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Genome Project Aims to Shed Light on Lichens

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Not counting a dedicated few researchers, it is probably safe to say most people could go months without ever thinking about a lichen or picking up the latest copy of The Lichenologist. For the uninitiated, lichens are symbiotic entities made up of a fungus and a photobiont, which is commonly a strain of green algae. They are incredibly diverse and are so adaptable that they can even survive unprotected in space for days at a time.

One researcher trying to apply genomics to lichenology is Daniele Armaleo, an associate professor at Duke University, who is helping to direct a project that aims to sequence an entire lichen genome within two years. With seed funding from the Institute for Genomic Sciences and Policy at Duke, Armaleo and his colleagues recently kicked off efforts to unveil more about lichens and, in the process, hopefully shed some light on other symbiotic systems of interest to the genomics community.

"It's a symbiosis, so it's a system in which two completely separate organisms are interacting with one another to form a new entity," says Armaleo. "And the interaction between lichen fungi and lichen algae is evolutionarily connected with the interaction between plant pathogenic fungi and their hosts." They therefore hope the project will help offer insight into how other fungi become parasitic to plants.

One difficulty in sequencing a lichen "genome" is due to the fact that natural lichens are an assembly of multiple organisms, and therefore multiple genomes. When wild lichens are ground up for DNA extraction, the result is a mix of not only both symbionts together, but also DNA from other organisms that grow in and around the lichen. That is why Armaleo is working with Cladonia grayi, a lichen species whose symbionts can be teased apart and grown separately in pure lab cultures. "To start a genome project using a wild lichen is a very difficult and tricky endeavor, whereas if you're starting from pure cultures in the lab we know exactly what sequences come from whom," he says. "So the fact we were able to cultivate these things in the lab is an advantage over other lichens."

The fact that lichens, which to date include more than 15,000 known species, also take a really long time to grow doesn't help matters, although Armaleo's Cladonia strain is more forgiving. According to Armaleo, because the researchers are trying to understand how the symbionts relate to each other and how they construct the lichen itself, culturing samples in the lab is a less than ideal experimental scenario. "When you actually grow them separately from one another in the lab, they are not particularly exciting. They're just little green colonies on a petri dish and the fungus forms little brown colonies on a petri," he says. "The lichen is very difficult to reconstruct in the laboratory, but when the symbionts get together in the wild they produce this very complex structure and organism with differentiations."

And because these organisms have been coevolving in intimate contact for more than 100 million years, Armaleo expects that some gene transfer has taken place. So far, initial sequencing work has helped confirm this idea. He and his team managed to find in the lichen fungus a few genes that were not similar to genes of other fungi but were similar to genes from photosynthetic organisms. They turned out to be ammonium transporter genes, responsible for getting ammonia into cells. "So although this is very preliminary, it seems pretty convincing that it is possible that these genes came from the photosynthetic partner of the lichen. They are definitely not typical fungal genes; they have come from some photosynthetic organisms and our bet is now that it is of course the organisms with which the lichen is or used to be associated," he says. "This was something that we were looking for."

 

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