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Fungal Symbiont Genome Sequence Hints at Secrets of Tree Relationships

NEW YORK (GenomeWeb News) - An international research group has sequenced the largest fungal genome yet, revealing the genetics behind the fungus’ symbiotic relationships with its tree hosts.
 
Researchers at the National Institute for Agricultural Research in Nancy, France, the US Department of Energy’s Joint Genome Institute, and elsewhere sequenced the genome of a fungus called Laccaria bicolor, which has symbiotic relationships with a number of tree species.
 
The findings, published this week in Nature today, reveal a complex genome with some features not previously seen in fungi. They also provide insight into the way L. bicolor draws nutrients from its host without damaging it.
 
Tree roots and soil fungi often team up underground in a process called mycorrhizal symbiosis, which benefits both organisms. In general, these “good” fungi help trees take up sometimes-scarce nutrients — in particular, phosphates and nitrogen. They may also protect the roots from harmful microbes. In return, the roots provide the fungi with carbon in the form of sugars. Roughly 85 percent of trees depend on some form of mycorrhizal symbiosis.
 
For this study, researchers focused on L. bicolor, a symbiotic fungus commonly found in North American birch, fir, and pine forests. It frequently forms symbiotic relationships with poplar, a tree whose genome has also been sequenced.
 
Lead author Francis Martin, a research physiologist with INRA, told GenomeWeb Daily News that they chose this species not only for its ecological relevance — L. bicolor is associated with many kinds of seedling and full-grown conifers and hardwood trees — but also because it’s easy to grow in the lab. The fungus is also commercially relevant, since it is used in tree nurseries in Europe and North America to bolster plant growth rate and overall vigor.
 
Martin and his colleagues sequenced the 65 million base pair L. bicolor genome at DOE’s JGI. They identified roughly 20,000 protein-coding genes, many belonging to expanded gene families. Some appear to have roles in processes such as protein-protein interactions and signal transduction, while others have yet-unknown functions.
 
“I think the most striking result is that you have many, many multigene families,” Martin said. He speculated that these new families may hold the keys to understanding the fungus’ symbiotic relationships with trees. For instance, the L. bicolor genome contains genes coding for a group of small secreted proteins. Similar fungal SSPs have been turning up over the past few years, but they’re usually associated with the “bad guys,” fungal pathogens.
 
“I didn’t expect to find that kind of SSP in the good guy — the symbiont,” Martin said.
 
As well, it seems L. bicolor has genes coding for hydrolytic enzymes that let it break down the cell walls of parasitic microorganisms, but lacks many of the cellulose enzymes that break down tree cell walls. This means the fungus can help with plant defenses, breaking invaders’ cell walls, leaving root cell walls unscathed. But this may also drive the fungi to plants, Martin said, if they have “no choice but to get to the plants to suck the carbon.”
 
The team was also surprised to find a large number of transposable elements — some 21 percent of the genome. This was unexpected, as this sort of repeated sequence with the ability to “jump” is relatively rare in the fungal genomes sequenced so far. It also complicated sequencing.
 
“We had troubles,” Martin said. “It was really a pain in the neck to have all the transposable elements.” To get around this problem, the team relied on two assembly programs, JGI’s in-house program Jazz as well as Arachne, genome assembly software used at the Broad Institute.
 
They also used NimbleGen custom oligoarrays to see whether predicted L. bicolor genes were expressed — and where. For instance, L. bicolor seems to preferentially express and secrete these SSP molecules in places where the fungus comes in contact with roots.
 
In the future, Martin hopes that sequencing more symbionts and comparing their genomes with those of fungal pathogens may uncover genetic markers associated with the most useful fungal symbionts. If so, this could help researchers build an understanding of the way trees and “good” fungi communicate and function interdependently. As well, such work could pinpoint the most promising naturally occurring symbionts for enhancing tree growth.