J. A. Kolmer, M. E. Ordonez, and J. V. Groth, The Rust Fungi, 2009.

R. P. Singh, D. P. Hodson, J. Huerta-espino, J. Y. Bhavani, and S. , The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production, Annual Review of Phytopathology, vol.49, 2011.

J. Pinon and P. Frey, Structure of Melampsora larici-populina populations on wild and cultivated poplar, European Journal of Plant Pathology, vol.103, pp.159-173, 1997.
URL : https://hal.archives-ouvertes.fr/hal-02696112

Z. A. Pretorius, R. P. Singh, T. S. Wagoire, and T. S. Payne, Detection of virulence of wheat stem rust resistance gene Sr31 in Puccinia graminis f. sp. tritici in Uganda, Plant Disease, vol.84, pp.203-203, 2000.

D. Hodson, Shifting boundaries: challenges for rust monitoring, Euphytica, vol.179, pp.93-104, 2011.

R. P. Singh, D. P. Hodson, J. Huerta-espino, J. Y. Njau, and P. , Will stem rust destroy the world's wheat crop?, Advances in Agronomy, vol.98, pp.271-309, 2008.

P. N. Dodds, G. J. Lawrence, A. M. Catanzariti, M. A. Ayliffe, and J. G. Ellis, The Melampsora lini AvrL567 avirulence genes are expressed in haustoria and their products are recognized inside plant cells, Plant Cell, vol.16, pp.755-768, 2004.

S. A. Hogenhout, R. A. Van-der-hoorn, R. Terauchi, and S. Kamoun, Emerging concepts in effector biology of plant-associated organisms, Mol Plant Microbe Interact, vol.22, pp.115-122, 2009.

S. C. Whisson, P. C. Boevink, L. Moleleki, A. O. Avrova, and J. G. Morales, A translocation signal for delivery of oomycete effector proteins into host plant cells, Nature, vol.450, pp.115-118, 2007.

M. Rafiqi, P. H. Gan, M. Ravensdale, G. J. Lawrence, and J. G. Ellis, Internalization of flax rust avirulence proteins into flax and tobacco cells can occur in the absence of the pathogen, Plant Cell, vol.22, pp.2017-2032, 2010.

E. Kemen, A. C. Kemen, M. Rafiqi, U. Hempel, and K. Mendgen, Identification of a protein from rust fungi transferred from haustoria into infected plant cells, Mol Plant Microbe Interact, vol.18, pp.1130-1139, 2005.

C. H. Khang, R. Berruyer, M. C. Giraldo, P. Kankanala, and S. Y. Park, Translocation of Magnaporthe oryzae effectors into rice cells and their subsequent cell-to-cell movement, Plant Cell, vol.22, pp.1388-1403, 2010.

H. C. Rooney, J. W. Van't-klooster, R. A. Van-der-hoorn, M. H. Joosten, and J. D. Jones, Cladosporium Avr2 inhibits tomato Rcr3 protease required for Cf-2-dependent disease resistance, Science, vol.308, pp.1783-1786, 2005.

L. S. Boutemy, S. King, J. Win, R. K. Hughes, and T. A. Clarke, Structures of Phytophthora RXLR effector proteins: a conserved but adaptable fold underpins functional diversity, Journal of Biological Chemistry, 2011.

S. Kang, J. A. Sweigard, and B. Valent, The PWL host specificity gene family in the blast fungus Magnaporthe grisea, Mol Plant Microbe Interact, vol.8, pp.939-948, 1995.

H. J. Newton, F. M. Sansom, J. Dao, A. D. Mcalister, and J. Sloan, Sel1 repeat protein LpnE is a Legionella pneumophila virulence determinant that influences vacuolar trafficking, Infect Immun, vol.75, pp.5575-5585, 2007.

X. Liu, X. Nie, Y. Ding, and J. Chen, Asc1, a WD-repeat protein, is required for hyphal development and virulence in Candida albicans, Acta Biochim Biophys Sin (Shanghai), vol.42, pp.793-800, 2010.

W. B. Shim, U. S. Sagaram, Y. E. Choi, J. So, and H. H. Wilkinson, FSR1 is essential for virulence and female fertility in Fusarium verticillioides and F. graminearum, Mol Plant Microbe Interact, vol.19, pp.725-733, 2006.

C. M. Pieterse, A. M. Derksen, J. Folders, and F. Govers, Expression of the Phytophthora infestans ipiB and ipiO genes in planta and in vitro, Mol Gen Genet, vol.244, pp.269-277, 1994.

S. Raffaele, J. Win, L. M. Cano, and S. Kamoun, Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans, BMC Genomics, vol.11, p.637, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01606572

T. Rouxel, J. Grandaubert, J. K. Hane, C. Hoede, and A. P. Van-de-wouw, Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations, Nat Commun, vol.2, p.202, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00841751

I. Stergiopoulos and P. J. De-wit, Fungal effector proteins, Annu Rev Phytopathol, vol.47, pp.233-263, 2009.

V. G. Vleeshouwers, H. Rietman, P. Krenek, N. Champouret, and C. Young, Effector genomics accelerates discovery and functional profiling of potato disease resistance and Phytophthora infestans avirulence genes, PLoS One, vol.3, p.2875, 2008.

V. Vleeshouwers, S. Raffaele, J. Vossen, N. Champouret, and R. Oliva, Understanding and exploiting late blight resistance in the age of effectors, Annual Review of Phytopathology, vol.49, pp.25-46, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02647856

M. Rep, Small proteins of plant-pathogenic fungi secreted during host colonization, FEMS Microbiol Lett, vol.253, pp.19-27, 2005.

L. Li, C. J. Stoeckert, J. Roos, and D. S. , OrthoMCL: identification of ortholog groups for eukaryotic genomes, Genome Res, vol.13, pp.2178-2189, 2003.

S. Duplessis, C. A. Cuomo, Y. C. Lin, A. Aerts, and E. Tisserant, Obligate biotrophy features unraveled by the genomic analysis of rust fungi, Proc Natl Acad Sci U S A, vol.108, pp.9166-9171, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000169

T. L. Bailey, M. Boden, F. A. Buske, M. Frith, and C. E. Grant, MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res, vol.37, pp.202-208, 2009.

D. Dou, S. D. Kale, X. Wang, Y. Chen, and Q. Wang, Conserved Cterminal motifs required for avirulence and suppression of cell death by Phytophthora sojae effector Avr1b, Plant Cell, vol.20, pp.1118-1133, 2008.

D. Godfrey, H. Bohlenius, C. Pedersen, Z. Zhang, and J. Emmersen, Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif, BMC Genomics, vol.11, p.317, 2010.

J. Ellis, A. M. Catanzariti, and P. Dodds, The problem of how fungal and oomycete avirulence proteins enter plant cells, Trends Plant Sci, vol.11, pp.61-63, 2006.

R. D. Kulkarni, H. S. Kelkar, and R. A. Dean, An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins, Trends Biochem Sci, vol.28, pp.118-121, 2003.

D. L. Joly, N. Feau, P. Tanguay, and R. C. Hamelin, Comparative analysis of secreted protein evolution using expressed sequence tags from four poplar leaf rusts (Melampsora spp, BMC Genomics, vol.11, p.422, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02660329

A. M. Catanzariti, P. N. Dodds, G. J. Lawrence, M. A. Ayliffe, and J. G. Ellis, Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors, Plant Cell, vol.18, pp.243-256, 2006.

C. Y. Szeto, G. S. Leung, and H. S. Kwan, Le.MAPK and its interacting partner, Le.DRMIP, in fruiting body development in Lentinula edodes, Gene, vol.393, pp.87-93, 2007.
URL : https://hal.archives-ouvertes.fr/hal-02059997

T. J. Milne, G. Abbenante, J. D. Tyndall, J. Halliday, and R. J. Lewis, Isolation and characterization of a cone snail protease with homology to CRISP proteins of the pathogenesis-related protein superfamily, J Biol Chem, vol.278, pp.31105-31110, 2003.

G. M. Gibbs, K. Roelants, and M. K. O'bryan, The CAP superfamily: cysteinerich secretory proteins, antigen 5, and pathogenesis-related 1 proteins-roles in reproduction, cancer, and immune defense, Endocr Rev, vol.29, pp.865-897, 2008.

J. J. Liu, R. Sturrock, and A. K. Ekramoddoullah, The superfamily of thaumatinlike proteins: its origin, evolution, and expression towards biological function, Plant Cell Rep, vol.29, pp.419-436, 2010.

X. Wang, P. Zafian, M. Choudhary, and M. Lawton, The PR5K receptor protein kinase from Arabidopsis thaliana is structurally related to a family of plant defense proteins, Proc Natl Acad Sci U S A, vol.93, pp.2598-2602, 1996.

B. Petre, I. Major, N. Rouhier, and S. Duplessis, Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar, BMC Plant Biol, vol.11, p.33, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02548481

A. L. De-oliveira, M. Gallo, L. Pazzagli, C. E. Benedetti, and G. Cappugi, The structure of the elicitor Cerato-platanin (CP), the first member of the CP fungal protein family, reveals a double psibeta-barrel fold and carbohydrate binding, J Biol Chem, vol.286, pp.17560-17568, 2011.

P. Tompa and D. Kovacs, Intrinsically disordered chaperones in plants and animals, Biochem Cell Biol, vol.88, pp.167-174, 2010.

L. Larous, A. Kameli, and D. M. Losel, Ultrastructural observations on Puccinia methae infections, Journal of Plant Pathology, vol.90, pp.185-190, 2008.

S. Kamoun, Groovy times: filamentous pathogen effectors revealed, Curr Opin Plant Biol, vol.10, pp.358-365, 2007.

P. N. Dodds, M. Rafiqi, P. H. Gan, A. R. Hardham, and D. A. Jones, Effectors of biotrophic fungi and oomycetes: pathogenicity factors and triggers of host resistance, New Phytol, vol.183, pp.993-1000, 2009.

B. J. Haas, S. Kamoun, M. C. Zody, R. H. Jiang, and R. E. Handsaker, Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans, Nature, vol.461, pp.393-398, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02668530

J. Xu, R. Linning, J. Fellers, M. Dickinson, and W. Zhu, Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi, BMC Genomics, vol.12, p.161, 2011.

T. Liu, W. Ye, Y. Ru, X. Yang, and B. Gu, Two host cytoplasmic effectors are required for pathogenesis of Phytophthora sojae by suppression of host defenses, Plant Physiol, vol.155, pp.490-501, 2011.

S. Schornack, M. Van-damme, T. O. Bozkurt, L. M. Cano, and M. Smoker, Ancient class of translocated oomycete effectors targets the host nucleus, Proc Natl Acad Sci U S A, vol.107, pp.17421-17426, 2010.

T. D. Kanneganti, X. Bai, C. W. Tsai, J. Win, and T. Meulia, A functional genetic assay for nuclear trafficking in plants, Plant J, vol.50, pp.149-158, 2007.

Q. H. Shen, Y. Saijo, S. Mauch, C. Biskup, and S. Bieri, Nuclear activity of MLA immune receptors links isolate-specific and basal disease-resistance responses, Science, vol.315, pp.1098-1103, 2007.

J. Jorda and A. V. Kajava, T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm, Bioinformatics, vol.25, pp.2632-2638, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00423755

S. Hacquard, C. Delaruelle, V. Legue, E. Tisserant, and A. Kohler, Laser capture microdissection of uredinia formed by Melampsora larici-populina revealed a transcriptional switch between biotrophy and sporulation, Mol Plant Microbe Interact, vol.23, pp.1275-1286, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02667759

G. Doehlemann, K. Van-der-linde, D. Assmann, D. Schwammbach, and A. Hof, Pep1, a secreted effector protein of Ustilago maydis, is required for successful invasion of plant cells, PLoS Pathog, vol.5, p.1000290, 2009.

, The Melampsora laricis-populina genome database

, The Puccinia group database

T. A. Torto, S. Li, A. Styer, E. Huitema, and A. Testa, EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora, Genome Res, vol.13, pp.1675-1685, 2003.

, Blast2go web server

C. Yin, X. Chen, X. Wang, Q. Han, and Z. Kang, Generation and analysis of expression sequence tags from haustoria of the wheat stripe rust fungus Puccinia striiformis f. sp. Tritici, BMC Genomics, vol.10, p.626, 2009.

K. Yoshida, H. Saitoh, S. Fujisawa, H. Kanzaki, and H. Matsumura, Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae, Plant Cell, vol.21, pp.1573-1591, 2009.

W. Li, B. Wang, J. Wu, G. Lu, and Y. Hu, The Magnaporthe oryzae avirulence gene AvrPiz-t encodes a predicted secreted protein that triggers the immunity in rice mediated by the blast resistance gene Piz-t, Mol Plant Microbe Interact, vol.22, pp.411-420, 2009.

C. A. Levesque, H. Brouwer, L. Cano, J. P. Hamilton, and C. Holt, Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire, Genome Biol, vol.11, p.73, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01605006

R. Nair and B. Rost, Better prediction of sub-cellular localization by combining evolutionary and structural information, Proteins, vol.53, pp.917-930, 2003.

A. Ceroni, A. Passerini, A. Vullo, and P. Frasconi, DISULFIND: a disulfide bonding state and cysteine connectivity prediction server, Nucleic Acids Res, vol.34, pp.177-181, 2006.

A. J. Enright, S. Van-dongen, and C. A. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, vol.30, pp.1575-1584, 2002.

R. D. Finn, J. Mistry, J. Tate, P. Coggill, and A. Heger, The Pfam protein families database, Nucleic Acids Res, vol.38, pp.211-222, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01294685

A. I. Saeed, V. Sharov, J. White, J. Li, and W. Liang, TM4: a free, opensource system for microarray data management and analysis, Biotechniques, vol.34, pp.374-378, 2003.