Eucalyptus genome successfully sequenced

The genetic blueprint of the Eucalyptus grandis (flooded gum) has been sequenced for the first time. The five-year effort to analyse the 640 million base-pair genome was conducted by 80 researchers from 30 institutions across 18 countries.

Eucalypts are the world’s most widely planted hardwood trees, grown in 100 countries across six continents, with their beneficial properties including wide adaptability, extremely fast growth and complex oil production. The trees help contribute to koala preservation, pest damage minimisation and antiseptic production, and are also used for timber, pulp and paper production.

The sequencing 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 (ORNL), 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.

South Africa’s Department of Science and Technology (DST), together with forestry companies Sappi and Mondi, funded the construction of the genome map used as a scaffold for genome assembly, as well as the sequencing of expressed genes used for annotation of the genome. The results were published in the journal Nature and the genome data are available through the DOE JGI’s comparative plant genomics portal Phytozome.

Dario Grattapaglia, Zander Myburg and Jerry Tuskan pose in front of Eucalyptus regnans in Tasmania. Image credit: Zander Myburg.

“We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis,” the researchers said, and discovered over 36,000 genes - almost double the number of genes in the human genome. The team’s analysis 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 the tree may have followed an evolutionary path that highlighted specific genes for woody biomass production.

The researchers also identified 113 genes responsible for synthesising terpenes - hydrocarbons which serve as chemical self-defences against pests, as well as providing the aromatic essential oils used in medicinal cough drops and in industrial processes. Furthermore, they found that among the family of terpene compounds naturally produced in plants and in particularly high abundance in Eucalyptus trees, derivatives of sesquiterpenes that contain 15 carbon atoms may be promising alternatives for petroleum-based fuels. Researchers have already made important breakthroughs in engineering aspects of terpene biosynthesis into microbes such as bacteria and yeast.

“This means that in future we could use specially selected Eucalyptus genes in bacteria and yeasts, turning them into bio-factories to manufacture advanced biofuels on a large scale,” Myburg said.

Tuskan added, “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.”

The researchers were particularly interesting in those genes which may influence the production of ‘chemical cellulose’ - 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, while the remaining biomass primarily comprises a glue-like material called lignin. The 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,” said Myburg.

“We have a keen interest in how wood is formed,” said Tuskan. “A major determinant of industrial processing efficiency lies in the composition and cross-linking of biopolymers in the thick secondary cell walls of woody fibres. 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.”

“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,” said Grattapaglia. “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.”

The extensive catalogue of genes contributed by the team will allow breeders to adapt Eucalyptus trees for sustainable energy production in regions where they cannot currently be grown.

“And, with this new knowledge about the molecular basis for superior growth and specific adaptations in plants, we can apply the same techniques to other woody plants that can be used as feedstock in the bio-economy of the future,” said Myburg.