1. Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle
- Author
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Alan Kuo, Rhyan B. Dockter, Juan Chen, Shingo Miyauchi, Thibaut Payen, Benjamin Noel, François Le Tacon, Jean-Marc Aury, Minou Nowrousian, Mei Wang, Emmanuelle Morin, Annegret Kohler, Claude Murat, Petr Baldrian, Laure Fauchery, Julie Poulain, Lucia Žifčáková, Julie Guy, Claudia Riccioni, Corinne Da Silva, Francis Martin, László Nagy, Patrick Wincker, Richard Splivallo, Beatrice Belfiori, Fabienne Malagnac, Anna Lipzen, Paola Bonfante, Stefanie Traeger, Francesco Paolocci, Alicia Clum, Mirco Iotti, Yaron Sitrit, Elisabetta Levati, Igor V. Grigoriev, Alessandra Zambonelli, Barbara Montanini, Erika Lindquist, Joseph W. Spatafora, Kerrie Barry, Mathieu Hainaut, Andrea Rubini, Simone Ottonello, Virginie Molinier, Krisztina Krizsán, Raffaella Balestrini, Nicolas Cichocki, Daniel Wipf, Bernard Henrissat, Antonietta Mello, Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Institute of medicinal plant development, Chinese Academy of Medical Sciences, Synthet & Syst Biol Unit, Hungarian Academy of Sciences (MTA), CNR, Ist Protez Piante, UOS Torino, Laboratory of Functional Genomics and Protein Engineering, Biochemistry and Molecular Biology Unit, Department of Life Sciences, University of Parma = Università degli studi di Parma [Parme, Italie], Dept Life Sci, Biochem & Mol Biol Unit, Lab Funct Genom & Prot Engn, Joint Genome Institute, United States Department of Energy, Plant Genetics Institute, Consiglio Nazionale delle Ricerche [Roma] (CNR), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Dipartimento Protez & Valorizzaz Agroalimentare, Alma Mater Studiorum University of Bologna (UNIBO), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Istituto per la Protezione delle Piante, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, IPF – Integrative Fungal Research, Goethe-Universität Frankfurt am Main, Institut für biologie und biotechnologie der pflanzen, Westfälische Wilhelms-Universität Münster (WWU), 0977 Unité associée de Biologie forestière, Institut National de la Recherche Agronomique (INRA), Institute of Microbiology of the CAS, Department of Botany and Plant Pathology, Oregon State University (OSU), Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Department of Biochemistry and Molecular Biology, Medical and Health Science Center, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Dipartimento di Biologia Vegetale, Università degli studi di Torino (UNITO), French National Research Agency through the project SYSTRUF ANR-14-CE06-0020, ANR-09-STRA-10, French National Research Agency through the project SYMWOOD (Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems) ANR-11-LABX 0002 01, Office of Science of the US Department of Energy DE-AC02-05CH11231, France Genomique ANR-10-INBS-09, Region Lorraine Research Council, European Commission (European Regional Development Fund), University of Parma, Interuniversity Consortium for Biotechnologies, Piedmont Region, Czech Science Foundation 16-08916S, German Research Foundation NO407/7-1, Department of General and Molecular Botany, ANR-14-CE06-0020,FUNTUNE,Cocktails enzymatiques inspirés de modèles fongiques pour la déconstruction contrôlée de la biomasse végétale(2014), ANR-10-STRA-0010,COMANCHE,Interactions écosystémiques et impacts anthropiques dans les populations de Coquilles St-Jacques de la Manche(2010), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), U.S. Department of Energy (DOE)-U.S. Department of Energy (DOE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Murat, Claude, Payen, Thibaut, Noel, Benjamin, Kuo, Alan, Morin, Emmanuelle, Chen, Juan, Kohler, Annegret, Krizsán, Krisztina, Balestrini, Raffaella, Da Silva, Corinne, Montanini, Barbara, Hainaut, Mathieu, Levati, Elisabetta, Barry, Kerrie W., Belfiori, Beatrice, Cichocki, Nicola, Clum, Alicia, Dockter, Rhyan B., Fauchery, Laure, Guy, Julie, Iotti, Mirco, Le Tacon, Françoi, Lindquist, Erika A., Lipzen, Anna, Malagnac, Fabienne, Mello, Antonietta, Molinier, Virginie, Miyauchi, Shingo, Poulain, Julie, Riccioni, Claudia, Rubini, Andrea, Sitrit, Yaron, Splivallo, Richard, Traeger, Stefanie, Wang, Mei, Žifčáková, Lucia, Wipf, Daniel, Zambonelli, Alessandra, Paolocci, Francesco, Nowrousian, Minou, Ottonello, Simone, Baldrian, Petr, Spatafora, Joseph W., Henrissat, Bernard, Nagy, Laszlo G., Aury, Jean-Marc, Wincker, Patrick, Grigoriev, Igor V., Bonfante, Paola, Martin, Francis M., Università degli studi di Parma = University of Parma (UNIPR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Unité associée de biologie forestière, Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Università degli studi di Torino = University of Turin (UNITO), and MURAT-FURMINIEUX, Claude
- Subjects
0301 basic medicine ,volatile organic compound ,tuber (truffles) ,[SDV]Life Sciences [q-bio] ,champignon ,Pezizomycetes ,truffle ,Tuber aestivum ,Mycorrhizae ,DNA, Fungal ,Life History Traits ,Phylogeny ,2. Zero hunger ,Truffle ,Genome ,biology ,Ecology ,composé organique volatil ,food and beverages ,Ecology, Evolution, Behavior and Systematics ,Tuberaceae ,Fungal ,expression différentielle ,Genome, Fungal ,Sequence Analysis ,tuber ,Evolution ,no key words ,03 medical and health sciences ,truffe ,Behavior and Systematics ,Ascomycota ,Phylogenetics ,ddc:570 ,Botany ,Choiromyces ,Genetics ,Symbiosis ,Comparative genomics ,Human Genome ,fungi ,Sequence Analysis, DNA ,DNA ,champignon ectomycorhizien ,15. Life on land ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematic ,030104 developmental biology ,Tuber melanosporum - Abstract
Tuberaceae is one of the most diverse lineages of symbiotic truffle-forming fungi. To understand the molecular underpinning of the ectomycorrhizal truffle lifestyle, we compared the genomes of Piedmont white truffle (Tuber magnatum), Périgord black truffle (Tuber melanosporum), Burgundy truffle (Tuber aestivum), pig truffle (Choiromyces venosus) and desert truffle (Terfezia boudieri) to saprotrophic Pezizomycetes. Reconstructed gene duplication/loss histories along a time-calibrated phylogeny of Ascomycetes revealed that Tuberaceae-specific traits may be related to a higher gene diversification rate. Genomic features in Tuber species appear to be very similar, with high transposon content, few genes coding lignocellulose-degrading enzymes, a substantial set of lineage-specific fruiting-body-upregulated genes and high expression of genes involved in volatile organic compound metabolism. Developmental and metabolic pathways expressed in ectomycorrhizae and fruiting bodies of T. magnatum and T. melanosporum are unexpectedly very similar, owing to the fact that they diverged ~100 Ma. Volatile organic compounds from pungent truffle odours are not the products of Tuber-specific gene innovations, but rely on the differential expression of an existing gene repertoire. These genomic resources will help to address fundamental questions in the evolution of the truffle lifestyle and the ecology of fungi that have been praised as food delicacies for centuries.
- Published
- 2018
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