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1. The challenge of West Nile virus in Europe: knowledge gaps and research priorities

Author

Sebastian Ulbert, Norbert Nowotny, Ana Moreno, Luisa Barzon, N. Pardigon, Penelope Koraka, Antonio Tenorio, Miguel Ángel Jiménez-Clavero, Jordi Figuerola, Paolo Cordioli, Niek N. Sanders, Byron E. E. Martina, Annapaola Rizzoli, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universita degli Studi di Padova, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Veterinary Medicine [Vienna] (Vetmeduni), Sultan Qaboos University (SQU), Institut Pasteur [Paris], Universiteit Gent = Ghent University [Belgium] (UGENT), Fraunhofer Institute for Cell Therapy and Immunology (Fraunhofer IZI), Fraunhofer (Fraunhofer-Gesellschaft), Instituto de Salud Carlos III [Madrid] (ISC), This paper is the product of a cooperative action promoted by the Coordinators and delegates of the EU funded projects on West Nile virus under the 7th European Programme, in particular the EuroWestNile project (www.eurowestnile.org, GA n. 261391), the EDENext project (www.edenext.eu , GA n. 261504) the Wings project (www.west-nile-shield-project.eu , GA n. 261426), and the Vectorie project (www.vectorie.eu , GA n. 261466). This study was partially funded by EU grant FP7-261504 EDENext and is catalogued by the EDENext Steering Committee as EDENext 142 (http://www.edenext.eu). AR was partially funded by the Autonomous Province of Trento grant LExEM (http://www.lexem.eu). The contents of this publication are the sole responsibility of the authors and don't necessarily reflect the views of the European Commission., This paper is dedicated to the memory of our wonderful colleague and friend, Dr Paolo Cordioli, who recently passed away. We thank the European Centre for Disease Prevention and Control (ECDC) for supporting this initiative and for promoting a stronger integration between public health and research in Europe. We also thank Dr Jolanta Kolodziejek of the Institute of Virology, University of Veterinary Medicine Vienna for establishing the phylogenetic trees and Matteo Marcantonio of the GIS/RS platform at the Edmund Mach Foundation for preparing the map in Figure 1, European Project: 261391,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EUROWESTNILE(2011), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), European Project: 261426,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,WINGS(2011), European Project: 261466,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,VECTORIE(2010), Virology, Università degli Studi di Padova = University of Padua (Unipd), Institut Pasteur [Paris] (IP), Universiteit Gent = Ghent University (UGENT), and Publica

Subjects
Health Knowledge, Attitudes, Practice, Veterinary medicine, Economic growth, WNV STRAINS, Epidemiology, viruses, MESH: Health Knowledge, Attitudes, Practice, medicine.disease_cause, Disease Outbreaks, EXPERIMENTAL-INFECTION, ENVELOPE PROTEIN, Neuroinvasive disease, Medicine and Health Sciences, MESH: Genetic Variation, MESH: Disease Outbreaks, MESH: Phylogeny, Phylogeny, media_common, EARLY WARNING SYSTEM, biology, SUBSTITUTION, AMINO-ACID, 3. Good health, Europe, MESH: Research, Geography, Population Surveillance, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, West Nile virus, SPARROWS PASSER-DOMESTICUS, media_common.quotation_subject, Ecology (disciplines), MESH: Population Surveillance, SDG 3 - Good Health and Well-being, Virology, medicine, Humans, media_common.cataloged_instance, Veterinary Sciences, European union, TIME RT-PCR, Settore VET/06 - PARASSITOLOGIA E MALATTIE PARASSITARIE DEGLI ANIMALI, MESH: West Nile virus, MESH: West Nile Fever, MESH: Humans, Research, LINEAGE 1 STRAIN, Public Health, Environmental and Occupational Health, Genetic Variation, Outbreak, biology.organism_classification, USUTU VIRUS, Early warning system, MESH: Europe, CULEX-PIPIENS MOSQUITOS, Usutu virus, West Nile Fever, Diversity (politics)
Abstract

West Nile virus (WNV) is continuously spreading across Europe, and other continents, i.e. North and South America and many other regions of the world. Despite the overall sporadic nature of outbreaks with cases of West Nile neuroinvasive disease (WNND) in Europe, the spillover events have increased and the virus has been introduced into new areas. The high genetic diversity of the virus, with remarkable phenotypic variation, and its endemic circulation in several countries, require an intensification of the integrated and multidisciplinary research efforts built under the 7th Framework Programme of the European Union (FP7). It is important to better clarify several aspects of WNV circulation in Europe, including its ecology, genomic diversity, pathogenicity, transmissibility, diagnosis and control options, under different environmental and socio-economic scenarios. Identifying WNV endemic as well as infection-free areas is becoming a need for the development of human vaccines and therapeutics and the application of blood and organs safety regulations. This review, produced as a joint initiative among European experts and based on analysis of 118 scientific papers published between 2004 and 2014, provides the state of knowledge on WNV and highlights the existing knowledge and research gaps that need to be addressed with high priority in Europe and neighbouring countries.

Published
2015

2. Accounting for competition in multi-environment tree genetic evaluations: a case study with hybrid pines

Author

Nuno Borralho, Eduardo P. Cappa, Ector Belaber, Maria Elena Gauchat, Cristian Damián Schoffen, Facundo Muñoz, Leopoldo Sanchez, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), RAIZ – Forestry & Paper Research Institut, Instituto Superior Técnico, Universidade Técnica de Lisboa, Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and This study was funded by the National Institute of Agricultural Technology (INTA) (grant numbers PNFOR-01104062, MSNES-1242204/5). E.P.C.’s research was partially supported by the National Agency for the Promotion of Science and Technology of Argentina (ANPCYT, PICT-2016 1048). F.M.’s research is partially supported by research grant MTM2016-77501-P from the State Research Agency of the Spanish Ministry of Science, Innovation and Universities jointly with the European Regional Development Fund, FEDER.

Subjects
Additive and competition genotype–environment interaction, 0106 biological sciences, Mixed model, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Accounting, Tree breeding, 010603 evolutionary biology, 01 natural sciences, Genetic correlation, Competition (biology), Competition model, Genetic variation, Gene–environment interaction, media_common, Mathematics, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, business.industry, Diameter at breast height, Forestry, 15. Life on land, Total heritable variance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, 010606 plant biology & botany
Abstract

International audience; Key message: A novel multi-environment competition individual-tree mixed model resulted in better fit, and greater individual narrow- and broad-sense heritabilities than the model without competition, notably for traits showing competition. In multi-environment tests, the proposed model would allow tree breeders to select genotypes with the best performance in both additive direct and competition breeding values, increasing forest productivity. Context: Genetic merit of trees is known to be affected and interact with local competition effects as well as changes across environmental conditions. Recent studies showed that competition genetic effects can affect the genetic variance and bias the tree breeding values, and its covariance with direct breeding values has been variable across traits. Aims: The present paper extends a mixed-model methodology to the problem of accounting for competition in a multi-environment set of forest genetic trials and exploring its impact on genetic variances as well as the multi-environment genetic correlation. Methods: The proposed model is illustrated using data from two full-sib trials of Pinus elliottii var. elliottii × Pinus caribaea var. hondurensis F1. Dispersion parameters and (co)variance of total breeding values were estimated for diameter at breast height, total tree height, and stem straightness at age 10. Results: For traits showing competition effects (diameter at breast height and total tree height), the proposed multi-environment competition model gave better fit than the simpler model. Accounting for competition increased the direct additive variance, reduced the residual variances, and did not change significantly the across-site additive genetic correlation. However, for diameter at breast height, top 5% best genetic rankings showed differences. Conclusion: When traits are strongly affected by inter-tree competition, the use of the proposed model in multi-environment analyses can efficiently identify the phenomenon with general benefits in the fitting of genetic components and open the door to select on the basis of competitiveness.

Published
2021

3. Quantitative genetic parameters for growth and wood properties in Eucalyptus 'urograndis' hybrid using near-infrared phenotyping and genome-wide SNP-based relationships

Author

Orzenil B. Silva-Junior, Bruno Marco de Lima, Shawn D. Mansfield, Carla Garcia, Dario Grattapaglia, Eduardo P. Cappa, BRUNO MARCO DE LIMA, USP, EDUARDO P. CAPPA, INSTITUTO NACIONAL DE TECNOLOGI´A AGROPECUARIA (INTA), ARGENTINA, ORZENIL BONFIM DA SILVA JUNIOR, Cenargen, CARLA GARCIA, INTERNATIONAL PAPER DO BRASIL ROD, SHAWN D. MANSFIELD, UNIVERSITY OF BRITISH COLUMBIA, CANADA, and DARIO GRATTAPAGLIA, Cenargen.

Subjects
0106 biological sciences, 0301 basic medicine, Heredity, Plant Science, 01 natural sciences, Lignin, Trees, Spectrum Analysis Techniques, NEAR-INFRARED PEHNOTYPING, Data Management, education.field_of_study, Eucalyptus, Multidisciplinary, Spectroscopy, Near-Infrared, Organic Compounds, Plant Anatomy, Eukaryota, near-Infrared Spectroscopy, Phylogenetic Analysis, Genomics, Plants, Wood, Phylogenetics, Polimorfismo de un Solo Nucleótido, Chemistry, Phenotypes, Phenotype, Genetic gain, Physical Sciences, Medicine, Brazil, Genome, Plant, Research Article, Genetic Research, Computer and Information Sciences, Genética Cuantitativa, Genotype, Science, Population, Infrared Spectroscopy, Quantitative trait locus, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, Quantitative Genetics, 03 medical and health sciences, Quantitative Trait, Heritable, MOLECULAR RELATIONSHIP, Species Specificity, Genetic variation, Genetics, Evolutionary Systematics, PEDIGREE RELATIONSHIP, education, Cellulose, Fenotipos, Hybrid, Taxonomy, Evolutionary Biology, Models, Genetic, Directional selection, Organic Chemistry, Organisms, Chemical Compounds, Biology and Life Sciences, Heritability, purl.org/becyt/ford/4.5 [https], Plant Breeding, 030104 developmental biology, Evolutionary biology, Single Nucleotide Polymorphism, Tree breeding, Hybridization, Genetic, purl.org/becyt/ford/4 [https], 010606 plant biology & botany
Abstract

A thorough understanding of the heritability, genetic correlations and additive and non-additive variance components of tree growth and wood properties is a requisite for effective tree breeding. This knowledge is essential to maximize genetic gain, that is, the amount of increase in trait performance achieved annually through directional selection. Understanding the genetic attributes of traits targeted by breeding is also important to sustain decade-long genetic progress, that is, the progress made by increasing the average genetic value of the offspring as compared to that of the parental generation. In this study, we report quantitative genetic parameters for fifteen growth, wood chemical and physical traits for the world-famous Eucalyptus urograndis hybrid (E. grandis × E. urophylla). These traits directly impact the optimal use of wood for cellulose pulp, paper, and energy production. A population of 1,000 trees sampled in a progeny trial was phenotyped directly or following the development and use of near-infrared spectroscopy calibration models. Trees were genotyped with 33,398 SNPs and 24,001 DArT-seq genome-wide markers and genomic realized relationship matrices (GRM) were used for parameter estimation with an individual-tree additive-dominant mixed model. Wood chemical properties and wood density showed stronger genetic control than growth, cellulose and fiber traits. Additive effects are the main drivers of genetic variation for all traits, but dominance plays an equally or more important role for growth, singularly in this hybrid. GRM´s with >10,000 markers provided stable relationships estimates and more accurate parameters than pedigrees by capturing the full genetic relationships among individuals and disentangling the non-additive from the additive genetic component. Low correlations between growth and wood properties indicate that simultaneous selection for wood traits can be applied with minor effects on genetic gain for growth. Conversely, moderate to strong correlations between wood density and chemical traits exist, likely due to their interdependency on cell wall structure such that responses to selection will be connected for these traits. Our results illustrate the advantage of using genomewide marker data to inform tree breeding in general and have important consequences for operational breeding of eucalypt urograndis hybrids. Fil: de Lima, Bruno Marco. Universidade de Sao Paulo; Brasil. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Silva Junior, Orzenil B.. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil. Universidade Católica de Brasília; Brasil Fil: Garcia, Carla. No especifíca; Fil: Mansfield, Shawn D.. University of British Columbia; Canadá Fil: Grattapaglia, Dario. Ministerio da Agricultura Pecuaria e Abastecimento de Brasil. Empresa Brasileira de Pesquisa Agropecuaria; Brasil. Universidade Católica de Brasília; Brasil

Published
2019

4. A test for gene-environment interaction in the presence of measurement error in the environmental variable

Author

Hugues Aschard, Donna Spiegelman, Molin Wang, Vincent Laville, Pete Kraft, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Harvard T.H. Chan School of Public Health, The authors thank the reviewers for their helpful comments that have improved the paper. This research is supported by grant R01CA050597 from the National Cancer Institute (NCI) and R21HG007687 from the National Human Genome Research Institute (NHGRI). The authors have no conflict of interest to declare., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Epidemiology, Genome-wide association study, Breast Neoplasms, MESH: Logistic Models, Interaction, Logistic regression, 01 natural sciences, Article, Correlation, 010104 statistics & probability, 03 medical and health sciences, Bias, Statistics, Linear regression, MESH: Bias, Humans, normal discriminant analysis, MESH: Genetic Variation, MESH: Models, Genetic, 0101 mathematics, Gene–environment interaction, gene-environment interaction test, Genetics (clinical), Mathematics, [STAT.AP]Statistics [stat]/Applications [stat.AP], Observational error, MESH: Humans, Models, Genetic, Genetic Variation, Reproducibility of Results, MESH: Gene-Environment Interaction, Linear discriminant analysis, 3. Good health, MESH: Reproducibility of Results, 030104 developmental biology, Logistic Models, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, genome-wide association studies, MESH: Genome-Wide Association Study, Gene-Environment Interaction, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [STAT.ME]Statistics [stat]/Methodology [stat.ME], measurement error, MESH: Breast Neoplasms, Genome-Wide Association Study
Abstract

International audience; The identification of gene-environment interactions in relation to risk of human diseases has been challenging. One difficulty has been that measurement error in the exposure can lead to massive reductions in the power of the test, as well as in bias toward the null in the interaction effect estimates. Leveraging previous work on linear discriminant analysis, we develop a new test of interaction between genetic variants and a continuous exposure that mitigates these detrimental impacts of exposure measurement error in ExG testing by reversing the role of exposure and the diseases status in the fitted model, thus transforming the analysis to standard linear regression. Through simulation studies, we show that the proposed approach is valid in the presence of classical exposure measurement error as well as when there is correlation between the exposure and the genetic variant. Simulations also demonstrated that the reverse test has greater power compared to logistic regression. Finally, we confirmed that our approach eliminates bias from exposure measurement error in estimation. Computing times are reduced by as much as fivefold in this new approach. For illustrative purposes, we applied the new approach to an ExGWAS study of interactions with alcohol and body mass index among 1,145 cases with invasive breast cancer and 1,142 controls from the Cancer Genetic Markers of Susceptibility study.

Published
2018

5. Genome-scale rates of evolutionary change in bacteria

Author

Jane Hawkey, David J. Edwards, Simon Le Hello, Kathryn E. Holt, Mathieu Fourment, Edward C. Holmes, François-Xavier Weill, Sebastián Duchêne, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Centre for Systems Genomics, The University of MelbourneParkville, VIC, Australia., Department of Biochemistry and Molecular Biology, Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris] (IP), This research was funded by the NHMRC (Australia Fellowship#AF30 to E. C. H., Career Development Fellowship #1061409 toK. E. H.). S. D. was supported by a McKenzie fellowship from the University of Melbourne.This paper was supported by the following grant(s):National Health and Medical Research Council 1061409.National Health and Medical Research Council GNT1037231., and Institut Pasteur [Paris]

Subjects
0301 basic medicine, 0106 biological sciences, Mechanisms of Evolution, Evolutionary change, Genome scale, Bacterial genome size, phylogeny, Genome, 010603 evolutionary biology, 01 natural sciences, Orders of magnitude (bit rate), Evolution, Molecular, 03 medical and health sciences, Phylogenetics, evolution, Molecular clock, Evolutionary dynamics, 030304 developmental biology, Whole genome sequencing, Genetics, 0303 health sciences, biology, Bacteria, Models, Genetic, molecular clock, Genetic Variation, General Medicine, biology.organism_classification, Biological Evolution, 030104 developmental biology, Ancient DNA, 13. Climate action, Evolutionary biology, time-dependency, Microbial Evolution and Epidemiology, Mutation, Human genome, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, substitution rates, Genome, Bacterial, Research Paper
Abstract

Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ancient DNA” data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10−6 to 10−8 nucleotide substitutions site-1 year-1. This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.

Published
2016

6. 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