The genome of Eucalyptus grandis
Alexander A. Myburg1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaDário Grattapaglia1] Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, Brazil [2] Programa de Ciências Genômicas e Biotecnologia - Universidade Católica de Brasília SGAN 916, 70790-160 Brasília, BrazilGerald A. Tuskan1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USAUffe HellstenUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USARichard D. HayesUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAJane GrimwoodHudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USAJerry JenkinsHudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USAErika LindquistUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAHope TiceUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USADiane BauerUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USADavid GoodsteinUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAInna DubchakUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAAlexandre PoliakovUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAEshchar Mizrachi1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaAnand R. K. Kullan1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaSteven G. Hussey1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaDesré Pinard1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaKaren van der Merwe1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaPooja Singh1] Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South AfricaIda van JaarsveldBioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South AfricaOrzenil B. Silva‐JuniorLaboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, BrazilRoberto Coiti TogawaLaboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, BrazilMarilia R. PappasLaboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, BrazilDanielle Assis de FariaLaboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, BrazilCarolina SansaloniLaboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, BrazilCésar Daniel PetroliLaboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, 70770-917 Brasília, BrazilXiaohan YangBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USAPriya RanjanBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USATimothy J. TschaplinskiBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USAChuyu YeBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USATing LiBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USALieven SterckDepartment of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Technologiepark 927, B-9000 Ghent, BelgiumKevin VannesteDepartment of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Technologiepark 927, B-9000 Ghent, BelgiumFlorent MuratMarçal SolerLaboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, FranceHélène San ClementeLaboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, FranceMohamed Najib SaïdiLaboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, FranceHua WangLaboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, FranceChristophe DunandLaboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, FranceCharles A. Hefer1] Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver V6T 1Z4, CanadaErich Bornberg‐BauerEvolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, D-48149, Muenster, GermanyAnna R. Kersting1] Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Muenster, Huefferstrasse 1, D-48149, Muenster, Germany [2] Department of Bioinformatics, Institute for Computer Science, University of Duesseldorf, Universitätsstrasse 1, 40225 Düsseldorf, GermanyKelly ViningDepartment of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USAVindhya AmarasingheDepartment of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USAMartin RanikDepartment of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USASushma Naithani1] Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USAJustin ElserDepartment of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USAAlexander E. BoydCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USAAaron Liston1] Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USAJoseph W. Spatafora1] Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USAPalitha DharmwardhanaDepartment of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USARajani RajaDepartment of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USAChristopher M. SullivanCenter for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USAElisson Romanel1] Laboratório de Biologia Evolutiva Teórica e Aplicada, Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, Brazil [2] Departamento de Biotecnologia, Escola de Engenharia de Lorena-Universidade de São Paulo (EEL-USP), CP116, 12602-810, Lorena-SP, Brazil [3] Laboratório de Genética Molecular Vegetal (LGMV), Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, BrazilMárcio Alves‐FerreiraLaboratório de Genética Molecular Vegetal (LGMV), Departamento de Genética, Universidade Federal do Rio de Janeiro (UFRJ), Av. Prof. Rodolpho Paulo Rocco, 21949900 Rio de Janeiro, BrazilCarsten KülheimResearch School of Biology, Australian National University, Canberra 0200, AustraliaWilliam J. FoleyResearch School of Biology, Australian National University, Canberra 0200, AustraliaVíctor Carocha1] Laboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, France [2] IICT/MNE; Palácio Burnay - Rua da Junqueira, 30, 1349-007 Lisboa, Portugal [3] IBET/ITQB, Av. República, Quinta do Marquês, 2781-901 Oeiras, PortugalJorge A. P. Paiva1] IICT/MNE; Palácio Burnay - Rua da Junqueira, 30, 1349-007 Lisboa, Portugal [2] IBET/ITQB, Av. República, Quinta do Marquês, 2781-901 Oeiras, PortugalDavid KudrnaArizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USASérgio Hermínio BrommonschenkelDep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa 36570-000, BrazilGiancarlo PasqualiCentro de Biotecnologia, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, BrazilMargaret ByrneScience and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Western Australia 6983, AustraliaPhilippe RigaultJosquin TibbitsDepartment of Environment and Primary Industries, Victorian Government, Melbourne, Victoria 3085, AustraliaAntanas SpokeviciusMelbourne School of Land and Environment, University of Melbourne, Melbourne, Victoria 3010, AustraliaRebecca C. JonesSchool of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, AustraliaDorothy A. Steane1] School of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia [2] Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Queensland 4558, AustraliaRené E. VaillancourtSchool of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, AustraliaBM PottsSchool of Biological Sciences and National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, AustraliaFourie Joubert1] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, Private bag X20, Pretoria 0028, South AfricaKerrie BarryUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAΓεώργιος ΠαππάςDepartamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, BrazilSteven H. StraussDepartment of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon 97331, USAPankaj Jaiswal1] Department of Botany and Plant Pathology, Oregon State University, 2082-Cordley Hall, Corvallis, Oregon 97331, USA [2] Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USAJacqueline Grima‐PettenatiLaboratoire de Recherche en Sciences Végétales, UMR 5546, Université Toulouse III, UPS, CNRS, BP 42617, 31326 Castanet Tolosan, FranceJérôme SalseYves Van de Peer1] Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria 0028, South Africa [2] Department of Plant Biotechnology and Bioinformatics (VIB), Ghent University, Technologiepark 927, B-9000 Ghent, BelgiumDaniel S. RokhsarUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USAJeremy Schmutz1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA
2014en
ABI
Аннотация
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. The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. Fast-growing Eucalyptus trees form the basis of an international pulp, paper and chemical cellulose industry and they are also seen as potential biomass feedstocks for bioenergy and biomaterials. The genome of Eucalyptus grandis has now been sequenced. It contains the greatest number of tandem duplications so far found in a plant genome, as well as the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils. Comparison with the sister species E. globulus and with other E. grandis lines reveals dynamic genome evolution and hotspots of inbreeding depression. The availability of comprehensive genomic data will be of use in work on accelerating breeding cycles for productivity and wood quality and developing eucalypt strains suited to a variety of habitats.
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