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USDA-Led Team Publishes Draft Genome of Bee Parasite

NEW YORK (GenomeWeb News) – In a paper appearing online today in PLoS Pathogens, researchers from the US Department of Agriculture, the University of Maryland, Columbia University, and Roche 454 Life Sciences reported that they have sequenced and analyzed the draft genome of Nosema ceranae, a honey bee-parasitizing microsporidian fungus found throughout Europe and North America.

Using pyrosequencing, the team sequenced the nearly eight million bases of the N. ceranae genome. Based on this sequence, they estimated that the genome contains more than 2,600 protein-coding genes — about half of which have homologs in Encephalitozoon cuniculi, a related microsporidian that parasitizes mammals. Along with providing insights into genes that may contribute to microsporidian virulence, those involved say the work sets the stage for future studies of Nosema and related pathogens.

N. ceranae, which belongs to a group of highly derived fungi called microsporidians, is an obligate parasite found in bee guts. It was originally detected in the Asian honey bee, Apis cerana, but made the jump to the European honey bee, A. mellifera, relatively recently. Over the past three or four years, N. ceranae has become widespread in North America, senior author Jay Evans, a researcher at the USDA-Agricultural Research Service's Bee Research Lab, told GenomeWeb Daily News.

Researchers suspect the parasite may contribute to — or exacerbate — colony collapse disorder, a mysterious condition that has dramatically reduced honey bee numbers in recent years, threatening the multi-billion dollar bee industry. Even so, there are several potential CCD culprits. And since N. ceranae has been detected in seemingly healthy colonies, Evans explained, it seems likely that other fungi and/or viruses are involved as well.

In an effort to better understand N. ceranae and its effect on bees, Evans and his team decided to sequence and assess the 7.86 million or so bases in the parasite's genome. To do this, they extracted DNA from N. ceranae spores in the guts of bees at a USDA-ARS Bee Research Laboratory colony in Maryland and used Roche 454 sequencing to sequence the genome.

Assembling the genome was tricky, lead author Scott Cornman, a post-doctoral researcher in Evans' lab, told GenomeWeb Daily News, because the genome has a strong bias toward A and T nucleotides. Roughly three-quarters of the N. ceranae genome is composed of A's and T's.

The genome also contained numerous homopolymer runs and repetitive elements. And in contrast to the microsatellite repeats detected in other types of fungi, Evans noted, the repeats in the N. ceranae genome tended to be longer and more similar to those seen in vertebrates.

The team's analysis suggests the N. ceranae genome contains about 2,614 protein-coding genes. Of these, roughly 1,366 are homologous to genes found in the parasite's closest sequenced relative, E. cuniculi.

When the researchers compared the N. ceranae and E. cuniculi genomes with that of a distantly related fungus — the yeast Saccharomyces cerevisiae — they found that the microsporidians resembled one another but were distinct from other yeast and fungi. Both microsporidian genomes contained fewer genes involved in transport and chemical response than free-living fungi, but more genes involved in growth-related processes.

But while they were able to find genes unique to microsporidians, so far the researchers don't have functional information that could help them tease apart which genes, if any, contribute to virulence in bees. "We're still kind of hacking through that," Evan said, noting that identifying such genes will likely require analyses of gene expression and activity levels associated with virulence.

He and his team are starting to do baseline experiments to determine which polymorphisms are the most variable and/or informative for tracking the parasite's migration and other traits. "We're thinking of the genome sequence really as a tool to start with," Evans said.

With the N. ceranae draft genome in hand, the researchers also have a template for assembling and investigating related genomes. "We have a prototype that we can now use to characterize other strains," co-author Ian Lipkin, director of the Columbia University Mailman School of Public Health's Center for Infection and Immunity, told GenomeWeb Daily News.

In the future, Evans and his team plan to try to use this and other data to try to figure out how N. ceranae moved so quickly into North American bees. They also hope to find new clues about genetic differences that might make some parasites more dangerous to honey bee colonies.

"The characterization of the N. ceranae genome presented here should advance our understanding and eventual mitigation of Nosema parasitism," the authors wrote. "The identification of conserved and novel genes and domains is an initial step in unraveling the many enigmatic aspects of Nosema-honey bee interactions."

The N. ceranae genome sequence and annotations are available online as Genome Project ID 32973 in Genbank.

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