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International Team Reports on Initial Findings from Eucalyptus Genome

NEW YORK (GenomeWeb News) – In a study published online today in Nature, an international team led by investigators in the US, South Africa, Brazil, and Australia presented initial findings from the newly sequenced eucalyptus tree genome.

Using Sanger sequencing, the researchers produced a reference genome for Eucalyptus grandis, a species of eucalyptus tree commonly known as flooded gum, rose gum, or gum trees. After annotating the genome, they compared the genome to sequences from forest trees and domesticated woody plants and re-sequenced plants from both E. grandis and a sister species grown in temperate climates.

Such data made it possible for the team to take a look back at evolutionary events shaping the eucalyptus genome, while tracking down sequences important to eucalyptus traits of interest — from the plant's fast-growing hardwood to its essential oils.

"Now that we understand which genes determine specific characteristics in these trees, we can breed trees that grow faster, have higher quality wood, use water more efficiently and will cope better with climate change," corresponding author Zander Myburg, with the University of Pretoria, said in a statement. "Even more, we can turn well-managed Eucalyptus plantations into bio-factories to produce specific kinds of sought-after materials and chemicals."

Hundreds of eucalyptus tree species have been identified so far. The hardwood trees — which are native to Australia, but now grown in temperate and tropical zones — are widely cultivated for use in the pulp, paper, and timber industries. Eucalyptus plants have also attracted interest as potential biofuel sources, the study authors noted. And the essential oils they produce are already used in medical or industrial settings.

For their genome sequencing effort, the researchers used whole-genome Sanger sequencing to analyze genomic DNA from an E. grandis representative belonging to the BRASUZI genotype produced by self-crossing eucalyptus plants for a generation to decrease heterogeneity in the genome.

Using those sequences, together with bacterial artificial chromosome sequences and a genetic linkage map, the team put together an E. grandis genome assembly that spans more than 94 percent of the plant's predicted 640 million base sequence at an average depth of nearly seven-fold.

To that, they added RNA sequences representing different eucalyptus tissue types and developmental stages. The genomes of a sub-tropical representative from E. grandis BRASUZI and a temperate eucalyptus species called E. globulus were re-sequenced with Illumina instruments.

With the help of E. grandis transcriptome sequences, the team annotated the genome, identifying 36,376 predicted protein-coding eucalyptus genes. Around one-third of those turned up in sequences stemming from tandem duplications, highlighting the importance of repeat sequences in the genome.

By comparing the plant's sequences and gene content to those found in 17 other plant species, the researchers got a look at relationships between the plants as well as genetic insights into characteristic eucalyptus features.

For example, the team saw signs of a whole-genome duplication event in the eucalyptus lineage that it pegged at roughly 110 million years ago, around the time that Australia became isolated from other landmasses.

As part of their analysis of distinctive eucalyptus features, the researchers found a varied set of genes involved in producing pest-deterring compounds such as terpenes and other metabolites in the plant's aromatic oils.

They also narrowed in on genes involved in producing the sugar-based cellulose and hemicellulose compounds in the cell wall material that are held together by lignin and make up the plant's woody biomass. Those included genes suspected of participating in 18 enzymatically controlled steps that lead to the formation of cellulose and a hemicellulose compound called xylan.

"We have a keen interest in how wood is formed," Oak Ridge National Laboratory's Jerry Tuskan, co-author on the study, said in a statement. He noted that the biopolymer composition and cross-linking in the secondary cell walls of woody fibers in such plants is particularly important to efficiently processing the material in an industrial setting, for example.

"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," Tuskan said.