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; Jeremy Schmutz

doi:10.1038/nature13308

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 JaarsveldOrzenil 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, Jeremy Schmutz

Research output: Contribution to journal › Article › peer-review

673 Scopus citations

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.

Original language	English
Pages (from-to)	356-362
Number of pages	7
Journal	Nature
Volume	510
Issue number	7505
DOIs	https://doi.org/10.1038/nature13308
State	Published - 2014

Funding

Acknowledgements The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231. The research and writing of the manuscript was supported, in part, by the Office of Biological and Environmental Research in the US Department of Energy Office of Science under contract DE-AC05-00OR22725 as part of the US DOE Bioenergy Center. Funding for additional components of the study was provided by the Brazilian Ministry of Science, Technology and Innovation (MCTI) through its research funding agencies (CNPq and FINEP), the Brazilian Federal District Research Foundation (FAP-DF), the public-private Genolyptus network of Brazilian forestry companies, the Tree Biosafety and Genomics Research Cooperative (TBGRC, Oregon State University), South African forestry companies Sappi and Mondi, the Technology and Human Resources for Industry Programme (THRIP, UID 80118), the South African Department of Science and Technology (DST) and National Research Foundation (NRF, UID 18312 and 86936), the Laboratoire d’Excellence (LABEX TULIP ANR-10-LABX-41), the Agence Nationale pour la Recherche (Project Tree For Joules ANR-2010-KBBE-007-01; Fundação para a Ciência e Tecnologia (FCT, P-KBBE/ AGR_GPL/0001/2010), the Centre National pour la Recherche Scientifique (CNRS), the University Paul Sabatier Toulouse III (UPS). Part of this work was carried out using the Stevin Supercomputer Infrastructure at Ghent University, funded by Ghent University, the Hercules Foundation, and the Flemish Government–department EWI. We also acknowledge S. Oda and E. Gonzalez of Suzano Paper and Pulp for providing genetic material of E. grandis genotypes BRASUZ1, G7J1, M35D2 and their progeny used for genome sequencing and resequencing, Forestal Mininco (Chile) for genetic material of X46, the E. globulus genotype used for genome resequencing, M. Hinchee and W. Rottmann of ArborGen for EST sequences used to support gene annotation, Sappi (South Africa) for genetic material of the population used for genetic linkage mapping, and Sappi and Mondi (South Africa) for E. grandis tissues used for RNA sequencing. We acknowledge M. O’Neill of the University of Pretoria for technical assistance with E. grandis RNA sequencing.

Funders	Funder number
Brazilian Federal District Research Foundation
Brazilian Ministry of Science, Technology and Innovation
FAP-DF
Flemish Government–department EWI
National Research Foundation	86936, UID 18312
Office of Biological and Environmental Research in the US Department of Energy Office of Science	DE-AC05-00OR22725
South African Department of Science and Technology
South African forestry companies Sappi and Mondi
Technology and Human Resources for Industry Programme	UID 80118
Tree Biosafety and Genomics Research Cooperative
US Department of Energy	DE-AC02-05CH11231
US Department of Energy Joint Genome Institute
National Science Foundation	1238305
U.S. Department of Energy
Office of Science
Oregon State University
Hercules Foundation
Department of Science and Technology, Republic of South Africa
Ministério da Ciência, Tecnologia e Inovação
Conselho Nacional de Desenvolvimento Científico e Tecnológico
Labex	TULIP ANR-10-LABX-41
Universiteit Gent
Centre National de la Recherche Scientifique
Financiadora de Estudos e Projetos
Agence Nationale pour le Développement de la Recherche en Santé	ANR-2010-KBBE-007-01
Centre National pour la Recherche Scientifique et Technique
Instituto Nacional de Ciência e Tecnologia para Excitotoxicidade e Neuroproteção
Fundació Catalana de Trasplantament	P-KBBE/ AGR_GPL/0001/2010
Université Toulouse III - Paul Sabatier

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10.1038/nature13308

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Myburg, A. A., Grattapaglia, D., Tuskan, G. A., Hellsten, U., Hayes, R. D., Grimwood, J., Jenkins, J., Lindquist, E., Tice, H., Bauer, D., Goodstein, D. M., Dubchak, I., Poliakov, A., Mizrachi, E., Kullan, A. R. K., Hussey, S. G., Pinard, D., Van Der Merwe, K., Singh, P., ... Schmutz, J. (2014). The genome of Eucalyptus grandis. Nature, 510(7505), 356-362. https://doi.org/10.1038/nature13308

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title = "The genome of Eucalyptus grandis",

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.",

author = "Myburg, {Alexander A.} and Dario Grattapaglia and Tuskan, {Gerald A.} and Uffe Hellsten and Hayes, {Richard D.} and Jane Grimwood and Jerry Jenkins and Erika Lindquist and Hope Tice and Diane Bauer and Goodstein, {David M.} and Inna Dubchak and Alexandre Poliakov and Eshchar Mizrachi and Kullan, {Anand R.K.} and Hussey, {Steven G.} and Desre Pinard and {Van Der Merwe}, Karen and Pooja Singh and {Van Jaarsveld}, Ida and Silva-Junior, {Orzenil B.} and Togawa, {Roberto C.} and Pappas, {Marilia R.} and Faria, {Danielle A.} and Sansaloni, {Carolina P.} and Petroli, {Cesar D.} and Xiaohan Yang and Priya Ranjan and Tschaplinski, {Timothy J.} and Ye, {Chu Yu} and Ting Li and Lieven Sterck and Kevin Vanneste and Florent Murat and Mar{\c c}al Soler and Clemente, {H{\'e}l{\`e}ne San} and Naijib Saidi and Hua Cassan-Wang and Christophe Dunand and Hefer, {Charles A.} and Erich Bornberg-Bauer and Kersting, {Anna R.} and Kelly Vining and Vindhya Amarasinghe and Martin Ranik and Sushma Naithani and Justin Elser and Boyd, {Alexander E.} and Aaron Liston and Spatafora, {Joseph W.} and Palitha Dharmwardhana and Rajani Raja and Christopher Sullivan and Elisson Romanel and Marcio Alves-Ferreira and Carsten K{\"u}lheim and William Foley and Victor Carocha and Jorge Paiva and David Kudrna and Brommonschenkel, {Sergio H.} and Giancarlo Pasquali and Margaret Byrne and Philippe Rigault and Josquin Tibbits and Antanas Spokevicius and Jones, {Rebecca C.} and Steane, {Dorothy A.} and Vaillancourt, {Ren{\'e} E.} and Potts, {Brad M.} and Fourie Joubert and Kerrie Barry and Pappas, {Georgios J.} and Strauss, {Steven H.} and Pankaj Jaiswal and Jacqueline Grima-Pettenati and J{\'e}r{\^o}me Salse and {Van De Peer}, Yves and Rokhsar, {Daniel S.} and Jeremy Schmutz",

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doi = "10.1038/nature13308",

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volume = "510",

pages = "356--362",

journal = "Nature",

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Myburg, AA, Grattapaglia, D, Tuskan, GA, Hellsten, U, Hayes, RD, Grimwood, J, Jenkins, J, Lindquist, E, Tice, H, Bauer, D, Goodstein, DM, Dubchak, I, Poliakov, A, Mizrachi, E, Kullan, ARK, Hussey, SG, Pinard, D, Van Der Merwe, K, Singh, P, Van Jaarsveld, I, Silva-Junior, OB, Togawa, RC, Pappas, MR, Faria, DA, Sansaloni, CP, Petroli, CD, Yang, X , Ranjan, P , Tschaplinski, TJ, Ye, CY, Li, T, Sterck, L, Vanneste, K, Murat, F, Soler, M, Clemente, HS, Saidi, N, Cassan-Wang, H, Dunand, C, Hefer, CA, Bornberg-Bauer, E, Kersting, AR, Vining, K, Amarasinghe, V, Ranik, M, Naithani, S, Elser, J, Boyd, AE, Liston, A, Spatafora, JW, Dharmwardhana, P, Raja, R, Sullivan, C, Romanel, E, Alves-Ferreira, M, Külheim, C, Foley, W, Carocha, V, Paiva, J, Kudrna, D, Brommonschenkel, SH, Pasquali, G, Byrne, M, Rigault, P, Tibbits, J, Spokevicius, A, Jones, RC, Steane, DA, Vaillancourt, RE, Potts, BM, Joubert, F, Barry, K, Pappas, GJ, Strauss, SH, Jaiswal, P, Grima-Pettenati, J, Salse, J, Van De Peer, Y, Rokhsar, DS & Schmutz, J 2014, 'The genome of Eucalyptus grandis', Nature, vol. 510, no. 7505, pp. 356-362. https://doi.org/10.1038/nature13308

TY - JOUR

T1 - The genome of Eucalyptus grandis

AU - Myburg, Alexander A.

AU - Grattapaglia, Dario

AU - Tuskan, Gerald A.

AU - Hellsten, Uffe

AU - Hayes, Richard D.

AU - Grimwood, Jane

AU - Jenkins, Jerry

AU - Lindquist, Erika

AU - Tice, Hope

AU - Bauer, Diane

AU - Goodstein, David M.

AU - Dubchak, Inna

AU - Poliakov, Alexandre

AU - Mizrachi, Eshchar

AU - Kullan, Anand R.K.

AU - Hussey, Steven G.

AU - Pinard, Desre

AU - Van Der Merwe, Karen

AU - Singh, Pooja

AU - Van Jaarsveld, Ida

AU - Silva-Junior, Orzenil B.

AU - Togawa, Roberto C.

AU - Pappas, Marilia R.

AU - Faria, Danielle A.

AU - Sansaloni, Carolina P.

AU - Petroli, Cesar D.

AU - Yang, Xiaohan

AU - Ranjan, Priya

AU - Tschaplinski, Timothy J.

AU - Ye, Chu Yu

AU - Li, Ting

AU - Sterck, Lieven

AU - Vanneste, Kevin

AU - Murat, Florent

AU - Soler, Marçal

AU - Clemente, Hélène San

AU - Saidi, Naijib

AU - Cassan-Wang, Hua

AU - Dunand, Christophe

AU - Hefer, Charles A.

AU - Bornberg-Bauer, Erich

AU - Kersting, Anna R.

AU - Vining, Kelly

AU - Amarasinghe, Vindhya

AU - Ranik, Martin

AU - Naithani, Sushma

AU - Elser, Justin

AU - Boyd, Alexander E.

AU - Liston, Aaron

AU - Spatafora, Joseph W.

AU - Dharmwardhana, Palitha

AU - Raja, Rajani

AU - Sullivan, Christopher

AU - Romanel, Elisson

AU - Alves-Ferreira, Marcio

AU - Külheim, Carsten

AU - Foley, William

AU - Carocha, Victor

AU - Paiva, Jorge

AU - Kudrna, David

AU - Brommonschenkel, Sergio H.

AU - Pasquali, Giancarlo

AU - Byrne, Margaret

AU - Rigault, Philippe

AU - Tibbits, Josquin

AU - Spokevicius, Antanas

AU - Jones, Rebecca C.

AU - Steane, Dorothy A.

AU - Vaillancourt, René E.

AU - Potts, Brad M.

AU - Joubert, Fourie

AU - Barry, Kerrie

AU - Pappas, Georgios J.

AU - Strauss, Steven H.

AU - Jaiswal, Pankaj

AU - Grima-Pettenati, Jacqueline

AU - Salse, Jérôme

AU - Van De Peer, Yves

AU - Rokhsar, Daniel S.

AU - Schmutz, Jeremy

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

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U2 - 10.1038/nature13308

DO - 10.1038/nature13308

M3 - Article

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AN - SCOPUS:84903203459

SN - 0028-0836

VL - 510

SP - 356

EP - 362

JO - Nature

JF - Nature

IS - 7505

ER -

The genome of Eucalyptus grandis

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