J. Pinon and P. Frey, Interactions between poplar clones and Melampsora populations and their implications for breeding for durable resistance, CAB International, pp.139-154, 2005.

E. M. Rubin, Genomics of cellulosic biofuels, Nature, vol.454, issue.7206, pp.841-845, 2008.

S. Nagarajan and D. V. Singh, Long-distance dispersion of rust pathogens, Annual Review of Phytopathology, vol.28, pp.139-153, 1990.

B. Barrès, F. Halkett, C. Dutech, A. Andrieux, J. Pinon et al., Genetic structure of the poplar rust fungus Melampsora larici-populina: evidence for isolation by distance in Europe and recent founder effects overseas, Infection, Genetics and Evolution, vol.8, issue.5, pp.577-587, 2008.

S. Duplessis, I. T. Major, F. Martin, and A. Séguin, Poplar and pathogen interactions: insights from populus genomewide analyses of resistance and defense gene families and gene expression profiling, Critical Reviews in Plant Sciences, vol.28, issue.5, pp.309-334, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02665788

F. Laurans and G. Pilate, Histological aspects of a hypersensitive response in poplar to Melampsora larici-populina, Phytopathology, vol.89, issue.3, pp.233-238, 1999.
URL : https://hal.archives-ouvertes.fr/hal-02695574

C. Rinaldi, A. Kohler, and P. Frey, Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina, Plant Physiology, vol.144, issue.1, pp.347-366, 2007.
URL : https://hal.archives-ouvertes.fr/hal-01194961

B. Boyle, V. Levée, L. P. Hamel, M. C. Nicole, and A. Séguin, Molecular and histochemical characterisation of two distinct poplar Melampsora leaf rust pathosystems, Plant Biology, vol.12, issue.2, pp.364-376, 2010.

S. Hacquard, C. Delaruelle, and V. Legué, Laser capture microdissection of uredinia formed by Melampsora laricipopulina revealed a transcriptional switch between biotrophy and sporulation, Molecular Plant-Microbe Interactions, vol.23, issue.10, pp.1275-1286, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02667759

S. Hacquard, C. Veneault-fourrey, C. Delaruelle, P. Frey, F. Martin et al., Validation of Melampsora laricipopulina reference genes for in planta RT-quantitative PCR expression profiling during time-course infection of poplar leaves, Physiological and Molecular Plant Pathology, vol.75, issue.3, pp.106-112, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02644005

M. Miranda, S. G. Ralph, and R. Mellway, The transcriptional response of hybrid poplar (Populus trichocarpa x P. deltoides) to infection by Melampsora medusae leaf rust involves induction of flavonoid pathway genes leading to the accumulation of proanthocyanidins, Molecular Plant-Microbe Interactions, vol.20, issue.7, pp.816-831, 2007.

G. A. Tuskan, S. Difazio, and S. Jansson, The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, vol.313, issue.5793, pp.1596-1604, 2006.
URL : https://hal.archives-ouvertes.fr/hal-02669155

F. Martin, A. Aerts, and D. Ahrén, The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis, Nature, vol.452, issue.7183, pp.88-92, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00261893

F. Martin, V. Gianinazzi-pearson, and M. Hijri, The long hard road to a completed Glomus intraradices genome, New Phytologist, vol.180, issue.4, pp.747-750, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02655504

S. Duplessis, C. A. Cuomo, and Y. C. Lin, Obligate biotrophy features unraveled by the genomic analysis of rust fungi, Proceedings of the National Academy of Sciences of the United States of America, vol.108, pp.9166-9171, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000169

X. Yang, U. C. Kalluri, and S. P. Difazio, Poplar genomics: state of the science, Critical Reviews in Plant Sciences, vol.28, issue.5, pp.285-308, 2009.

D. L. Joly, S. Hacquard, and N. Feau, Chasing effectors in the secretome of Melampsora larici-populina, International Society for Molecular Plant-Microbe Interactions, vol.7, 2010.

A. H. Paterson, M. Freeling, H. Tang, and X. Wang, Insights from the comparison of plant genome sequences, Annual Review of Plant Biology, vol.61, pp.349-372, 2010.

A. Kohler, C. Rinaldi, and S. Duplessis, Genome-wide identification of NBS resistance genes in Populus trichocarpa, Plant Molecular Biology, vol.66, issue.6, pp.619-636, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02669184

J. D. Jones and J. L. Dangl, The plant immune system, Nature, vol.444, issue.7117, pp.323-329, 2006.

P. N. Dodds and J. P. Rathjen, Plant immunity: towards an integrated view of plant-pathogen interactions, Nature Reviews Genetics, vol.11, issue.8, pp.539-548, 2010.

A. Bresson, V. Jorge, and A. Dowkiw, Qualitative and quantitative resistances to leaf rust finaly mapped within two nucleotide-binding site leucine-rich repeat (NBS-LRR)-rich genomic regions of chromosome 19 in poplar, New Phytologist, vol.192, issue.1, pp.151-163, 2011.

R. W. Innes, C. Ameline-torregrosa, and T. Ashfield, Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean, Plant Physiology, vol.148, issue.4, pp.1740-1759, 2008.

H. Germain and A. Séguin, Innate immunity: has poplar made its BED?, New Phytologist, vol.189, issue.3, pp.678-687, 2011.

L. Aravind, The BED finger, a novel DNA-binding domain in chromatin-boundary-element-binding proteins and transposases, Trends in Biochemical Sciences, vol.25, issue.9, pp.421-423, 2000.

L. C. Van-loon, M. Rep, and C. M. Pieterse, Significance of inducible defense-related proteins in infected plants, Annual Review of Phytopathology, vol.44, pp.135-162, 2006.

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

J. P. Zhao and X. H. Su, Patterns of molecular evolution and predicted function in thaumatin-like proteins of Populus trichocarpa, Planta, vol.232, issue.4, pp.949-962, 2010.

P. D. Spanu, J. C. Abbott, and J. Amselem, Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism, Science, vol.330, issue.6010, pp.1543-1546, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02664949

L. Baxter, S. Tripathy, and N. Ishaque, Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome, Science, vol.330, issue.6010, pp.1549-1551, 2010.

I. Stergiopoulos and P. J. De-wit, Fungal effector proteins, Annual Review of Phytopathology, vol.47, pp.233-263, 2009.

B. M. Tyler, Entering and breaking: virulence effector proteins of oomycete plant pathogens, Cellular Microbiology, vol.11, issue.1, pp.13-20, 2009.

G. Aguileta, G. Refrégier, R. Yockteng, E. Fournier, and T. Giraud, Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protists, Infection, Genetics and Evolution, vol.9, issue.4, pp.656-670, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02333119

R. Terauchi and K. Yoshida, Towards population genomics of effector-effector target interactions, New Phytologist, vol.187, issue.4, pp.929-939, 2010.

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, issue.1, p.422, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02660329

D. J. Schneider and A. Collmer, Studying plant-pathogen interactions in the genomics era: beyond molecular Koch's postulates to systems biology, Annual Review of Phytopathology, vol.48, pp.457-479, 2010.

M. Rep, Small proteins of plant-pathogenic fungi secreted during host colonization, FEMS Microbiology Letters, vol.253, issue.1, pp.19-27, 2005.

S. Kamoun, A catalogue of the effector secretome of plant pathogenic oomycetes, Annual Review of Phytopathology, vol.44, pp.41-60, 2006.

D. Godfrey, H. Böhlenius, C. Pedersen, Z. Zhang, J. Emmersen et al., Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif, BMC Genomics, vol.11, issue.1, p.317, 2010.

S. C. Whisson, P. C. Boevink, and L. Moleleki, A translocation signal for delivery of oomycete effector proteins into host plant cells, Nature, vol.450, issue.7166, pp.115-118, 2007.

R. H. Jiang, S. Tripathy, F. Govers, and B. M. Tyler, RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members, Proceedings of the National Academy of Sciences of the United States of America, vol.105, issue.12, pp.4874-4879, 2008.

S. D. Kale, B. Gu, and D. G. Capelluto, External lipid PI3P mediates entry of eukaryotic pathogen effectors into plant and animal host cells, Cell, vol.142, issue.2, pp.284-295, 2010.

J. Win, W. Morgan, and J. Bos, Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes, The Plant Cell, vol.19, issue.8, pp.2349-2369, 2007.

M. M. Van-der-merwe, M. W. Kinnear, and L. G. Barrett, Positive selection in AvrP4 avirulence gene homologues across the genus Melampsora, Proceedings of the Royal Society B, vol.276, issue.1669, pp.2913-2922, 2009.

R. L. Allen, P. D. Bittner-eddy, and L. J. Grenville-briggs, Host-parasite coevolutionary conflict between Arabidopsis and downy mildew, Science, vol.306, issue.5703, pp.1957-1960, 2004.

A. P. Rehmany, A. Gordon, and L. E. Rose, Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines, The Plant Cell, vol.17, issue.6, pp.1839-1850, 2005.

L. G. Barrett, P. H. Thrall, and P. N. Dodds, Diversity and evolution of effector loci in natural populations of the plant pathogen Melampsora lini, Molecular Biology and Evolution, vol.26, issue.11, pp.2499-2513, 2009.

M. Both, M. Csukai, M. P. Stumpf, and P. D. Spanu, Gene expression profiles of Blumeria graminis indicate dynamic changes to primary metabolism during development of an obligate biotrophic pathogen, The Plant Cell, vol.17, issue.7, pp.2107-2122, 2005.

A. Azaiez, B. Boyle, V. Levée, and A. Séguin, Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi, Molecular Plant-Microbe Interactions, vol.22, issue.2, pp.190-200, 2009.

V. Levée, I. Major, C. Levasseur, L. Tremblay, J. Mackay et al., Expression profiling and functional analysis of Populus WRKY23 reveals a regulatory role in defense, New Phytologist, vol.184, issue.1, pp.48-70, 2009.

Y. Tao, Z. Xie, and W. Chen, Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae, The Plant Cell, vol.15, issue.2, pp.317-330, 2003.

S. Duplessis, S. Hacquard, and C. Delaruelle, Melampsora larici-populina transcript profiling during germination and time-course infection of poplar leaves reveals dynamic expression patterns associated with virulence and biotrophy, Molecular Plant-Microbe Interactions, vol.24, issue.7, pp.808-818, 2011.

R. T. Voegele, M. Hahn, and K. Mendgen, The uredinales: cytology, biochemistry, and molecular biology, The Mycota, H. B. Deising, vol.5, pp.69-98, 2009.

M. Hahn and K. Mendgen, Isolation by ConA binding of haustoria from different rust fungi and comparison of their surface qualities, Protoplasma, vol.170, issue.3-4, pp.95-103, 1992.

M. Hahn and K. Mendgen, Characterization of in plantainduced rust genes isolated from a haustorium-specific cDNA library, Molecular Plant-Microbe Interactions, vol.10, issue.4, pp.427-437, 1997.

A. M. Catanzariti, R. Mago, J. Ellis, and P. Dodds, Constructing haustorium-specific cDNA libraries from rust fungi, Methods in Molecular Biology, vol.712, pp.79-87, 2011.

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, The Plant Cell, vol.18, issue.1, pp.243-256, 2006.

H. Takahara, A. Dolf, E. Endl, and R. O'connell, Flow cytometric purification of Colletotrichum higginsianum biotrophic hyphae from Arabidopsis leaves for stage-specific transcriptome analysis, Plant Journal, vol.59, issue.4, pp.672-683, 2009.

J. R. Alfano, Roadmap for future research on plant pathogen effectors, Molecular Plant Pathology, vol.10, issue.6, pp.805-813, 2009.

K. H. Sohn, R. Lei, A. Nemri, and J. D. Jones, The downy mildew effector proteins ATR1 and ATR13 promote disease susceptibility in Arabidopsis thaliana, The Plant Cell, vol.19, issue.12, pp.4077-4090, 2007.

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, The Plant Cell, vol.16, issue.3, pp.755-768, 2004.

M. Rafiqi, P. H. Gan, and M. Ravensdale, Internalization of flax rust avirulence proteins into flax and tobacco cells can occur in the absence of the pathogen, The Plant Cell, vol.22, issue.6, pp.2017-2032, 2010.

M. Bernoux, T. Ve, and S. Williams, Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, signaling, and autoregulation, Cell Host & Microbe, vol.9, issue.3, pp.200-211, 2011.

E. Markljung, L. Jiang, and J. D. Jaffe, ZBED6, a novel transcription factor derived from a domesticated DNA transposaon regulates IGF2 expression and muscle growth, Plos Biology, vol.7, issue.12, 2009.

J. Liu, R. Sturrock, and A. K. Ekramoddoullah, The superfamily of thaumatin-like proteins: its origin, evolution, and expression towards biological function, Plant Cell Reports, vol.29, issue.5, pp.419-436, 2010.

C. Tsai, S. A. Harding, T. J. Tschaplinski, R. L. Lindroth, and Y. Yuan, Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus, New Phytologist, vol.172, issue.1, pp.47-62, 2006.

B. Hamberger, M. Ellis, M. Friedmann, C. Souza, B. Barbazuk et al., Genome-wide analyses of phenylpropanoid-related genes in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa: the Populus lignin toolbox and conservation and diversification of angiosperm gene families, Canadian Journal of Botany, vol.85, issue.12, pp.1182-1201, 2007.

P. Bednarek and A. Osbourn, Plant-microbe interactions: chemical diversity in plant defense, Science, vol.324, issue.5928, pp.746-748, 2009.

A. Barakat, P. K. Wall, S. Diloreto, C. W. , and J. E. Carlson, Conservation and divergence of microRNAs in Populus, BMC Genomics, vol.8, p.481, 2007.

M. Tronchet, C. Balagué, T. Kroj, L. Jouanin, and D. Roby, Cinnamyl alcohol dehydrogenases-C and D, key enzymes in lignin biosynthesis, play an essential role in disease resistance in Arabidopsis, Molecular Plant Pathology, vol.11, issue.1, pp.83-92, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01203884

X. Ye, B. G. Kang, L. D. Osburn, Y. Li, and Z. M. Cheng, Identification of the flavin-dependent monooxygenase-encoding YUCCA gene family in Populus trichocarpa and their expression in vegetative tissues and in response to hormone and environmental stresses, Plant Cell, Tissue and Organ Culture, vol.97, issue.3, pp.271-283, 2009.

M. R. Grant and J. D. Jones, Hormone (dis)harmony moulds plant health and disease, Science, vol.324, issue.5928, pp.750-752, 2009.

U. C. Kalluri, S. P. Difazio, A. M. Brunner, and G. A. Tuskan, Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa, BMC Plant Biology, vol.7, p.59, 2007.

J. Zhuang, B. Cai, and R. H. Peng, Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa, Biochemical and Biophysical Research Communications, vol.371, issue.3, pp.468-474, 2008.

N. Gutterson and T. L. Reuber, Regulation of disease resistance pathways by AP2/ERF transcription factors, Current Opinion in Plant Biology, vol.7, issue.4, pp.465-471, 2004.

O. Wilkins, H. Nahal, J. Foong, N. J. Provart, and M. M. Campbell, Expansion and diversification of the Populus R2R3-MYB family of transcription factors, Plant Physiology, vol.149, issue.2, pp.981-993, 2009.

R. D. Mellway, L. T. Tran, M. B. Prouse, M. M. Campbell, and C. P. Constabel, The wound-, pathogen-, and ultraviolet Bresponsive MYB134 gene encodes an R2R3 MYB transcription factor that regulates proanthocyanidin synthesis in poplar, Plant Physiology, vol.150, issue.2, pp.924-941, 2009.

X. C. Zhang, X. Wu, and S. Findley, Molecular evolution of lysin motif-type receptor-like kinases in plants, Plant Physiology, vol.144, issue.2, pp.623-636, 2007.

J. Wan, X. Zhang, and D. Neece, A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis, The Plant Cell, vol.20, issue.2, pp.471-481, 2008.

Q. Liu, C. Zhang, Y. Yang, and X. Hu, Genome-wide and molecular evolution analyses of the phospholipase D gene family in Poplar and Grape, BMC Plant Biology, vol.10, p.117, 2010.

X. Wang, Regulatory functions of phospholipase D and phosphatidic acid in plant growth, development, and stress responses, Plant Physiology, vol.139, issue.2, pp.566-573, 2005.

M. Garcia-lorenzo, A. Sjodin, S. Jansson, and C. Funk, Protease gene families in Populus and Arabidopsis, BMC Plant Biology, vol.6, issue.30, 2006.

M. Solomon, B. Belenghi, M. Delledonne, E. Menachem, and A. Levine, The involvement of cysteine proteases and protease inhibitor genes in the regulation of programmed cell death in plants, The Plant Cell, vol.11, issue.3, pp.431-444, 1999.

X. H. Yang, U. C. Kalluri, and S. Jawdy, The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants, Plant Physiology, vol.148, issue.3, pp.1189-1200, 2008.

A. Block, G. Li, Z. Q. Fu, and J. R. Alfano, Phytopathogen type III effector weaponry and their plant targets, Current Opinion in Plant Biology, vol.11, issue.4, pp.396-403, 2008.

I. T. Major and C. P. Constabel, Functional analysis of the kunitz trypsin inhibitor family in poplar reveals biochemical diversity and multiplicity in defense against herbivores, Plant Physiology, vol.146, issue.3, pp.888-903, 2008.

J. Li, G. Brader, and E. T. Palva, Kunitz trypsin inhibitor: an antagonist of cell death triggered by phytopathogens and fumonisin b1 in Arabidopsis, Molecular Plant, vol.1, issue.3, pp.482-495, 2008.

L. Peal, N. Jambunathan, and R. Mahalingam, Phylogenetic and expression analysis of RNA-binding proteins with triple RNA recognition motifs in plants, Molecules and Cells, vol.31, issue.1, pp.55-64, 2010.

Z. Q. Fu, M. Guo, and B. R. Jeong, A type III effector ADPribosylates RNA-binding proteins and quells plant immunity, Nature, vol.447, issue.7142, pp.284-288, 2007.

T. Lan, Z. Yang, X. Yang, Y. Liu, X. Wang et al., Extensive functional diversification of the Populus glutathione S-transferase supergene family, The Plant Cell, vol.21, issue.12, pp.3749-3766, 2009.

D. P. Dixon, M. Skipsey, and R. Edwards, Roles for glutathione transferases in plant secondary metabolism, Phytochemistry, vol.71, issue.4, pp.338-350, 2010.

J. Couturier, J. Jacquot, and N. Rouhier, Evolution and diversity of glutaredoxins in photosynthetic organisms, Cellular and Molecular Life Sciences, vol.66, issue.15, pp.2539-2557, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02668190

N. Rouhier, S. D. Lemaire, and J. Jacquot, The role of glutathione in photosynthetic organisms: emerging functions for glutaredoxins and glutathionylation, Annual Review of Plant Biology, vol.59, pp.143-166, 2008.
URL : https://hal.archives-ouvertes.fr/hal-02660326