2. Arthropod pests in the poultry industry

Background Adult house flies, Musca domestica L., are mechanical vectors of more than 100 devastating diseases that have severe consequences for human and animal health. House fly larvae play a vital role as decomposers of animal wastes, and thus live in intimate association with many animal pathogens. Results We have sequenced and analyzed the genome of the house fly using DNA from female flies. The sequenced genome is 691 Mb. Compared with Drosophila melanogaster, the genome contains a rich resource of shared and novel protein coding genes, a significantly higher amount of repetitive elements, and substantial increases in copy number and diversity of both the recognition and effector components of the immune system, consistent with life in a pathogen-rich environment. There are 146 P450 genes, plus 11 pseudogenes, in M. domestica, representing a significant increase relative to D. melanogaster and suggesting the presence of enhanced detoxification in house flies. Relative to D. melanogaster, M. domestica has also evolved an expanded repertoire of chemoreceptors and odorant binding proteins, many associated with gustation. Conclusions This represents the first genome sequence of an insect that lives in intimate association with abundant animal pathogens. The house fly genome provides a rich resource for enabling work on innovative methods of insect control, for understanding the mechanisms of insecticide resistance, genetic adaptation to high pathogen loads, and for exploring the basic biology of this important pest. The genome of this species will also serve as a close out-group to Drosophila in comparative genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0466-3) contains supplementary material, which is available to authorized users.

Stomoxys flies are mechanical vectors of pathogens present in the blood and skin of their animal hosts, especially livestock, but occasionally humans. In livestock, their direct effects are disturbance, skin lesions, reduction of food intake, stress, blood loss, and a global immunosuppressive effect. They also induce the gathering of animals for mutual protection; meanwhile they favor development of pathogens in the hosts and their transmission. Their indirect effect is the mechanical transmission of pathogens. In case of interrupted feeding, Stomoxys can re-start their blood meal on another host. When injecting saliva prior to blood-sucking, they can inoculate some infected blood remaining on their mouthparts. Beside this immediate transmission, it was observed that Stomoxys may keep some blood in their crop, which offers a friendly environment for pathogens that could be regurgitated during the next blood meal; thus a delayed transmission by Stomoxys seems possible. Such a mechanism has a considerable epidemiological impact since it allows inter-herd transmission of pathogens. Equine infectious anemia, African swine fever, West Nile, and Rift Valley viruses are known to be transmitted by Stomoxys, while others are suspected. Rickettsia (Anaplasma, Coxiella), other bacteria and parasites (Trypanosoma spp., Besnoitia spp.) are also transmitted by Stomoxys. Finally, Stomoxys was also found to act as an intermediate host of the helminth Habronema microstoma and may be involved in the transmission of some Onchocerca and Dirofilaria species. Being cosmopolite, Stomoxys calcitrans might have a worldwide and greater impact than previously thought on animal and human pathogen transmission.