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Researchers Sequence Leaf-cutter Ant Genome

By Andrea Anderson

NEW YORK (GenomeWeb News) – The obligate symbiotic relationship between a leaf-cutter ant species and the fungus it farms coincides with a loss of some nutrient acquisition genes and other changes to the ant's genome, a new sequencing study suggests.

An international research team used Roche 454 sequencing to take on the genome of the leaf-cutter ant Atta cephalotes — one of dozens of leaf-cutter species found in the New World tropics. In the process, they uncovered new genetic clues about the ant's lifestyle, caste system, and relationship with the fungus that it farms. The research appeared online last night in PLoS Genetics.

"The genome allows us to understand interactions in this insect-microbial system," co-corresponding author Cameron Currie, who is affiliated with the University of Wisconsin at Madison, the US Department of Energy's Great Lakes Bioenergy Research Center, and the Smithsonian Tropical Research Institute in Panama, said in a statement. "It improves our ability to understand the evolution of symbiosis and fungus farming in ants in a major way."

The study is the latest in a series of new ant genome projects: late last month, a trio of papers in the Proceedings of the National Academy of Sciences described efforts to sequence the Argentine, red harvester, and fire ant genomes.

Leaf-cutter ants are known for their obligate symbiotic relationships with fungi that they farm. Although there are hundreds of species of fungus-growing ants, Currie told GenomeWeb Daily News, only leaf-cutters actually cut, collect, and cart leaves along elaborate trails to their massive fungal gardens.

"Only the most derived groups of fungus growing ants are called the leaf-cutters and they form the really large colonies," he said. "There's a lot of diversity in fungus-growing ants and leaf-cutting ants."

For the current study, he and his colleagues focused on A. cephalotes, one of three Atta species found in Panama. Ants in this genus are known for producing very large colonies, Currie noted, and tend to show dramatic social structure, biology, and life history patterns.

Through the Roche Applied Sciences 10 Gigabase Sequencing program, the team used the Roche 454 GS FLX Titanium to sequence DNA libraries from three male leaf-cutter ants. They also used the same platform to sequence RNA pooled from nearly 200 worker ants to aid in annotation of the genome.

In the process, the researchers generated an estimated 18 to 20 times coverage of the ant's 300 million base genome, identifying 18,093 predicted protein-coding genes.

They then turned their attention to looking for genetic clues in the newly sequenced genome that might help explain A. cephalotes' relationship with its fungal symbiont.

"We looked in the genome for evidence of how this relationship might have changed the genome of the ant itself," co-corresponding author Garret Suen, a researcher affiliated with the University of Wisconsin at Madison and the DOE Great Lakes Bioenergy Research Center, told GWDN.

"We focused mainly on nutrition because that's the main role that we know of that the fungus is providing for the ants," Suen added. "The fungus feeds pretty much all of the developing brood in the colonies."

Indeed, the team's comparison between the leaf-cutter ant genome and sequences from bees, wasps, and other insects — as well as comparisons with some previously sequenced ant genomes — support the notion that some gene functions have been lost from the leaf-cutter ant genome, including serine protease enzymes and the pathway for producing the amino acid arginine.

On the other hand, Suen noted, the A. cephalotes genome appears to contain additional neuronal genes and an over-representation of certain genes that may contribute to caste development in these ants.

The researchers also detected some predicted genes with unknown functions, Suen explained, fueling speculation that some of these sequences could have roles in the ant's biology, caste development, communication with the fungus, and so on.

In the future, the team plans to continue exploring these and other interactions by studying each player in the leaf-cutter ant system — from the ant and its fungal symbiont to other microbes that seem to hinder or support this relationship.

"We're basically trying to get a community genome of the symbiosis that's more than just the two players," Suen said.

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