The genome of Eucalyptus grandis

Alexander A. Myburg (), Dario Grattapaglia, Gerald A. Tuskan, Uffe Hellsten, Richard D. Hayes, Jane Grimwood, Jerry Jenkins, Erika Lindquist, Hope Tice, Diane Bauer, David M. Goodstein, Inna Dubchak, Alexandre Poliakov, Eshchar Mizrachi, Anand R. K. Kullan, Steven G. Hussey, Desre Pinard, Karen van der Merwe, Pooja Singh, Ida van Jaarsveld, Orzenil B. Silva-Junior, Roberto C. Togawa, Marilia R. Pappas, Danielle A. Faria, Carolina P. Sansaloni, Cesar D. Petroli, Xiaohan Yang, Priya Ranjan, Timothy J. Tschaplinski, Chu-Yu Ye, Ting Li, Lieven Sterck, Kevin Vanneste, Florent Murat, Marçal Soler, Hélène San Clemente, Naijib Saidi, Hua Cassan-Wang, Christophe Dunand, Charles A. Hefer, Erich Bornberg-Bauer, Anna R. Kersting, Kelly Vining, Vindhya Amarasinghe, Martin Ranik, Sushma Naithani, Justin Elser, Alexander E. Boyd, Aaron Liston, Joseph W. Spatafora, Palitha Dharmwardhana, Rajani Raja, Christopher Sullivan, Elisson Romanel, Marcio Alves-Ferreira, Carsten Külheim, William Foley, Victor Carocha, Jorge Paiva, David Kudrna, Sergio H. Brommonschenkel, Giancarlo Pasquali, Margaret Byrne, Philippe Rigault, Josquin Tibbits, Antanas Spokevicius, Rebecca C. Jones, Dorothy A. Steane, René E. Vaillancourt, Brad M. Potts, Fourie Joubert, Kerrie Barry, Georgios J. Pappas, Steven H. Strauss, Pankaj Jaiswal, Jacqueline Grima-Pettenati, Jérôme Salse, Yves Van de Peer, Daniel S. Rokhsar and Jeremy Schmutz
Additional contact information
Alexander A. Myburg: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Dario Grattapaglia: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Gerald A. Tuskan: 2800 Mitchell Drive
Uffe Hellsten: 2800 Mitchell Drive
Richard D. Hayes: 2800 Mitchell Drive
Jane Grimwood: HudsonAlpha Institute for Biotechnology, 601 Genome Way
Jerry Jenkins: HudsonAlpha Institute for Biotechnology, 601 Genome Way
Erika Lindquist: 2800 Mitchell Drive
Hope Tice: 2800 Mitchell Drive
Diane Bauer: 2800 Mitchell Drive
David M. Goodstein: 2800 Mitchell Drive
Inna Dubchak: 2800 Mitchell Drive
Alexandre Poliakov: 2800 Mitchell Drive
Eshchar Mizrachi: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Anand R. K. Kullan: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Steven G. Hussey: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Desre Pinard: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Karen van der Merwe: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Pooja Singh: Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Ida van Jaarsveld: Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa
Orzenil B. Silva-Junior: Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Roberto C. Togawa: Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Marilia R. Pappas: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Danielle A. Faria: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Carolina P. Sansaloni: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Cesar D. Petroli: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil
Xiaohan Yang: Oak Ridge National Laboratory
Priya Ranjan: Oak Ridge National Laboratory
Timothy J. Tschaplinski: Oak Ridge National Laboratory
Chu-Yu Ye: Oak Ridge National Laboratory
Ting Li: Oak Ridge National Laboratory
Lieven Sterck: Ghent University, Technologiepark 927, B-9000 Ghent, Belgium
Kevin Vanneste: Ghent University, Technologiepark 927, B-9000 Ghent, Belgium
Florent Murat: INRA/UBP UMR 1095, 5 Avenue de Beaulieu, 63100 Clermont Ferrand, France
Marçal Soler: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Hélène San Clemente: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Naijib Saidi: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Hua Cassan-Wang: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Christophe Dunand: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Charles A. Hefer: Bioinformatics and Computational Biology Unit, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa
Erich Bornberg-Bauer: Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany
Anna R. Kersting: Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany
Kelly Vining: Oregon State University
Vindhya Amarasinghe: Oregon State University
Martin Ranik: Oregon State University
Sushma Naithani: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Justin Elser: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Alexander E. Boyd: Center for Genome Research and Biocomputing, Oregon State University
Aaron Liston: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Joseph W. Spatafora: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Palitha Dharmwardhana: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Rajani Raja: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Christopher Sullivan: Center for Genome Research and Biocomputing, Oregon State University
Elisson Romanel: Laboratório de Biologia Evolutiva Teórica e Aplicada, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil
Marcio Alves-Ferreira: Laboratório de Genética Molecular Vegetal (LGMV), Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil
Carsten Külheim: Research School of Biology, Australian National University, Canberra 0200, Australia
William Foley: Research School of Biology, Australian National University, Canberra 0200, Australia
Victor Carocha: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Jorge Paiva: IICT/MNE; Palácio Burnay - Rua da Junqueira, 30, 1349-007 Lisboa, Portugal
David Kudrna: Arizona Genomics Institute, University of Arizona
Sergio H. Brommonschenkel: Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-000, Brazil
Giancarlo Pasquali: Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
Margaret Byrne: Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, Australia
Philippe Rigault: GYDLE, 1363 av. Maguire, suite 301, Québec, Quebec G1T 1Z2, Canada
Josquin Tibbits: Victorian Government, Melbourne, Victoria 3085, Australia
Antanas Spokevicius: Melbourne School of Land and Environment, University of Melbourne, Melbourne, Victoria 3010, Australia
Rebecca C. Jones: School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
Dorothy A. Steane: School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
René E. Vaillancourt: School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
Brad M. Potts: School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
Fourie Joubert: Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Kerrie Barry: 2800 Mitchell Drive
Georgios J. Pappas: Universidade de Brasília, Brasília 70910-900, Brazil
Steven H. Strauss: Oregon State University
Pankaj Jaiswal: Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA
Jacqueline Grima-Pettenati: Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France
Jérôme Salse: INRA/UBP UMR 1095, 5 Avenue de Beaulieu, 63100 Clermont Ferrand, France
Yves Van de Peer: Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa
Daniel S. Rokhsar: 2800 Mitchell Drive
Jeremy Schmutz: 2800 Mitchell Drive

Nature, 2014, vol. 510, issue 7505, 356-362

Abstract: Abstract 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.

Date: 2014
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DOI: 10.1038/nature13308

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