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Sébastien Duplessis


Director of the Tree-Microbe Interactions Department (UMR 1136 IAM)

Université de Lorraine / INRAE Centre Grand-Est, Nancy - Labex ARBRE

Bio: BSc in Biology at Bordeaux University (1995). MSc in Cell Biology and Physiology (1998) and PhD in Plant and Forest Sciences (2001) at Nancy University. Silver medal of the French Academy of Agriculture (2001). Hired research scientist in 2001 at INRA. 1 year sabbatical at Exeter University (2003-2004). HDR diploma from Lorraine University (2012). Region Lorraine Researcher Award (2012). Académie Stanislas Zivi Award (2012). INRA Research Director DR2 (2013). Appointed head of the Ecogenomic of interactions team in 2013, appointed Deputy head of the Tree-Microbe Interactions department in 2019. Appointed head of the INRAE/Lorraine University Tree-Microbe Interactions Department in January 2020.

My early research was on functional genomics of the ectomycorrhizal symbiosis in the group of Francis Martin (INRA Nancy). I spent 1 year in Nick Talbot’s lab at Exeter University to extend my background in molecular phytopathology (2003-2004), and since 2005, my research in the Ecogenomics team has mostly focused on the poplar-poplar rust interaction. I am currently coordinating a transversal scientific project called Mechanism and evolution of the poplar-poplar rust interaction within the Tree-Microbe Interactions department at INRAE Nancy, and co-leading the WP1 of the Labex ARBRE (Integrative Biology) with Nicolas Rouhier.

Resume: My research at INRA aims at elucidating how trees respond to pathogens and how biotroph pathogens are able to develop and feed on trees. Our model is the poplar-poplar rust pathosystem. I mainly use genomics and functional approaches to identify and characterize molecular determinants involved in disease resistance and defense response in poplar, and pathogenicity in the rust fungus Melampsora larici-populina as my main model pathosystem. In recent years, I have diversified my research in the frame of international projects using genomics in order to better understand the biology of rust fungi.  Progress made in understanding rust fungal biotrophy will help setting new strategies to contain rust diseases.


Journal articles71 documents

  • Si-Qi Tao, Lucas Auer, Emmanuelle Morin, Ying-Mei Liang, Sébastien Duplessis. Transcriptome Analysis of Apple Leaves Infected by the Rust Fungus Gymnosporangium yamadae at Two Sporulation Stages. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2020, 33 (3), pp.444-461. ⟨10.1094/MPMI-07-19-0208-R⟩. ⟨hal-02989882⟩
  • Benjamin Petre, Cécile Lorrain, Eva Stukenbrock, Sébastien Duplessis. Host-specialized transcriptome of plant-associated organisms. Current Opinion in Plant Biology, Elsevier, 2020, 56, pp.81-88. ⟨10.1016/j.pbi.2020.04.007⟩. ⟨hal-02990650⟩
  • Cécile Lorrain, Karen Cristine Gonçalves dos Santos, Hugo Germain, Arnaud Hecker, Sébastien Duplessis. Advances in understanding obligate biotrophy in rust fungi. New Phytologist, Wiley, 2019, 222 (3), pp.1190-1206. ⟨10.1111/nph.15641⟩. ⟨hal-02181079⟩
  • Karine de Guillen, Cécile Lorrain, Pascale Tsan, Philippe Barthe, Benjamin Petre, et al.. Structural genomics applied to the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine knot and NTF2-like protein folds. Scientific Reports, Nature Publishing Group, 2019, 9 (1), pp.18084. ⟨10.1038/s41598-019-53816-9⟩. ⟨hal-02548559⟩
  • Si-Qi Tao, Bin Cao, Emmanuelle Morin, Ying-Mei Liang, Sébastien Duplessis. Comparative transcriptomics of Gymnosporangium spp. teliospores reveals a conserved genetic program at this specific stage of the rust fungal life cycle. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-6099-x⟩. ⟨hal-02905570⟩
  • Christophe Plomion, Jean-Marc Aury, Joelle Amselem, Thibault Leroy, Florent Murat, et al.. Oak genome reveals facets of long lifespan. Nature Plants, Nature Publishing Group, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩. ⟨hal-01820559⟩
  • Cécile Lorrain, Clémence Marchal, Stéphane Hacquard, Christine Delaruelle, Jeremy Petrowski, et al.. The Rust Fungus Melampsora larici-populina Expresses a Conserved Genetic Program and Distinct Sets of Secreted Protein Genes During Infection of Its Two Host Plants, Larch and Poplar. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2018, 31 (7), pp.695-706. ⟨10.1094/MPMI-12-17-0319-R⟩. ⟨hal-01893935⟩
  • Hugo Germain, David L Joly, Caroline Mireault, Mélodie B Plourde, Claire Letanneur, et al.. Infection assays in Arabidopsis reveal candidate effectors from the poplar rust fungus that promote susceptibility to bacteria and oomycete pathogens. Molecular Plant Pathology, Wiley, 2018, 19 (1), pp.191-200. ⟨10.1111/mpp.12514⟩. ⟨hal-01771813⟩
  • Zhen Zeng, Hui Sun, Eeva J. Vainio, Tommaso Raffaello, Andriy Kovalchuk, et al.. Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors. BMC Genomics, BioMed Central, 2018, 19 (1), ⟨10.1186/s12864-018-4610-4⟩. ⟨hal-01844924⟩
  • Cécile Lorrain, Benjamin Petre, Sébastien Duplessis. Show me the way: Rust effector targets in heterologous plant systems. Current Opinion in Microbiology, Elsevier, 2018, 46, pp.19-25. ⟨10.1016/j.mib.2018.01.016⟩. ⟨hal-02154538⟩
  • Md Bulbul Ahmed, Karen Cristine Gonçalves Dos Santos, Ingrid Benerice Sanchez, Benjamin Petre, Cécile Lorrain, et al.. A rust fungal effector binds plant DNA and modulates transcription. Scientific Reports, Nature Publishing Group, 2018, 8 (1), pp.1-14. ⟨10.1038/s41598-018-32825-0⟩. ⟨hal-02548542⟩
  • M. Catherine Aime, Alistair R. Mctaggart, Stephen J. Mondo, S. Duplessis. Phylogenetics and Phylogenomics of Rust Fungi. Advances in Genetics, Elsevier, 2017, 100, pp.267-307. ⟨10.1016/bs.adgen.2017.09.011⟩. ⟨hal-02626920⟩
  • Jana Sperschneider, Peter Dodds, Jennifer Taylor, Sébastien Duplessis. Computational Methods for Predicting Effectors in Rust Pathogens. News (National Library of Medicine), Bethesda, Md. : The Library, 2017, pp.73-83. ⟨10.1007/978-1-4939-7249-4_7⟩. ⟨hal-02989876⟩
  • Benjamin Petre, Diane G O Saunders, Jan Sklenar, Cécile Lorrain, Ksenia V. Krasileva, et al.. Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE, Public Library of Science, 2016, 11 (2), pp.e0149035. ⟨10.1371/journal.pone.0149035⟩. ⟨hal-01329212⟩
  • Guus Bakkeren, David. L. Joly, Sébastien Duplessis. Editorial: Genomics Research on Non-model Plant Pathogens: Delivering Novel Insights into Rust Fungus Biology. Frontiers in Plant Science, Frontiers, 2016, 7, pp.216. ⟨10.3389/fpls.2016.00216⟩. ⟨hal-01579570⟩
  • Benjamin Petre, Arnaud Hecker, Hugo Germain, Pascale Tsan, Jan Sklenar, et al.. The Poplar Rust-Induced Secreted Protein (RISP) Inhibits the Growth of the Leaf Rust Pathogen Melampsora larici-populina and Triggers Cell Culture Alkalinisation. Frontiers in Plant Science, Frontiers, 2016, 7, pp.e1001732. ⟨10.3389/fpls.2016.00097⟩. ⟨hal-01579575⟩
  • Benjamin Petre, Cécile Lorrain, Diane G.O. Saunders, Joe Win, Jan Sklenar, et al.. Rust fungal effectors mimic host transit peptides to translocate into chloroplasts. Cellular Microbiology, Wiley, 2016, 18 (4), pp.453-465. ⟨10.1111/cmi.12530⟩. ⟨hal-02548525⟩
  • Christophe Plomion, Catherine Bastien, Marie-Béatrice Bogeat-Triboulot, Laurent Bouffier, Annabelle Déjardin, et al.. Forest tree genomics: 10 achievements from the past 10 years and future prospects. Annals of Forest Science, Springer Verlag/EDP Sciences, 2016, 73 (1), pp.77-103. ⟨10.1007/s13595-015-0488-3⟩. ⟨hal-01330031⟩
  • Michael H Perlin, Joelle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, et al.. Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics, BioMed Central, 2015, 16 (461), ⟨10.1186/s12864-015-1660-8⟩. ⟨hal-01186421⟩
  • Cécile Lorrain, Arnaud Hecker, Sébastien Duplessis. Effector-Mining in the Poplar Rust Fungus Melampsora larici-populina Secretome. Frontiers in Plant Science, Frontiers, 2015, 6 (3), pp.597 - 608. ⟨10.3389/fpls.2015.01051⟩. ⟨hal-01577939⟩
  • Benjamin Petre, Diane G O Saunders, Jan Sklenar, Cécile Lorrain, Joe Win, et al.. Candidate Effector Proteins of the Rust Pathogen Melampsora larici-populina Target Diverse Plant Cell Compartments. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2015, 28 (6), pp.689-700. ⟨10.1094/MPMI-01-15-0003-R⟩. ⟨hal-01269166⟩
  • Diogo N. Silva, Sébastien Duplessis, Pedro Talhinhas, Helena Azinheira, Octávio S. Paulo, et al.. Genomic Patterns of Positive Selection at the Origin of Rust Fungi. PLoS ONE, Public Library of Science, 2015, 10 (12), pp.1-22. ⟨10.1371/journal.pone.0143959⟩. ⟨hal-01269480⟩
  • Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Tina Alaeitabar, Valérie Barbe, et al.. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.. Molecular Ecology Resources, Wiley/Blackwell, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩. ⟨hal-01579667⟩
  • Henri Pégeot, Cha San Koh, Benjamin Petre, Sandrine Mathiot, Sébastien Duplessis, et al.. The poplar Phi class glutathione transferase: expression, activity and structure of GSTF1. Frontiers in Plant Science, Frontiers, 2014, 5, article 712 (15 p.). ⟨10.3389/fpls.2014.00712⟩. ⟨hal-01521321⟩
  • Benjamin Petre, David L. Joly, Sébastien Duplessis. Effector proteins of rust fungi. Frontiers in Plant Science, Frontiers, 2014, 5, pp.938-47. ⟨10.3389/fpls.2014.00416⟩. ⟨hal-01579674⟩
  • Benjamin Petre, Stéphane Hacquard, Sébastien Duplessis, Nicolas Rouhier. Genome analysis of poplar LRR-RLP gene clusters reveals RISP, a defense-related gene coding a candidate endogenous peptide elicitor. Frontiers in Plant Science, Frontiers, 2014, 5, ⟨10.3389/fpls.2014.00111⟩. ⟨hal-02548502⟩
  • Marco Loehrer, Alexander Vogel, Bruno Huettel, Richard Reinhardt, Vladimir Benes, et al.. On the current status of [i]Phakopsora pachyrhizi[/i] genome sequencing. Frontiers in Plant Science, Frontiers, 2014, 5 (377), 5 p. ⟨10.3389/fpls.2014.00377⟩. ⟨hal-01268956⟩
  • Michaël Pernaci, Stéphane de Mita, Axelle Andrieux, Jeremy Petrowski, Fabien Halkett, et al.. Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Frontiers in Plant Science, Frontiers, 2014, 5, ⟨10.3389/fpls.2014.00454⟩. ⟨hal-01269013⟩
  • Antoine Persoons, Emmanuelle Morin, Christine Delaruelle, Thibaut Payen, Fabien Halkett, et al.. Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. Frontiers in Plant Science, Frontiers, 2014, 5, ⟨10.3389/fpls.2014.00450⟩. ⟨hal-01269012⟩
  • Pedro Talhinhas, Helena G. Azinheira, Bruno Vieira, Andreia Loureiro, Silvia Tavares, et al.. Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection. Frontiers in Plant Science, Frontiers, 2014, 5, ⟨10.3389/fpls.2014.00088⟩. ⟨hal-01268536⟩
  • Stéphane Hacquard, Christine Delaruelle, Pascal Frey, Emilie Tisserant, Annegret Kohler, et al.. Transcriptome analysis of poplar rust telia reveals overwintering adaptation and tightly coordinated karyogamy and meiosis processes. Frontiers in Plant Science, Frontiers, 2013, 4, ⟨10.3389/fpls.2013.00456⟩. ⟨hal-01268532⟩
  • Louis-Phillipe Hamel, Marie-Claude Nicole, Sébastien Duplessis, Brian Ellis. Mitogen-activated protein kinase signaling in plant-interacting fungi: distinct messages from conserved messengers. The Plant cell, American Society of Plant Biologists (ASPB), 2012, 24 (4), pp.1327-1351. ⟨10.1105/tpc.112.096156⟩. ⟨hal-01267888⟩
  • Benjamin Petre, Emmanuelle Morin, Emilie Tisserant, Stéphane Hacquard, Corinne da Silva, et al.. RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter. PLoS ONE, Public Library of Science, 2012, 7 (8), pp.1-12. ⟨10.1371/journal.pone.0044408⟩. ⟨hal-01267887⟩
  • Stéphane Hacquard, David L. Joly, Yao-Cheng Lin, Emilie Tisserant, Nicolas Feau, et al.. A comprehensive analysis of genes encoding small secreted proteins identifies candidate effectors in Melampsora larici-populina (poplar leaf rust).. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2012, 25 (3), pp.279-293. ⟨10.1094/MPMI-09-11-0238⟩. ⟨hal-01267890⟩
  • Diana Fernandez, Emilie Tisserant, Pedro Talhinhas, Helena Azinheira, Ana Vieira, et al.. 454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction.. Molecular Plant Pathology, Wiley, 2012, 13 (1), pp.17-37. ⟨10.1111/j.1364-3703.2011.00723.x⟩. ⟨hal-01267893⟩
  • Ana Vieira, Pedro Talhinhas, Andreia Loureiro, Johannes Thürich, Sébastien Duplessis, et al.. Expression profiling of genes involved in the biotrophic colonisation of [i]Coffea arabica[/i] leaves by [i]Hemileia vastatrix[/i]. European Journal of Plant Pathology, Springer Verlag, 2012, 133 (1), pp.266-277. ⟨10.1007/s10658-011-9864-5⟩. ⟨hal-01267894⟩
  • Ake Olson, Andrea Aerts, Fred Asiegbu, Lassaâd Belbahri, Ourdia Bouzid, et al.. Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen.. New Phytologist, Wiley, 2012, 194 (4), pp.1001-1013. ⟨10.1111/j.1469-8137.2012.04128.x⟩. ⟨hal-02649642⟩
  • Mehdi Kaytoue, Sergei O. Kuznetsov, Amedeo Napoli, Sébastien Duplessis. Mining gene expression data with pattern structures in formal concept analysis. Information Sciences, Elsevier, 2011, 181 (10), pp.1989-2001. ⟨hal-00541100⟩
  • Stéphane Hacquard, Benjamin Petre, Pascal Frey, Arnaud Hecker, Nicolas Rouhier, et al.. The Poplar-Poplar Rust Interaction: Insights from Genomics and Transcriptomics. Journal of Pathogens, 2011, 2011, pp.1-11. ⟨10.4061/2011/716041⟩. ⟨hal-02548474⟩
  • Benjamin Petre, Ian Major, Nicolas Rouhier, Sébastien Duplessis. Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar. BMC Plant Biology, BioMed Central, 2011, 11 (1), pp.33. ⟨10.1186/1471-2229-11-33⟩. ⟨hal-02548481⟩
  • Floriane l'Haridon, Sébastien Aimé, Sébastien Duplessis, Claude Alabouvette, Christian Steinberg, et al.. Isolation of differentially expressed genes during interactions between tomato cells and a protective or a non-protective strain of Fusarium oxysporum. Physiological and Molecular Plant Pathology, Elsevier, 2011, 76 (1), pp.9-19. ⟨10.1016/j.pmpp.2011.07.001⟩. ⟨hal-02644850⟩
  • Stéphane Hacquard, Claire Veneault-Fourrey, Christine Delaruelle, Pascal Frey, Francis Martin, et al.. Validation of Melampsora larici-populina reference genes for in planta RT-quantitative PCR expression profiling during time-course infection of poplar leaves. Physiological and Molecular Plant Pathology, Elsevier, 2011, 75 (3), pp.106-112. ⟨10.1016/j.pmpp.2010.10.003⟩. ⟨hal-02644005⟩
  • Stéphane Hacquard, Benjamin Petre, Pascal Frey, Arnaud Hecker, Nicolas Rouhier, et al.. The poplar-poplar rust interaction: insights from genomics and transcriptomics. Journal of Pathogens, 2011, EPUB 2011. ⟨hal-02642064⟩
  • Mehdi Kaytoue, Sergei O. Kuznetsov, Amedeo Napoli, Sébastien Duplessis. Mining gene expression data with pattern structures in formal concept analysis. Information Sciences, Elsevier, 2011, 181 (10), pp.1989-2001. ⟨hal-02651138⟩
  • Sébastien Duplessis, Stéphane Hacquard, Christine Delaruelle, Emilie Tisserant, Pascal Frey, et al.. Melampsora larici-populina transcript profiling during germination and timecourse infection of poplar leaves reveals dynamic expression patterns associated with virulence and biotrophy.. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2011, 24 (7), pp.808-818. ⟨10.1094/MPMI-01-11-0006⟩. ⟨hal-02650884⟩
  • Ana Vieira, Pedro Talhinhas, Andreia Loureiro, Sébastien Duplessis, Diana Fernandez, et al.. Validation of RT-qPCR reference genes for in planta expression studies in Hemileia vastatrix, the causal agent of coffee leaf rust.. Fungal Biology, Elsevier, 2011, 115 (9), pp.891-901. ⟨10.1016/j.funbio.2011.07.002⟩. ⟨hal-02646996⟩
  • Sébastien Duplessis, Christina A Cuomo, Yao-Cheng Lin, Andrea Aerts, Emilie Tisserant, et al.. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2011, 108 (22), pp.9166-9171. ⟨10.1073/pnas.1019315108⟩. ⟨hal-01000169⟩
  • Ian T. Major, Marie-Claude Nicole, Sébastien Duplessis, Armand Séguin. Photosynthetic and respiratory changes in leaves of poplar elicited by rust infection. Photosynthesis Research, Springer Verlag, 2010, 104 (1), pp.41-48. ⟨10.1007/s11120-009-9507-2⟩. ⟨hal-02663764⟩
  • Stéphane Hacquard, Christine Delaruelle, Valérie Legué, Emilie Tisserant, Annegret Kohler, et al.. Laser capture microdissection of uredinia formed by Melampsora larici-populina revealed a transcriptional switch between biotrophy and sporulation. Molecular Plant-Microbe Interactions, American Phytopathological Society, 2010, 23 (10), pp.1275-1286. ⟨10.1094/MPMI-05-10-0111⟩. ⟨hal-02667759⟩
  • Francis Martin, Annegret Kohler, Claude Murat, Raffaella Balestrini, Pedro M. Coutinho, et al.. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature, Nature Publishing Group, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩. ⟨cea-00907731⟩
  • Minna Kemppainen, Sébastien Duplessis, Francis Martin, Alejandro G. Pardo. RNA silencing in the model mycorrhizal fungus Laccaria bicolor: gene knock-down of nitrate reductase results in inhibition of symbiosis with Populus. Environmental Microbiology, Wiley-Blackwell, 2009, 11 (7), pp.1878-1896. ⟨10.1111/j.1462-2920.2009.01912.x⟩. ⟨hal-02658986⟩
  • Sébastien Duplessis, Ian Major, Francis Martin, Armand Séguin. Poplar and pathogen interactions: Insights from populus genome-wide analyses of resistance and defense gene families and gene expression profiling. Critical Reviews in Plant Sciences, Taylor & Francis, 2009, 28 (5), pp.309-334. ⟨10.1080/07352680903241063⟩. ⟨hal-02665788⟩
  • Thierry Rouxel, Sébastien Duplessis, Muriel Viaud, Joelle Amselem, Marc-Henri Lebrun. La génomique fongique. Biofutur, Elsevier - Cachan : Lavoisier, 2009, 296 (Février), pp.31-35. ⟨hal-02654166⟩
  • Thierry Rouxel, Sébastien Duplessis, Muriel Viaud, Joelle Amselem, Marc-Henri Lebrun. La génomique des champignons pathogènes des plantes en France. Biofutur, Elsevier - Cachan : Lavoisier, 2009, Fev. (296), pp.35. ⟨hal-02654230⟩
  • Fernando Guerra, Sébastien Duplessis, Annegret Kohler, Francis Martin, Jaime Tapia, et al.. Gene expression analysis of Populus deltoides roots subjected to copper stress. Environmental and Experimental Botany, Elsevier, 2009, 67 (2), pp.335-344. ⟨10.1016/j.envexpbot.2009.08.004⟩. ⟨hal-02655593⟩
  • Sébastien Duplessis, H. Kuhn. Secretomic climax in plant–fungal interactions. New Phytologist, Wiley, 2008, 179 (4), pp.907-910. ⟨10.1111/j.1469-8137.2008.02594.x⟩. ⟨hal-02660039⟩
  • Minna Kemppainen, Sébastien Duplessis, Francis Martin, Alejandro G. Pardo. T-DNA insertion, plasmid rescue and integration analysis in the model mycorrhizal fungus Laccaria bicolor. Microbial Biotechnology, Wiley, 2008, 1 (3), pp.258-269. ⟨10.1111/j.1751-7915.2008.00029.x⟩. ⟨hal-02665900⟩
  • Annegret Kohler, Cécile Rinaldi, Sébastien Duplessis, Marie Baucher, Danny Geelen, et al.. Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Molecular Biology, Springer Verlag (Germany), 2008, 66 (6), pp.619-636. ⟨10.1007/s11103-008-9293-9⟩. ⟨hal-02669184⟩
  • F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, et al.. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature, Nature Publishing Group, 2008, 452 (7183), pp.88-93. ⟨10.1038/nature06556⟩. ⟨halsde-00261893⟩
  • Cecile Rinaldi, Annegret Kohler, Pascal Frey, Frédéric Duchaussoy, Francois Ningre, et al.. Transcript Profiling of Poplar Leaves upon Infection with Compatible and Incompatible Strains of the Foliar Rust Melampsora larici-populina. Plant Physiology, American Society of Plant Biologists, 2007, 144 (1), pp.347-366. ⟨10.1104/pp.106.094987⟩. ⟨hal-01194961⟩
  • Francis Martin, Annegret Kohler, Sébastien Duplessis. Living in harmony in the wood underground: ectomycorrhizal genomics. Current Opinion in Plant Biology, Elsevier, 2007, 10 (2), pp.204-210. ⟨10.1016/j.pbi.2007.01.006⟩. ⟨hal-02660158⟩
  • Marc-André Selosse, Sébastien Duplessis. More complexity in the mycorrhizal word. New Phytologist, Wiley, 2006, 172 (4), pp.600-604. ⟨10.1111/j.1469-8137.2006.01929.x⟩. ⟨hal-02653524⟩
  • Gerald A. Tuskan, Stephen Difazio, Stefan Jansson, Jörg Bohlmann, Igor Grigoriev, et al.. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, American Association for the Advancement of Science, 2006, 313 (5793), pp.1596-1604. ⟨10.1126/science.1128691⟩. ⟨hal-02669155⟩
  • S. Gabella, S. Abbà, Sébastien Duplessis, Barbara Montanini, F. Martin, et al.. Transcript profiling reveals novel marker genes involved in fruiting body formation in Tuber borchii. Eukaryotic Cell, American Society for Microbiology, 2005, 4 (9), pp.1599-1602. ⟨hal-02671240⟩
  • A.G. Pardo, Minna Kemppainen, D. Valdemoros, Sébastien Duplessis, Francis Martin, et al.. T-DNA transfer from Agrobacterium tumefaciens to the ectomycorrhizal fungus Pisolithus microcarpus. Revista Argentina de Microbiología, Asociación Argentina de Microbiología, 2005, 37, pp.69-72. ⟨hal-02681826⟩
  • P. Gupta, Sébastien Duplessis, H. White, F. Martin, G.K. Podila. Gene expression patterns of trembling aspen trees following long-term exposure to interacting elevated CO2 and tropospheric O3. New Phytologist, Wiley, 2005, 167, pp.129-142. ⟨hal-02678558⟩
  • Sébastien Duplessis, Pierre-Emmanuel Courty, Denis Tagu, F. Martin. Transcript patterns associated with ectomycorrhiza development in Eucalyptus globulus and Pisolithus microcarpus. New Phytologist, Wiley, 2005, 165, pp.599-611. ⟨hal-02680580⟩
  • Nicolas Rouhier, Eric Gelhaye, J.M. Gualberto, M.N. Jordy, E. de Fay, et al.. Poplar peroxiredoxin Q. A thioredoxin-linked chloroplast antioxidant functional in pathogen defense. Plant Physiology, American Society of Plant Biologists, 2004, 134 (3), pp.1027-1036. ⟨hal-02680157⟩
  • Magali Peter, Pierre-Emmanuel Courty, A. Kohler, Christine Delaruelle, D. Martin, et al.. Analysis of expressed sequence tags from the ectomycorhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus. New Phytologist, Wiley, 2003, 159 (1), pp.117-129. ⟨hal-02680906⟩
  • C. Voiblet, Sébastien Duplessis, N. Encelot, F. Martin. Identification of symbiosis-regulated genes in Eucalyptus globulus-Pisolithus tinctorius ectomycorrhiza by differential hybridization of arrayed cDNAs. Plant Journal, Wiley, 2001, 25 (3), pp.1-12. ⟨hal-02673611⟩
  • Sébastien Duplessis, Céline Sorin, Catherine Voiblet, Béatrice Palin, Francis Martin, et al.. Cloning and expression analysis of a new hydrophobin cDNA from the ectomycorrhizal basidiomycete Pisolithus. Current Genetics, Springer Verlag, 2001, ⟨10.1007/s002940100224⟩. ⟨hal-02915287⟩

Conference papers35 documents

  • Xavier Manival, Lucas Nussbaum, Sébastien Duplessis, Emmanuelle Montargès-Pelletier, Pierre Humbert. Table ronde sur les aspects "utilisateurs" : intérêts et retours d’expériences de chercheurs et enseignants-chercheurs du site. Colloque Sciences ouvertes : expériences, enjeux et perspectives, Université de Lorraine; Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation, Oct 2018, Vandœuvre-lès-Nancy, France. ⟨hal-01885979⟩
  • Joëlle Amselem, Nicolas Francillonne, Célia Michotey, Thomas Letellier, Jean-Marc Aury, et al.. An integrated information system dedicated to oak genomics and genetics. PAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides. ⟨hal-01839185⟩
  • Michaël Pernaci, Agathe Maupetit, Stéphane de Mita, Bénédicte Fabre, S. Duplessis, et al.. Genome-wide QTL mapping of aggressiveness traits in the poplar rust fungus. International Conference on Population Genomics of Fungal and Oomycete Diseases of Animals and Plants, May 2017, Monte Verità Conference Center, Ascona, Switzerland. ⟨hal-02785090⟩
  • Fabien Halkett, Antoine Persoons, Agathe Maupetit, S. Duplessis, Pascal Frey, et al.. Demographic and genomic consequences of a major selective event in the poplar rust. International Conference on Population Genomics of Fungal and Oomycete Diseases of Animals and Plants, May 2017, Ascona, Switzerland. ⟨hal-02790211⟩
  • S. Duplessis, Stéphane de Mita, Fabien Halkett, Pascal Frey. Update on Melampsora larici-populina genomics. 11. Rencontres de Phytopathologie - Mycologie - JJC 2016 Journée Jean Chevaugeon, Jan 2016, Aussois, France. ⟨hal-02741208⟩
  • Joelle Amselem, Jean Marc Aury, Nicolas Francillonne, Tina Alaeitabar, Corinne da Silva, et al.. Annotation of the oak genome sequence and associated bioinformatic resources. IUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p. ⟨hal-02741128⟩
  • Michaël Pernaci, Stéphane de Mita, Bénédicte Fabre, S. Duplessis, Fabien Halkett, et al.. Mapping QTL of aggressiveness traits in the poplar rust fungus. 5. International Conference on Genetics of Tree-Parasite Interactions : Novel challenges and opportunities for resistance to pests and pathogens, Aug 2015, Orléans, France. ⟨hal-02793206⟩
  • Antoine Persoons, Fabien Halkett, Stéphane de Mita, S. Duplessis. Identification of candidate effectors in the poplar rust fungus Melampsora larici-populina through a population genomics approach. 28. Fungal Genetics Conference, Mar 2015, Asilomar, Pacific Grove, CA, United States. ⟨hal-02792660⟩
  • Michaël Pernaci, Stéphane de Mita, Bénédicte Fabre, S. Duplessis, Fabien Halkett, et al.. On the road to mapping QTLs of morphological and aggressiveness traits in the poplar rust fungus. Réunion annuelle 2015 du Réseau Ecologie des Interactions Durables, Mar 2015, Lyon, France. ⟨hal-02792666⟩
  • Michaël Pernaci, Stéphane de Mita, Bénédicte Fabre, S. Duplessis, Fabien Halkett, et al.. Mapping QTL of aggressiveness traits in the poplar rust fungus. 9eme Colloque de la Société Française de Phytopathologie, Jun 2015, Colmar, France. ⟨hal-02792933⟩
  • Antoine Persoons, Emmanuelle Morin, Christine Delaruelle, Thibaut Payen, Fabien Halkett, et al.. Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors. Max-Planck-ARBRE inter-departmental workshop on plant-fungus interactions, Nov 2014, Nancy, France. ⟨hal-02794927⟩
  • Benjamin Petre, Stéphane Hacquard, Antoine Persoons, Emilie Tisserant, Emmanuelle Morin, et al.. Genomics, transcriptomics and effectoromics of the poplar leaf rust fungus Melampsora larici-populina. IUFRO Joint Meeting on Genetics of Five-Needle Pines and Rusts in Mountain Landscapes, Jun 2014, Fort Collins, United States. ⟨hal-02801804⟩
  • Antoine Persoons, Stéphane de Mita, Fabien Halkett, S. Duplessis. Identification d’effecteurs de Melampsora larici-populina par une approche originale : de la génomique des populations à la génomique fonctionnelle. 10. Rencontres de Phytopathologie - Mycologie - JJC 2014 Journée Jean Chevaugeon, Jan 2014, Aussois, France. 116 p. ⟨hal-02742734⟩
  • N. Feau, Pascal Frey, Sébastien Duplessis, R. C. Hamelin. Genome-wide signature of adaptation in a recently introduced pathogen. APS-MSA Joint Meeting, Aug 2013, Austin, Texas, United States. ⟨hal-01268359⟩
  • Christophe Plomion, Joelle Amselem, Jean-Marc Aury, Catherine Bodenes, Emilie Chancerel, et al.. Development of genomic resources to study the structure, function and evolution of the oak genome. IUFRO working group "Genetics of Quercus and Nothofagus", Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p. ⟨hal-01019850⟩
  • Diogo N. Silva, Ana Vieira, Pedro Talhinhas, Helena Gil Azinheira, Maria Do Ceu Silva, et al.. Phylogenetic analysis of Hemileia vastatrix and related taxa using a genome-scale approach. 24. International Conference on Coffee Science. ASIC 2012, Nov 2012, San Jose, Costa Rica. ⟨hal-01267895⟩
  • Joelle Amselem, Timothée Flutre, Victoria Fabia Dominguez del Angel, Jonathan Kreplak, Sébastien Duplessis, et al.. Fungal genome analysis of transposable elements: expansion vs RIP silencing. Plant and Animal Genome: 19. Conference, Jan 2011, San Diego, United States. n.p. ⟨hal-00956370⟩
  • Benjamin Petre, Ian Major, Pascal Frey, Francis Martin, Nicolas Rouhier, et al.. Les apports de la génomique pour l’étude des familles multigéniques : exemple des thaumatin-like proteins (TLPs) chez le peuplier. Séminaire de l’Ecole Doctorale RP2E. Biodiversité, Ingénierie écologique, Jan 2011, Vandoeuvre-lès-Nancy, France. 8 p. ⟨hal-02746248⟩
  • Arnaud Dowkiw, Catherine Bastien, Véronique Jorge, Marc Villar, Elodie Voisin, et al.. Breeding poplars with durable resistance to Melampsora larici-populina leaf rust : a multidisciplinary approach to understand and delay pathogen adaptation. 4. International Workshop on the Genetics of Host-Parasite Interactions in Forestry : "Disease and Insect Resistance in Forest Trees", United States Department of Agriculture - USDA (USA) (USDA). Forest service, Ville service, USA., Jul 2011, Eugene, Oregon, United States. 112 p. ⟨hal-02748005⟩
  • Ana Vieira, Pedro Talhinhas, Andreia Loureiro, Sébastien Duplessis, Diana Fernandez, et al.. Hemileia vastatrix gene expression during the infection process of coffee leaves. 23. International Conference on Coffee Science - ASIC 2010, Oct 2010, Bali, Indonesia. ⟨hal-02745179⟩
  • Pedro Talhinhas, Helena Gil Azinheira, Andreia Loureiro, Dora Batista, B Vieira, et al.. Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix. 23. International Conference on Coffee Science - ASIC 2010, Oct 2010, Bali, Indonesia. ⟨hal-02745180⟩
  • Arnaud Dowkiw, Véronique Jorge, Elodie Voisin, Patricia Faivre-Rampant, Alois Bresson, et al.. No resistance is sacrosanct: unveiling the genes controlling quantitative resistance to Melampsora larici-populina in interspecific hybrid poplars and quantifying potential adaptation of the pathogen. 4. International Rusts of Forest Trees Conference. IUFRO Working Party 02.07.05, May 2010, Florence, Italy. ⟨hal-02754692⟩
  • Catherine Bastien, Arnaud Dowkiw, Véronique Jorge, Elodie Voisin, Vanina Guérin, et al.. Towards broad-spectrum resistance to Melampsora larici-populina rust in poplar: new genetic constructions and potential adaptation of the pathogen. 5. International Poplar Symposium;IPS V, Sep 2010, Orvieto, Italy. ⟨hal-02753480⟩
  • Sébastien Duplessis, Mehdi Kaytoue, Amedeo Napoli. L’analyse formelle de concepts pour l’extraction de connaissances dans les données d’expression de gènes. Extraction et gestion des connaissances (EGC’2009), Jan 2009, Strasbourg, France. pp.439-440. ⟨hal-02756939⟩
  • Mehdi Kaytoue, Sébastien Duplessis, Sergei O. Kuznetsov, Amedeo Napoli. Two FCA-Based Methods for Mining Gene Expression Data. Formal Concept Analysis, 7th International Conference, ICFCA 2009, Apr 2009, Darmstadt, Germany. pp.251-266, ⟨10.1007/978-3-642-01815-2_19⟩. ⟨inria-00600200⟩
  • Mehdi Kaytoue, Sébastien Duplessis, Amedeo Napoli. L'analyse formelle de concepts pour l'extraction de connaissances dans les données d'expression de gènes. Extraction et gestion des connaissances, Jan 2009, Strasbourg, France. pp.439-440. ⟨inria-00600217⟩
  • David L Joly, Stéphane Hacquard, Nicolas Feau, Philippe Tanguay, Francis Martin, et al.. Chasing effectors in the secretome of Melampsora larici-populina. 14. International Congress on Molecular Plant-Microbe Interactions, Jul 2009, Québec, Canada. ⟨hal-02752437⟩
  • Véronique Jorge, Sébastien Duplessis, Céline Lalanne, Alois Bresson, Arnaud Dowkiw, et al.. Joint transcriptomic and proteomic approaches to precise the molecular basis of a major QTL (RUS) controlling quantitative rust resistance in poplar. Plant genomics and beyond, Jul 2009, Evry, France. ⟨hal-02756173⟩
  • Mehdi Kaytoue-Uberall, Sébastien Duplessis, Amedeo Napoli. Using Formal Concept Analysis for the Extraction of Groups of Co-expressed Genes. 4.International Conference on Intelligent Computing, Sep 2008, Shanghai, China. ⟨hal-02757987⟩
  • Mehdi Kaytoue, Sébastien Duplessis, Amedeo Napoli. Using Formal Concept Analysis for the Extraction of Groups of Co-expressed Genes. Modelling, Computation and Optimization in Information Systems and Management Sciences, Sep 2008, Metz, France. pp.439-449, ⟨10.1007/978-3-540-87477-5_47⟩. ⟨inria-00600212⟩
  • Mehdi Kaytoue, Sébastien Duplessis, Amedeo Napoli. Toward the discovery of itemsets with significant variations in gene expression matrices. First joint meeting of the Société Francophone de Classification and the Classification and Data Analysis Group of the Italian Statistical Society - SFC - CLADAG 2008, Jun 2008, Caserta, Italy. ⟨inria-00600224⟩
  • Céline Lalanne, Catherine Bastien, Pascal Frey, Arnaud Dowkiw, Véronique Jorge, et al.. Molecular characterisation of a major QTL for rust resistance in poplar using a proteomic approach. IUFRO - Tree Biotechnology, Jun 2007, Ponta Delgada, Azores, Portugal. ⟨hal-02754112⟩
  • Marie-Béatrice Bogeat-Triboulot, Aude Hummel, Sébastien Duplessis, Annegret Kohler. Effet du stress osmotique sur la croissance racinaire du peuplier : approche par génomique fonctionnelle à l'échelle de la zone de croissance. IFR 110, Nov 2006, Nancy, France. 17 p. ⟨hal-02812516⟩
  • Francis Martin, Annegret Kohler, Anne Jambois, Sébastien Duplessis, Frédéric Lapeyrie. The wood underground: a glimpse of the interactions between trees and ectomycorrhizal fungi. 12. New Phytologist Symposium. Functional genomics of environmental adaptation in Populus, Oct 2004, Gatlinburg, United States. 1 p. ⟨hal-02829957⟩
  • Sébastien Duplessis, Annegret Kohler, Cécile Rinaldi, Pascal Frey, Francis Martin. Characterization of the early response of poplar to rust infection using expression profiling. 12. New Phytologist Symposium. Functional genomics of environmental adaptation in Populus, Oct 2004, Gatlinburg, United States. 1 p. ⟨hal-02830800⟩

Poster communications3 documents

  • Agathe Maupetit, Michaël Pernaci, Bénédicte Fabre, S. Duplessis, Stéphane de Mita, et al.. Genetic architecture of pathogenicity-related life history traits in the poplar rust fungus. 11. Rencontres de Phytopathologie - Mycologie - JJC 2016 Journée Jean Chevaugeon, Jan 2016, Aussois, France. 96 p., 2016, 11èmes Journées Jean Chevaugeon. 25–29 janvier 2016. Centre Paul Langevin, Aussois (France). ⟨hal-02740999⟩
  • Aude Hummel, Cécile Rinaldi, Annegret Kohler, Sébastien Duplessis, Rémy Merret, et al.. Croissance de la racine de peuplier en réponse au stress osmotique : approche moléculaire dans la zone de croissance. 10. Rencontre du Groupe de Biologie Moléculaire des Ligneux, May 2008, Nancy, France. 1 p., 2008. ⟨hal-02818246⟩
  • Véronique Jorge, Arnaud Dowkiw, Mary Juteau, Vanina Guérin, Patrick Poursat, et al.. INTERPOPGER: Interactions between natural and artificial poplar stands and selection pressures associated with their management in French landscape. Poster.. Population genetics and genomics of forest trees : from gene function to evolutionary dynamics and conservation; A joint conference of IUFRO working groups 2.04.01 (population, ecological and conservation genetics) and 2.04.10 (genomics), and COST Action E-28 (genosilva : european forest genomics network), Oct 2006, Madrid, Spain. 1 p., 2006, Population genetics and genomics of forest trees: from gene function to evolutionary dynamics and conservation. Programme and conference abstract book. ⟨hal-02755567⟩

Book sections7 documents

  • Sébastien Duplessis, Guus Bakkeren, Richard Hamelin. Advancing knowledge on biology of rust fungi through genomics. Fungi, 70, Academic Press - Elsevier, 488 p., 2014, Advances in Botanical Research, 978-0-12-397940-7. ⟨10.1016/B978-0-12-397940-7.00006-9⟩. ⟨hal-01268872⟩
  • Sébastien Duplessis, Pietro D Spanu, Jan Schirawski. Biotrophic Fungi (Powdery Mildews, Rusts, and Smuts). The Ecological Genomics of Fungi, John Wiley & Sons, Inc, pp.149-168, 2013, 9781119946106. ⟨hal-01941016⟩
  • Sébastien Duplessis, David Joly, Peter N. Dodds. Rust effectors. Effectors in Plant-Microbe Interactions, Willey-Blackwell, pp.155-193, 2012, 978-0-470-95822-3. ⟨hal-01267889⟩
  • Mehdi Kaytoue, Sébastien Duplessis, Amedeo Napoli. Toward the Discovery of Itemsets with Significant Variations in Gene Expression Matrices. Fichet, Bernard and Piccolo, Domenico and Verde, Rosanna and Vichi, Maurizio. Classification and Multivariate Analysis for Complex Data Structures, Springer Berlin Heidelberg, pp.463--471, 2011, Studies in Classification, Data Analysis, and Knowledge Organization, 978-3-642-13312-1. ⟨10.1007/978-3-642-13312-1_49⟩. ⟨inria-00600233⟩
  • Christophe Plomion, Delphine Vincent, Franck Bedon, Johann Joets, Ludovic Bonhomme, et al.. Poplar proteomics: update and future challenges. Genetics, Genomics and Breeding of Poplar, CRC Press, 390 p., 2011, Genetics, genomics and breeding of crop plants, 9781578087143. ⟨hal-00964339⟩
  • Francis Martin, Sébastien Duplessis, Annegret Kohler, Denis Tagu. Exploring the transcriptome of the ectomycorrhizal symbiosis. Molecular genetics and breeding of forest trees, Haworth Press, 2004, 1560229586. ⟨hal-02829658⟩
  • Denis Tagu, Sébastien Duplessis, Francis M. Martin. Living together underground: a molecular glimpse of the ectomycorrhizal symbiosis. Heinz D. Osiewacz. Molecular biology of fungal development, Marcel Dekker, 2002, 0-8247-0744-3. ⟨hal-02915362⟩

Directions of work or proceedings1 document

  • Mehdi Kaytoue-Uberall, Sébastien Duplessis, Amedeo Napoli. Toward the discovery of itemsets with significant variations in gene expression matrices. 1. Joint meeting of the Société francophone de classification and the Classification and data analysis group of SIS (SFC-CLADAG), Jun 2008, Caserta, Italy. pp.333-336, 2008. ⟨hal-02817806⟩

Reports1 document

  • Catherine Bastien, Jose-Luis Almeida Falcon, Nicolas Chenault, Arnaud Dowkiw, Vanina Guérin, et al.. INTERPOPGER Interactions entre peupleraies naturelles et cultivées et pressions évolutives liées à leurs modes de gestion. Bilan scientifique 2005‐2008. 2008. ⟨hal-02824228⟩

Theses2 documents

  • Sébastien Duplessis. Caractérisation par ingénierie génomique des profils d'expression génique de Pisolithus tinctorius et d'Eucalyptus globulus au cours du développement de la symbiose ectomycorhizienne. Biologie végétale. Université Henri Poincaré - Nancy 1, 2001. Français. ⟨NNT : 2001NAN10019⟩. ⟨tel-01748571⟩
  • Sébastien Duplessis. Caractérisation par ingénierie génomique des profils d'expression génique de Pisolithus tinctorius et d'Eucalyptus globulus au cours du développement de la symbiose ectomycorhizienne. Sciences du Vivant [q-bio]. Université Henri Poincaré (Nancy 1), 2001. Français. ⟨tel-02834183⟩

Habilitation à diriger des recherches1 document

  • Sébastien Duplessis. Génomique fonctionnelle des interactions arbre-champignon biotrophe. Sciences du Vivant [q-bio]. Université de Lorraine, 2012. ⟨tel-02809355⟩