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House Fly Genome Deciphered in Hunt for Pest, Pathogen Control Clues

NEW YORK (GenomeWeb) – A Cornell University-led team has sequenced and started analyzing the genome of the domestic house fly, Musca domestica, in the hopes of detecting genetic clues for dealing with the pest and pathogens it carries.

As they reported online today in Genome Biology, the researchers pooled genomic DNA from half a dozen female house flies, using it as a template to generate sequence reads that were then assembled into a 691 million base M. domestica genome.

By spelling out protein-coding genes in the genome and comparing the house fly sequence to that of the fruit fly, Drosophila melanogaster, the team has endeavored to unravel genetic factors coinciding with house fly features. For example, the M. domestica genome housed almost 150 cytochrome P450 enzyme-coding genes, consistent with a potentially bolstered detoxification system in the house fly.

"The house fly genome provides a rich resource for enabling work on innovative methods of insect control, for understanding the mechanisms of insecticide resistance, and genetic adaptation to high pathogen loads, and for exploring the basic biology of this important pest," corresponding author Jeffrey Scott, an entomology researcher at Cornell University, and his colleagues wrote.

Beyond their reputation as pests, house flies are known to act as a vector for transmitting parasitic bacteria, protozoa, viruses, and worms that cause a range of diseases in humans, livestock, and other animals, the researchers explained. For instance, they noted that house flies have been implicated in the spread of more than 100 infectious diseases, including cholera, amebic dysentery, eye infections, and leprosy.

"The mobility of house flies, their regular contact with excreta, carcasses, garbage, and other septic matter, and intimate association with animal pathogens and humans, all contribute to their roles in transmission of these diseases," Scott and his co-authors wrote.

Still, the team highlighted the important contributions fly larvae make in decomposing organic material — notably animal waste and byproducts. The fly's unusual attributes are of interest in other areas, too. For example, Scott noted that a better understanding of fly features could aid studies in fields such as developmental biology, physiology, and toxicology.

Of interest to those studying sex determination, for example, the house fly carries X and Y sex chromosomes, with the Y chromosome containing a male-determining "M" factor in the ancestral sex determination system. But maleness can also be achieved by tucking the M factor sequence away in one of the house fly's five autosomal chromosomes, too — and the sex determination has undergone even more subtle tweaks in various fly populations, the study's authors explained.

Moreover, given its ability to carry various pathogens without obvious detriments and to develop resistance to many of the insecticides that humans hurl at them, the house fly's genetic sequence is expected to offer hints about how it achieves these apparent forms of immunity.

To explore the genetics of these and other fly features, the researchers sequenced pooled genomic DNA from six adult female house flies belonging to an inbred strain called aabys. They also used Illumina's HiSeq 2000 instrument to do transcriptome sequencing on tissue samples from house fly adults and larvae.

Using these DNA and RNA sequences, the team put together — and annotated — a 691 million base assembly that spans more than three-quarters of the fly's complete genome sequence and contains an estimated 14,810 protein-coding genes. While most of those resembled genes described in Drosophila, some 1,934 genes appeared to be specific to the house fly lineage.

Relative to the fruit fly, the house fly genome contained far more repetitive sequence elements and copy number variants, the researchers noted, along with an especially robust representation of immune system components.

The house fly genome contained sequences for some 771 apparent immune-related genes, for example, including 355 that are not homologous to Drosophila immune genes. Members of the immune pathways appeared prone to copy number increases as well.

The team also found 146 different P450 cytochrome genes, along with genes coding for several other enzymes participating in metabolic processes that break down and detoxify drugs and other potentially dangerous compounds.

Consistent with their role as scent-based waste scavengers, the house flies had higher-than-usual representation by chemoreceptor and odorant-related genes in their genome, authors of the study noted.

The sequence data offered a peek at other fly features as well — from sex determination and sex-biased gene expression to house fly gene regulation. In the future, those involved in the work said the new genome is poised to inform studies of related species as well.

In particular, the study's authors noted that the availability of both the fruit fly and house fly genomes may help in annotating the genomes of mosquito species as they are sequenced.

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