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International Team Sequences Three Parasitoid Wasp Genomes

NEW YORK (GenomeWeb News) – Members of the Nasonia Genome Working Group reported online today in Science that they have sequenced and compared the genomes of three parasitoid wasp species belonging to the genus Nasonia.

The researchers used Sanger and Illumina methods to sequence the N. vitripennis, N. giraulti, and N. longicornis genomes. So far they have identified genes believed to contribute to everything from diet to venom production.

In addition, their analyses have uncovered other intriguing Nasonia genome features, including DNA methylation machinery, evidence of lateral gene transfer from bacteria and viruses, and rapid evolution of mitochondrial sequence and genes involved in interactions between the nucleus and mitochondria.

And, researchers say, the genome data is enhancing Nasonia's potential as a genetically tractable model organism.

"[Nasonia] is particularly useful for doing what we call the genetics of complex traits," co-lead author John (Jack) Werren, a biologist at the University of Rochester, told GenomeWeb Daily News. "By sequencing all three [species] it gives us a lot of powerful genetic tools."

Nasonia are cheap, easy to work with, and have short generation times, Werren explained. And although they're multi-cellular and relatively complex, males carry a single copy of the genome — a feature that simplifies genetic studies.

"Haploid genetics assist efficient genotyping, mutational screening, and evaluation of gene interactions (epistasis) without the added complexity of genetic dominance," the researchers wrote.

Along with their potential as a model organism, Werren and his co-workers explained, Nasonia species also have interesting — and useful — lifestyles. The wasps lay eggs in or on other insects, mites, and ticks. After these eggs hatch, the larvae feed on — and eventually kill — the host. Consequently, some parasitoid species are already used to help control certain pest insects.

In an effort to characterize Nasonia genomes, the team started out using Sanger sequencing to sequence the nearly 240 million base genome of an inbred N. vitripennis line to about six times coverage. They then sequenced the other two Nasonia species to one fold coverage with Sanger and about 12 times coverage with Illumina, aligning these to the N. vitripennis genome.

In addition, the team developed inter-species Nasonia crosses that they used to help put together sequence scaffolds, find mutations, and identify inter-species quantitative trait loci for everything from wing size and host preference to reproductive patterns.

Although a type of bacterium called Wolbachia usually lives inside the wasps, causing sexual incompatibility between different Nasonia species, the team eliminated this hurdle to cross breeding by treating the wasps with antibiotics.

Their subsequent analyses suggest some 60 percent of Nasonia genes are orthologous to human genes, while 18 percent are specific to arthropods and another 2.4 percent are specific to the Hymenoptera order, which also includes insects such as bees. Meanwhile, they report, 12 percent of the genes are either found in Nasonia alone or have uncertain orthology.

In general, they found that the parasitoid wasp genomes contain a slew of transposable elements, dozens of known and predicted microRNAs, as well as all of the machinery needed for DNA methylation.

Along with Nasonia's other features, this DNA methylation toolkit further recommends the wasp species as model organisms, Werren noted, though he said more research is needed to determine whether DNA methylation has a regulatory role in Nasonia.

By comparing the three Nasonia genomes to one another, the researchers narrowed in on genetic features related to species differences, speciation processes, and phylogenetic relationships between the wasps. These comparisons, combined with cross breeding experiments, also turned up evidence of rapid evolution in Nasonia's mitochondrial DNA and genes involved in interactions between the nucleus and mitochondria.

In addition, the team found patterns in the Nasonia genome that are consistent with recent lateral gene transfer, suggesting the wasps have swapped sequences with both Wolbachia bacteria and Pox viruses.

In the future, Werren predicted, such genetic and genomic information about Nasonia will likely have applications on several fronts. For instance, he noted, such tools are expected to improve Nasonia's usefulness as both a genetic model organism and an agent for controlling insect pests.

"[I]f we can harness their full potential, they would be vastly preferable to chemical pesticides, which broadly kill or poison many organisms in the environment, including us," Werren said in a statement.

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