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1. The genome of Eucalyptus grandis

Author

Anand Raj Kumar Kullan, Erich Bornberg-Bauer, Christopher M. Sullivan, Florent Murat, Elisson Romanel, Yves Van de Peer, Aaron Liston, Priya Ranjan, Dorothy A. Steane, Justin Elser, Pooja Singh, Victor Carocha, Orzenil B. Silva-Junior, Marçal Soler, Cesar Petroli, Inna Dubchak, Jane Grimwood, Carsten Külheim, Danielle A. Faria, Ida Van Jaarsveld, Chu-Yu Ye, Giancarlo Pasquali, Charles A. Hefer, Desre Pinard, Roberto C. Togawa, Richard D. Hayes, Eshchar Mizrachi, Fourie Joubert, Erika Lindquist, Kevin Vanneste, Philippe Rigault, Jérôme Salse, Karen Van der Merwe, David Kudrna, Palitha Dharmwardhana, Gerald A. Tuskan, Diane Bauer, Alexandre Poliakov, Marcio Alves-Ferreira, Kerrie Barry, Vindhya Amarasinghe, Ting Li, William J. Foley, Georgios J. Pappas, Carolina Sansaloni, René E. Vaillancourt, Marília de Castro Rodrigues Pappas, Uffe Hellsten, Daniel S. Rokhsar, Martin Ranik, Anna R. Kersting, Alexander Andrew Myburg, Hua Cassan-Wang, David Goodstein, Christophe Dunand, Naijib Saidi, Timothy J. Tschaplinski, Sushma Naithani, Dario Grattapaglia, Pankaj Jaiswal, Steven G. Hussey, Jeremy Schmutz, Rajani Raja, Brad M. Potts, Margaret Byrne, Antanas V. Spokevicius, Jorge A. P. Paiva, Jacqueline Grima-Pettenati, Xiaohan Yang, Alexander Boyd, Hope Tice, Joseph W. Spatafora, Lieven Sterck, Jerry Jenkins, Steven H. Strauss, Sérgio Hermínio Brommonschenkel, Josquin Tibbits, Rebecca C. Jones, Kelly J. Vining, Hélène San Clemente, BioSciences Division [Oak Ridge], Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, DOE Joint Genome Institute [Walnut Creek], Department of Epidemiology & Population Health, London School of Hygiene and Tropical Medicine (LSHTM), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, US Department of Energy Joint Genome Institute, University of California, Embrapa Uva e Vinho (BRAZIL), Technicolor R & I [Cesson Sévigné], Technicolor, Department of Plant Systems Biology, State University of Ghent, Ghent University [Belgium] (UGENT), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institute for Evolution and Biodiversity (IEB), Westfälische Wilhelms-Universität Münster (WWU), Department of Botany and Plant Pathology, Oregon State University (OSU), RAIZ – Forestry & Paper Research Institut, Laboratory of Plant Cell Biotechnology, ITQB/IBET, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, GYDLE, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bioinformatics and Computational Biology Unit, Faculty of Natural and Agricultural Sciences-University of Pretoria [South Africa], Institute of Continuing Medical Education of Ioannina, Plastes et différenciation cellulaire (PDC), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Universiteit Gent = Ghent University [Belgium] (UGENT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Dynamique et Evolution des Parois cellulaires végétales, Office of Science of the US Department of Energy [DE-AC02-05CH11231], Office of Biological and Environmental Research in the US Department of Energy Office of Science, US DOE Bioenergy Center [DE-AC05-00OR22725], Brazilian Ministry of Science, Technology and Innovation (MCTI) through (CNPq), Brazilian Ministry of Science, Technology and Innovation (MCTI) through (FINEP), Brazilian Federal District Research Foundation (FAP-DF), Technology and Human Resources for Industry Programme (THRIP) [UID 80118], South African Department of Science and Technology (DST), National Research Foundation (NRF) [UID 18312, 86936], Laboratoire d'Excellence [LABEX TULIP ANR-10-LABX-41], Agence Nationale pour la Recherche (Project Tree For Joules) [ANR-2010-KBBE-007-01], Fundacao para a Ciencia e Tecnologia (FCT) [P-KBBE/AGR_GPL/0001/2010], Centre National pour la Recherche Scientifique (CNRS), University Paul Sabatier Toulouse III (UPS), Ghent University, Hercules Foundation, Flemish Government-department EWI, Myburg, Alexander A., University of California (UC), Universiteit Gent = Ghent University (UGENT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)

Subjects
Genome evolution, DATABASE, phylogénomique, [SDV]Life Sciences [q-bio], Biology, Genome, DNA sequencing, Evolution, Molecular, Phylogenomics, Myrtales, Botany, Inbreeding depression, TOOL, Inbreeding, RNA-SEQ, PLANT, NUCLEAR-DNA, Phylogeny, ComputingMilieux_MISCELLANEOUS, Eucalyptus, Multidisciplinary, FOREST TREES, Biology and Life Sciences, Genetic Variation, métabolisme secondaire, 15. Life on land, biology.organism_classification, GENE, EVOLUTION, ALIGNMENT, biocarburant, Biofuels, Eucalyptus globulus, évolution du génome, WHOLE-GENOME, Secondary metabolism, Genome, Plant
Abstract

International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

Published
2014

2. RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans

Author

Jean-Yves Coppée, Gaëlle Lelandais, Odile Sismeiro, Sophie Lemoine, Frédéric Devaux, Stéphane Le Crom, Rajendra Prasad, Maria Bernard, Sanjiveeni Dhamgaye, Membrane Biology Laboratory, Jawaharlal Nehru University (JNU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris], Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), The work presented in this paper has been supported in part by grants to R.P. from Indo-French Center for the Promotion of Advanced Scientific Research (IFC-3403-2/2006) and DST INT/SWISS/P-31/2009., Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Institut Pasteur [Paris] (IP), BMC, Ed., Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Candida albicans, beta-Glucans, lcsh:QH426-470, lcsh:Biotechnology, Repressor, RNA-Seq, Drug resistance, Multidrug resistance, Fungal Proteins, 03 medical and health sciences, Drug Resistance, Fungal, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Transcriptional regulation, Genetics, CZF1, Gene, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Sequence Analysis, RNA, Gene Expression Profiling, biology.organism_classification, Yeast, 3. Good health, Multiple drug resistance, Gene expression profiling, lcsh:Genetics, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA-seq, Biotechnology, Transcription Factors, Research Article
Abstract

Background Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart. Results RNA-seq unveiled differential expression of 228 genes including a) genes previously identified as involved in CDR, b) genes not previously associated to the CDR phenotype, and c) novel transcripts whose function as a gene is uncharacterized. In particular, we show for the first time that CDR acquisition is correlated with an overexpression of the transcription factor encoding gene CZF1. CZF1 null mutants were susceptible to many drugs, independently of known multidrug resistance mechanisms. We show that CZF1 acts as a repressor of β-glucan synthesis, thus negatively regulating cell wall integrity. Finally, our RNA-seq data allowed us to identify a new transcribed region, upstream of the TAC1 gene, which encodes the major CDR transcriptional regulator. Conclusion Our results open new perspectives of the role of Czf1 and of our understanding of the transcriptional and post-transcriptional mechanisms that lead to the acquisition of drug resistance in C. albicans, with potential for future improvements of therapeutic strategies.

Published
2012