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[naturenews] from [nature.com]

[naturenews]
Published online 18 September 2009 | Nature | doi:10.1038/news.2009.928
News
Fungus genome boosts fight to save North American forests
DNA sequence could advance efforts to control pine beetle infestations.
By Elie Dolgin

The pine beetle is at the centre of a sustained sequencing effort.Ron Long, Simon Fraser University, Bugwood.orgCanadian researchers have decoded the DNA of the tree-killing fungus found in the mouths of mountain pine beetles, the destructive bugs that wipe out entire North American forests. Further genome sequencing of the beetle and pine tree species should help forest managers design better pest-control tactics, the authors say.

"It's really getting to a systems-level understanding of the mountain pine beetle epidemic," says study co-author Jörg Bohlmann, a chemical ecologist at the University of British Columbia in Vancouver, Canada, who is leading the Can$11.9m (US$11.1m) multi-species genome initiative. "What really happens in nature is not confined to one species, but is happening at the intersection when one species interacts with another."

Mountain pine beetles (Dendroctonus ponderosae) have eaten their way through vast swathes of western North American pine forests, including around 15 million hectares in British Columbia alone. As the burrowing beetles tunnel under the bark to feed and lay eggs, they release spores of the blue-stain fungus (Grosmannia clavigera), which stops the production of a protective toxic resin released by the tree and allows the beetles to continue to infest.

Dynamic decoding

Bohlmann and his colleagues assembled the fungus's 32.5-million-base-pair genome, which is around a hundredth the size of the human genome, using a combination of next-generation and traditional sequencing technologies — the first time that a complex eukaryotic organism has been sequenced from scratch using such a hybrid approach and then published in a peer-reviewed journal. The genome was reported online this month in the journal Genome Biology1.

"They've done a very careful analysis of what factors contribute to the different types of quality you can get" with next-generation sequencing, says Steve Rounsley, a genome researcher at the University of Arizona in Tucson, who was not involved in the study.

{“It's really going to push science in a big way.”
Brian Aukema
Canadian Forestry Service}

For the other two species — the beetle and the tree — the researchers are concentrating mainly on expressed gene sequences, fragments of the complete DNA sequence, rather than the genomes in their entirety. They've already amassed one of the largest insect libraries of gene transcripts for the bark beetle from more than a dozen beetle life stages and body parts. The lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana) are still at a much earlier stage of sequencing.

The goal, says Dezene Huber, a chemical ecologist at the University of Northern British Columbia in Prince George, Canada, is to predict the dynamics between the organisms under various climatic conditions. "We should be able to look at particular genes and say which population of trees is interacting with which population of fungus and which population of beetles," he says.

"It's really going to push science in a big way," says Brian Aukema of the Canadian Forestry Service in Prince George, who plans to incorporate the genomic data into landscape ecological models. "Once you have that information, you can hopefully feed that into models and understand where these beetle populations might be the most susceptible to treatments, intervention strategies and mitigation."

Fungal blues

Multi-species genomic interactions have been studied for some human diseases, including malaria, and a few symbiotic ecological relationships such as leaf-cutter ants and their microbial partners, but the approach has never before been applied on this scale for an outbreaking forest nuisance.

Already, the University of British Columbia researchers, led by mycologist Colette Breuil, have taken the fungus genome, pinpointed the gene responsible for staining the pine wood blue and created a knockout strain that does not produce any pigment. The blue staining reduces the commercial value of affected timber, but it is not clear what role the colouring plays in driving infestation. The researchers are now testing this strain to tease that apart.

But the full utility of the fungus genome might only be realized after other related species are also sequenced, says Diana Six, who studies the interaction between bark beetles and fungi at the University of Montana in Missoula. Comparing the blue-stain fungus with free-living or pathogenic fungi will shed light on how the beneficial fungus helps the beetles thrive, she says. "You need more than one [genome] to do that."

Using genomics to stop the bark beetles is a "bit of a long shot, for sure", admits Chris Keeling, a research associate in Bohlmann's lab. But it might offer the best strategy for containing the forest pests, which have already started to jump host species from lodgepole pine, which is found only west of the Rockies, to jack pine, which stretches east across the entire continent. "We might be able to tweak the system to reduce the beetle populations or prevent them from spreading further east," Keeling says.

References
1. DiGuistini, S. et al. Genome Biol. 10, R94 (2009) available online at http://genomebiology.com/2009/10/9/R94.