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International team sequences Eucalyptus genome; potential for improving biofuel and biomaterial production
14 June 2014
An international team of researchers has sequenced the genome of the eucalyptus tree (Eucalyptus grandis) and published the analysis in an open access paper in the journal Nature. With its prodigious growth habit, the eucalyptus tree, one of the world’s most widely planted hardwood trees, has the potential to enhance sustainable biofuels and biomaterials production, and to provide a stable year-round source of biomass that doesn’t compete with food crops.
The researchers reported the sequencing and assembly of more than 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, which can be substituted catalytically for jet fuel.
By having a library of these genes that control the synthesis of terpenes we are able to dissect which genes produce specific terpenes; then we can modify this biochemical pathway in the leaves so that we can develop the potential of Eucalyptus as an alternative source feedstock for jet fuel.—Gerald Tuskan, Oak Ridge National Laboratory
The international effort to sequence and analyze the genome of Eucalyptus grandis engaged more than 80 researchers from 30 institutions, representing 18 countries. The project was led by Alexander Myburg of the University of Pretoria (South Africa); Dario Grattapaglia of the Brazilian Agricultural Research Corporation (EMBRAPA) and Catholic University of Brasilia; Gerald Tuskan of the Oak Ridge National Laboratory and the BioEnergy Science Center and US Department of Energy Joint Genome Institute (DOE JGI); Dan Rokhsar of the DOE JGI and Jeremy Schmutz of the DOE JGI and the HudsonAlpha Institute for Biotechnology.
|“A major challenge for achieving a sustainable energy future is our understanding of the molecular basis of superior growth and adaptation in woody plants suitable for biomass production.” |
Trees play a significant role in the global carbon cycle. Collectively, they represent a major terrestrial repository of carbon and play both active CO2 capture and processing and passive storage roles. With these advantages in mind, Eucalyptus can be harvested from tropical and temperate zones and has more than 700 species that are rich in genetic variation.
Because of its wide adaptability, extremely fast growth rate and excellent wood and fiber properties, Eucalyptus trees, while native to Australia, are grown in 100 countries across six continents and account for over 40 million acres. Eucalyptus trees are planted worldwide mostly for the value of its wood; for the Department of Energy, their energy-rich cellulosic biomass makes them one of the principal candidate biomass energy crops.
Combing through the 36,000-plus genes found in Eucalyptus (nearly twice as many as in the human genome), the researchers homed in on those that may influence the production of secondary cell wall material that can be processed for pulp, paper, biomaterials and bioenergy applications.
Approximately 80% of the woody biomass in a Eucalyptus is made of cellulose and hemicellulose, both long chains of sugars, with the remaining biomass primarily comprised of lignin.
We have a keen interest in how wood is formed. A major determinant of industrial processing efficiency lies in the composition and cross-linking of biopolymers in the thick secondary cell walls of woody fibers. Our analysis provides a much more comprehensive understanding of the genetic control of carbon allocation towards cell wall biopolymers in woody plants—a crucial step toward the development of future biomass crops.—Gerald Tuskan
Our comparative analysis of the complex traits associated with the Eucalyptus genome and other large perennials offers new opportunities for accelerating breeding cycles for sustainable biomass productivity and optimal wood quality. In addition, insights into the trees’ evolutionary history and adaptation are improving our understanding of their response to environmental change, providing strategies to diminish the negative environmental impacts that threaten many species.—Dario Grattapaglia
The eucalyptus team identified genes encoding 18 final enzymatic steps for the production of cellulose and the hemicellulose xylan, both cell wall carbohydrates that can be used for biofuel production.
By tracing their evolutionary lineages and expression in woody tissues we defined a core set of genes as well as novel lignin-building candidates that are highly expressed in the development of xylem—the woody tissue that helps channel water throughout the plant—which serves to strengthen the tree.—Alexander Myburg
The team’s detailed analysis of the Eucalyptus genome revealed an ancient whole-genome duplication event estimated to have occurred about 110 million years ago, as well as an unusually high proportion of genes in tandem duplicate arrays. Their results, Tuskan said, highlight the major role of the phenomenon of tandem replication in shaping functional diversity in Eucalyptus and suggest that Eucalyptus may have followed an evolutionary path that highlighted specific genes for woody biomass production.
By comparison, Eucalyptus has three times the number of tandem repeat genes present in poplar, the first tree sequenced (by the DOE JGI and published on the cover of the journal Science in 2006).
The genetic architecture of inbreeding depression, often referred to as the converse of hybrid vigor, is largely unknown for trees and was also tackled in the study.
This poses a barrier to their rapid domestication and breeding improvements by way of self-pollination. Our results in Eucalyptus suggest that cumulative effects of many small genetic variants throughout the genome are responsible for these fundamental genetic phenomena. Favorably combined, they determine the height of a tree, which is one of our gauges for overall fitness.—Dario Grattapaglia
The extensive catalog of genes contributed by the team will allow breeders to adapt Eucalyptus trees for sustainable energy production in regions, such as the US Southeast, where it cannot currently be grown.
The Eucalyptus genome data are available publicly through the DOE JGI’s comparative plant genomics portal known as Phytozome, now in its 10th revision.
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 et al. (2014) “The genome of Eucalyptus grandis,” Nature doi: 10.1038/nature13308
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