 2007.
DOI : 10.1093/nar/gkl1046

URL : https://hal.archives-ouvertes.fr/inserm-00122555

L. Banyai and L. Patthy, Amoebapore homologs of Caenorhabditis elegans, Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, vol.1429, issue.1, pp.259-64, 1998.
DOI : 10.1016/S0167-4838(98)00237-4

T. Roeder, M. Stanisak, C. Gelhaus, I. Bruchhaus, J. Grotzinger et al., Caenopores are antimicrobial peptides in the nematode Caenorhabditis elegans instrumental in nutrition and immunity, Developmental & Comparative Immunology, vol.34, issue.2, pp.203-212, 2009.
DOI : 10.1016/j.dci.2009.09.010

J. Mysliwy, A. Dingley, M. Stanisak, S. Jung, I. Lorenzen et al., Caenopore-5: the threedimensional structure of an antimicrobial protein from Caenorhabditis elegans, Dev Comp Immunol, vol.34, issue.3, 2010.

D. Wong, D. Bazopoulou, N. Pujol, N. Tavernarakis, and J. Ewbank, Genome-wide investigation reveals pathogen-specific and shared signatures in the response of Caenorhabditis elegans to infection, Genome Biology, vol.8, issue.9
DOI : 10.1186/gb-2007-8-9-r194

A. Hoeckendorf and M. Leippe, SPP-3, a saposin-like protein of Caenorhabditis elegans, displays antimicrobial and pore-forming activity and is located in the intestine and in one head neuron, Developmental & Comparative Immunology, vol.38, issue.1, pp.181-187, 2012.
DOI : 10.1016/j.dci.2012.05.007

A. Hoeckendorf, M. Stanisak, and M. Leippe, and participates in defence against a natural bacterial pathogen, Biochemical Journal, vol.445, issue.2, pp.205-217, 2012.
DOI : 10.1042/BJ20112102

C. Drechsler, Some hyphomycetes parasitic on free-living terricolous nematodes, Phytopathology, vol.31, pp.773-802, 1941.
DOI : 10.2307/3754331

URL : http://www.biodiversitylibrary.org/handlers/modsdownload.ashx?pid=139454

H. Jansson, A. Jeyaprakash, and B. Zuckerman, Control of Root-Knot Nematodes on Tomato by the Endoparasitic Fungus Meria coniospora, J Nematol, vol.17, issue.3, pp.327-336, 1985.

S. Meyer, R. Huettel, and R. Sayre, Isolation of Fungi from Heterodera glycines and in vitro Bioassays for Their Antagonism to Eggs, J Nematol, vol.22, issue.4, pp.532-539, 1990.

G. Poinar and H. Jansson, Susceptibility of Neoaplectana spp. and Heterorhabditis heliothidis to the Endoparasitic Fungus Drechmeria coniospora, J Nematol. Epub, vol.18, issue.2, pp.225-234, 1986.

H. Jansson, Adhesion to nematodes of conidia from the nematophagous fungus Drechmeria coniospora, Journal of General Microbiology, vol.139, issue.8, pp.1899-906, 1993.
DOI : 10.1099/00221287-139-8-1899

P. Van-den-boogert, J. Dijksterhuis, H. Velvis, and M. Veenhuis, Adhesive knob formation by conidia of the nematophagous fungusDrechmeria coniospora, Antonie van Leeuwenhoek, vol.60, issue.3, pp.221-230, 1992.
DOI : 10.1007/BF00584228

J. Sun, S. Park, S. Kang, X. Liu, J. Qiu et al., Development of a transformation system for Hirsutella spp. and visualization of the mode of nematode infection by GFP-labeled H, minnesotensis. Sci Rep, vol.5, p.26190283, 2015.

L. Rosso, M. Finetti-sialer, P. Hirsch, A. Ciancio, B. Kerry et al., Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia, Applied Microbiology and Biotechnology, vol.12, issue.6, pp.1981-94, 2011.
DOI : 10.1007/s00253-011-3282-7

C. Olivares and L. Lopez-llorca, Fungal egg-parasites of plant-parasitic nematodes from Spanish soils, Rev Iberoam Micol, vol.19, issue.2, pp.104-114, 2002.

E. Larriba, M. Jaime, J. Carbonell-caballero, A. Conesa, J. Dopazo et al., Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia, Fungal Genetics and Biology, vol.65, pp.69-80, 2014.
DOI : 10.1016/j.fgb.2014.02.002

Q. Tahseen, I. Clark, S. Atkins, P. Hirsch, and B. Kerry, Impact of the nematophagous fungus Pochonia chlamydosporia on nematode and microbial populations, Commun Agric Appl Biol Sci, vol.70, issue.1, pp.81-87, 2005.

P. Mendoza-de-gives, K. Davies, S. Clark, and J. Behnke, Predatory behaviour of trapping fungi against srf mutants of Caenorhabditis elegans and different plant and animal parasitic nematodes, Parasitology, vol.119, issue.1, pp.95-104, 1999.
DOI : 10.1017/S0031182099004424

V. Migunova and B. Byzov, Determinants of trophic modes of the nematophagous fungus Arthrobotrys oligospora interacting with bacterivorous nematode Caenorhabditis elegans, Pedobiologia, vol.49, issue.2, pp.101-109, 2005.
DOI : 10.1016/j.pedobi.2004.08.003

X. Niu and K. Zhang, Arthrobotrys oligospora: a model organism for understanding the interaction between fungi and nematodes, Mycology, vol.2, issue.2, pp.59-78, 2011.
DOI : 10.1080/21501203.2011.562559

J. Van-den-brink and R. De-vries, Fungal enzyme sets for plant polysaccharide degradation, Applied Microbiology and Biotechnology, vol.58, issue.8, pp.1477-92, 2011.
DOI : 10.1007/s00253-011-3473-2

J. Dijksterhuis, W. Harder, U. Wyss, and M. Veenhuis, Colonization and digestion of nematodes by the endoparasitic nematophagous fungus Drechmeria coniospora, Mycological Research, vol.95, issue.7, pp.873-881, 1991.
DOI : 10.1016/S0953-7562(09)80052-X

A. Levasseur, E. Drula, V. Lombard, P. Coutinho, and B. Henrissat, Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes, Biotechnology for Biofuels, vol.6, issue.1, p.23514094, 2013.
DOI : 10.1186/1471-2148-12-186

URL : https://hal.archives-ouvertes.fr/hal-01268121

W. Fang, R. Leger, and . St, Mrt, a Gene Unique to Fungi, Encodes an Oligosaccharide Transporter and Facilitates Rhizosphere Competency in Metarhizium robertsii, PLANT PHYSIOLOGY, vol.154, issue.3, pp.1549-57, 2010.
DOI : 10.1104/pp.110.163014

E. Van-der-biezen and J. Jones, The NB-ARC domain: a novel signalling motif shared by plant resistance gene products and regulators of cell death in animals, Current Biology, vol.8, issue.7, pp.226-233, 1998.
DOI : 10.1016/S0960-9822(98)70145-9

W. Fang, M. Pava-ripoll, S. Wang, R. Leger, and . St, Protein kinase A regulates production of virulence determinants by the entomopathogenic fungus, Metarhizium anisopliae, Fungal Genetics and Biology, vol.46, issue.3, pp.277-85, 2009.
DOI : 10.1016/j.fgb.2008.12.001

J. Lu, H. Cao, L. Zhang, P. Huang, and F. Lin, Systematic analysis of Zn 2 Cys 6 transcription factors required for development and pathogenicity by high-throughput gene knockout in the rice blast fungus, PLoS Pathog, vol.10, issue.10, p.25299517, 2014.

J. Dijksterhuis, K. Sjollema, M. Veenhuis, and W. Harder, Competitive interactions between two nematophagous fungi during infection and digestion of the nematode Panagrellus redivivus, Mycological Research, vol.98, issue.12, pp.1458-62, 1994.
DOI : 10.1016/S0953-7562(09)81077-0

C. Zou, N. Tao, W. Liu, J. Yang, X. Huang et al., Regulation of subtilisin-like protease prC expression by nematode cuticle in the nematophagous fungus Clonostachys rosea, Environmental Microbiology, vol.12, issue.12, pp.3243-52, 2010.
DOI : 10.1111/j.1462-2920.2010.02296.x

A. Muszewska, J. Taylor, P. Szczesny, and M. Grynberg, Independent Subtilases Expansions in Fungi Associated with Animals, Molecular Biology and Evolution, vol.28, issue.12, pp.3395-404, 2011.
DOI : 10.1093/molbev/msr176

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3247792

L. Baxter, S. Tripathy, N. Ishaque, N. Boot, A. Cabral et al., Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome, Science, vol.452, issue.7183, pp.1549-51, 2010.
DOI : 10.1038/nature06556

J. Powell and F. Ausubel, Models of Caenorhabditis elegans Infection by Bacterial and Fungal Pathogens, Methods Mol Biol, vol.415, pp.403-430, 2008.
DOI : 10.1007/978-1-59745-570-1_24

P. Chomczynski and N. Sacchi, Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction, Analytical Biochemistry, vol.162, issue.1, pp.156-165, 1987.
DOI : 10.1016/0003-2697(87)90021-2

M. Grabherr, B. Haas, M. Yassour, J. Levin, D. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-52, 2011.

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571712

P. Gardner, J. Daub, J. Tate, E. Nawrocki, D. Kolbe et al., Rfam: updates to the RNA families database, Nucleic Acids Research, vol.37, issue.Database, pp.136-176, 2009.
DOI : 10.1093/nar/gkn766

URL : http://doi.org/10.1093/nar/gkn766

P. Jones, D. Binns, H. Chang, M. Fraser, W. Li et al., Genome-scale protein function classification, Bioinformatics, vol.5, issue.30, pp.1236-1276, 2014.
DOI : 10.1093/bioinformatics/btu031

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998142

C. Cuomo, U. Guldener, J. Xu, F. Trail, B. Turgeon et al., The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization, Science, vol.104, issue.4, pp.1400-1402, 2007.
DOI : 10.1016/j.fgb.2006.01.005

URL : https://hal.archives-ouvertes.fr/hal-00192479

L. Ma, H. Van-der-does, K. Borkovich, J. Coleman, M. Daboussi et al., Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium, Nature, vol.22, issue.7287, pp.367-73, 2010.
DOI : 10.1038/nature08850

URL : https://hal.archives-ouvertes.fr/hal-00574227

D. Martinez, R. Berka, B. Henrissat, M. Saloheimo, M. Arvas et al., Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina), Nature Biotechnology, vol.307, issue.5, pp.553-60, 2008.
DOI : 10.1038/nbt1403

T. Petersen, S. Brunak, G. Von-heijne, and H. Nielsen, SignalP 4.0: discriminating signal peptides from transmembrane regions, Nature Methods, vol.6, issue.10, pp.785-791, 2011.
DOI : 10.1016/0005-2795(75)90109-9

J. Hawkins and M. Boden, DETECTING AND SORTING TARGETING PEPTIDES WITH NEURAL NETWORKS AND SUPPORT VECTOR MACHINES, Journal of Bioinformatics and Computational Biology, vol.7, issue.01, pp.1-18, 2006.
DOI : 10.1093/bioinformatics/btg463

E. Sonnhammer, G. Von-heijne, and A. Krogh, A hidden Markov model for predicting transmembrane helices in protein sequences, Proc Int Conf Intell Syst Mol Biol, vol.623, issue.10, pp.175-82, 1998.

B. Neron, H. Menager, C. Maufrais, N. Joly, J. Maupetit et al., Mobyle: a new full web bioinformatics framework, Bioinformatics, vol.25, issue.22, pp.3005-3016, 2009.
DOI : 10.1093/bioinformatics/btp493

URL : https://hal.archives-ouvertes.fr/hal-01287963

J. Huerta-cepas, F. Serra, and P. Bork, ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data, Molecular Biology and Evolution, vol.33, issue.6, 2016.
DOI : 10.1093/molbev/msw046

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868116

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

V. Lombard, G. Ramulu, H. Drula, E. Coutinho, P. Henrissat et al., The carbohydrate-active enzymes database (CAZy) in 2013Database issue):D490?5, Nucleic Acids Res, vol.42, p.24270786, 2014.

B. Cantarel, P. Coutinho, C. Rancurel, T. Bernard, V. Lombard et al., The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics, Database issue):D233?8, p.18838391, 2008.
DOI : 10.1093/nar/gkn663

URL : http://doi.org/10.1093/nar/gkn663

T. Badet, R. Peyraud, and S. Raffaele, Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae, Frontiers in Plant Science, vol.29, issue.372, p.26442085, 2015.
DOI : 10.1093/bioinformatics/btt554

P. Horton, K. Park, T. Obayashi, N. Fujita, H. Harada et al., WoLF PSORT: protein localization predictor, Nucleic Acids Research, vol.35, issue.Web Server, pp.585-592, 2007.
DOI : 10.1093/nar/gkm259

URL : http://doi.org/10.1093/nar/gkm259

N. Ba, A. Pogoutse, A. Provart, N. Moses, and A. , NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction, BMC Bioinformatics. Epub, vol.10, p.202, 2009.

M. Brameier, A. Krings, and R. Maccallum, NucPred Predicting nuclear localization of proteins, Bioinformatics, vol.23, issue.9, pp.1159-6003, 2007.
DOI : 10.1093/bioinformatics/btm066

A. Theocharidis, S. Van-dongen, A. Enright, and T. Freeman, Network visualization and analysis of gene expression data using BioLayout Express(3D), Nat Protoc, vol.4, issue.10, 2009.
DOI : 10.1038/nprot.2009.177

A. Dobin, C. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/bts635

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905

S. Anders, P. Pyl, and W. Huber, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, issue.2, pp.166-175, 2015.
DOI : 10.1093/bioinformatics/btu638

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287950

B. Turgeon, B. Condon, J. Liu, and N. Zhang, Protoplast Transformation of Filamentous Fungi, Methods Mol Biol. Epub, vol.63820, pp.3-19, 2010.
DOI : 10.1007/978-1-60761-611-5_1