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Title: The genome of Eucalyptus grandis

Abstract

Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

Authors:
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Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1148848
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Nature (London)
Additional Journal Information:
Journal Volume: 510; Journal Issue: 7505; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Hellsten, Uffe, Hayes, Richard D., Grimwood, Jane, Jenkins, Jerry, Lindquist, Erika, Tice, Hope, Bauer, Diane, Goodstein, David M., Dubchak, Inna, Poliakov, Alexandre, Mizrachi, Eshchar, Kullan, Anand R. K., Hussey, Steven G., Pinard, Desre, van der Merwe, Karen, Singh, Pooja, van Jaarsveld, Ida, Silva-Junior, Orzenil B., Togawa, Roberto C., Pappas, Marilia R., Faria, Danielle A., Sansaloni, Carolina P., Petroli, Cesar D., Yang, Xiaohan, Ranjan, Priya, Tschaplinski, Timothy J., Ye, Chu-Yu, Li, Ting, Sterck, Lieven, Vanneste, Kevin, Murat, Florent, Soler, Marçal, Clemente, Hélène San, Saidi, Naijib, Cassan-Wang, Hua, Dunand, Christophe, Hefer, Charles A., Bornberg-Bauer, Erich, Kersting, Anna R., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Boyd, Alexander E., Liston, Aaron, Spatafora, Joseph W., Dharmwardhana, Palitha, Raja, Rajani, Sullivan, Christopher, Romanel, Elisson, Alves-Ferreira, Marcio, Külheim, Carsten, Foley, William, Carocha, Victor, Paiva, Jorge, Kudrna, David, Brommonschenkel, Sergio H., Pasquali, Giancarlo, Byrne, Margaret, Rigault, Philippe, Tibbits, Josquin, Spokevicius, Antanas, Jones, Rebecca C., Steane, Dorothy A., Vaillancourt, René E., Potts, Brad M., Joubert, Fourie, Barry, Kerrie, Pappas, Georgios J., Strauss, Steven H., Jaiswal, Pankaj, Grima-Pettenati, Jacqueline, Salse, Jérôme, Van de Peer, Yves, Rokhsar, Daniel S., and Schmutz, Jeremy. The genome of Eucalyptus grandis. United States: N. p., 2014. Web. doi:10.1038/nature13308.
Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Hellsten, Uffe, Hayes, Richard D., Grimwood, Jane, Jenkins, Jerry, Lindquist, Erika, Tice, Hope, Bauer, Diane, Goodstein, David M., Dubchak, Inna, Poliakov, Alexandre, Mizrachi, Eshchar, Kullan, Anand R. K., Hussey, Steven G., Pinard, Desre, van der Merwe, Karen, Singh, Pooja, van Jaarsveld, Ida, Silva-Junior, Orzenil B., Togawa, Roberto C., Pappas, Marilia R., Faria, Danielle A., Sansaloni, Carolina P., Petroli, Cesar D., Yang, Xiaohan, Ranjan, Priya, Tschaplinski, Timothy J., Ye, Chu-Yu, Li, Ting, Sterck, Lieven, Vanneste, Kevin, Murat, Florent, Soler, Marçal, Clemente, Hélène San, Saidi, Naijib, Cassan-Wang, Hua, Dunand, Christophe, Hefer, Charles A., Bornberg-Bauer, Erich, Kersting, Anna R., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Boyd, Alexander E., Liston, Aaron, Spatafora, Joseph W., Dharmwardhana, Palitha, Raja, Rajani, Sullivan, Christopher, Romanel, Elisson, Alves-Ferreira, Marcio, Külheim, Carsten, Foley, William, Carocha, Victor, Paiva, Jorge, Kudrna, David, Brommonschenkel, Sergio H., Pasquali, Giancarlo, Byrne, Margaret, Rigault, Philippe, Tibbits, Josquin, Spokevicius, Antanas, Jones, Rebecca C., Steane, Dorothy A., Vaillancourt, René E., Potts, Brad M., Joubert, Fourie, Barry, Kerrie, Pappas, Georgios J., Strauss, Steven H., Jaiswal, Pankaj, Grima-Pettenati, Jacqueline, Salse, Jérôme, Van de Peer, Yves, Rokhsar, Daniel S., & Schmutz, Jeremy. The genome of Eucalyptus grandis. United States. https://doi.org/10.1038/nature13308
Myburg, Alexander A., Grattapaglia, Dario, Tuskan, Gerald A., Hellsten, Uffe, Hayes, Richard D., Grimwood, Jane, Jenkins, Jerry, Lindquist, Erika, Tice, Hope, Bauer, Diane, Goodstein, David M., Dubchak, Inna, Poliakov, Alexandre, Mizrachi, Eshchar, Kullan, Anand R. K., Hussey, Steven G., Pinard, Desre, van der Merwe, Karen, Singh, Pooja, van Jaarsveld, Ida, Silva-Junior, Orzenil B., Togawa, Roberto C., Pappas, Marilia R., Faria, Danielle A., Sansaloni, Carolina P., Petroli, Cesar D., Yang, Xiaohan, Ranjan, Priya, Tschaplinski, Timothy J., Ye, Chu-Yu, Li, Ting, Sterck, Lieven, Vanneste, Kevin, Murat, Florent, Soler, Marçal, Clemente, Hélène San, Saidi, Naijib, Cassan-Wang, Hua, Dunand, Christophe, Hefer, Charles A., Bornberg-Bauer, Erich, Kersting, Anna R., Vining, Kelly, Amarasinghe, Vindhya, Ranik, Martin, Naithani, Sushma, Elser, Justin, Boyd, Alexander E., Liston, Aaron, Spatafora, Joseph W., Dharmwardhana, Palitha, Raja, Rajani, Sullivan, Christopher, Romanel, Elisson, Alves-Ferreira, Marcio, Külheim, Carsten, Foley, William, Carocha, Victor, Paiva, Jorge, Kudrna, David, Brommonschenkel, Sergio H., Pasquali, Giancarlo, Byrne, Margaret, Rigault, Philippe, Tibbits, Josquin, Spokevicius, Antanas, Jones, Rebecca C., Steane, Dorothy A., Vaillancourt, René E., Potts, Brad M., Joubert, Fourie, Barry, Kerrie, Pappas, Georgios J., Strauss, Steven H., Jaiswal, Pankaj, Grima-Pettenati, Jacqueline, Salse, Jérôme, Van de Peer, Yves, Rokhsar, Daniel S., and Schmutz, Jeremy. 2014. "The genome of Eucalyptus grandis". United States. https://doi.org/10.1038/nature13308.
@article{osti_1148848,
title = {The genome of Eucalyptus grandis},
author = {Myburg, Alexander A. and Grattapaglia, Dario and Tuskan, Gerald A. and Hellsten, Uffe and Hayes, Richard D. and Grimwood, Jane and Jenkins, Jerry and Lindquist, Erika and Tice, Hope and Bauer, Diane and Goodstein, David M. and Dubchak, Inna and Poliakov, Alexandre and Mizrachi, Eshchar and Kullan, Anand R. K. and Hussey, Steven G. and Pinard, Desre and van der Merwe, Karen and Singh, Pooja 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 Yang, Xiaohan and Ranjan, Priya and Tschaplinski, Timothy J. and Ye, Chu-Yu and Li, Ting and Sterck, Lieven and Vanneste, Kevin and Murat, Florent and Soler, Marçal and Clemente, Hélène San and Saidi, Naijib and Cassan-Wang, Hua and Dunand, Christophe and Hefer, Charles A. and Bornberg-Bauer, Erich and Kersting, Anna R. and Vining, Kelly and Amarasinghe, Vindhya and Ranik, Martin and Naithani, Sushma and Elser, Justin and Boyd, Alexander E. and Liston, Aaron and Spatafora, Joseph W. and Dharmwardhana, Palitha and Raja, Rajani and Sullivan, Christopher and Romanel, Elisson and Alves-Ferreira, Marcio and Külheim, Carsten and Foley, William and Carocha, Victor and Paiva, Jorge and Kudrna, David and Brommonschenkel, Sergio H. and Pasquali, Giancarlo and Byrne, Margaret and Rigault, Philippe and Tibbits, Josquin and Spokevicius, Antanas and Jones, Rebecca C. and Steane, Dorothy A. and Vaillancourt, René E. and Potts, Brad M. and Joubert, Fourie and Barry, Kerrie and Pappas, Georgios J. and Strauss, Steven H. and Jaiswal, Pankaj and Grima-Pettenati, Jacqueline and Salse, Jérôme and Van de Peer, Yves and Rokhsar, Daniel S. and Schmutz, Jeremy},
abstractNote = {Eucalypts are the world s most widely planted hardwood trees. Their broad adaptability, rich species diversity, fast growth and superior multipurpose wood, have made them a global renewable resource of fiber and energy that mitigates human pressures on natural forests. We sequenced and assembled >94% of the 640 Mbp genome of Eucalyptus grandis into its 11 chromosomes. A set of 36,376 protein coding genes were predicted revealing that 34% occur in tandem duplications, the largest proportion found thus far in any plant genome. Eucalypts also show the highest diversity of genes for plant specialized metabolism that act as chemical defence against biotic agents and provide unique pharmaceutical oils. Resequencing of a set of inbred tree genomes revealed regions of strongly conserved heterozygosity, likely hotspots of inbreeding depression. The resequenced genome of the sister species E. globulus underscored the high inter-specific genome colinearity despite substantial genome size variation in the genus. The genome of E. grandis is the first reference for the early diverging Rosid order Myrtales and is placed here basal to the Eurosids. This resource expands knowledge on the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.},
doi = {10.1038/nature13308},
url = {https://www.osti.gov/biblio/1148848}, journal = {Nature (London)},
issn = {0028-0836},
number = 7505,
volume = 510,
place = {United States},
year = {Wed Jun 11 00:00:00 EDT 2014},
month = {Wed Jun 11 00:00:00 EDT 2014}
}