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Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment.

Scott JG, Warren WC, Beukeboom LW, Bopp D, Clark AG, Giers SD, Hediger M, Jones AK, Kasai S, Leichter CA, Li M, Meisel RP, Minx P, Murphy TD, Nelson DR, Reid WR, Rinkevich FD, Robertson HM, Sackton TB, Sattelle DB, Thibaud-Nissen F, Tomlinson C, van de Zande L, Walden KK, Wilson RK, Liu N - Genome Biol. (2014)

Bottom Line: 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.Relative to D. melanogaster, M. domestica has also evolved an expanded repertoire of chemoreceptors and odorant binding proteins, many associated with gustation.The genome of this species will also serve as a close out-group to Drosophila in comparative genomic studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA. jgs5@cornell.edu

ABSTRACT

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.

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Tep phylogeny. Maximum likelihood amino acid phylogeny of D. melanogaster and M. domestica Teps. D. melanogaster proteins are labeled Tep1 to Tep5. M. domestica Teps are labeled XP_NNNNNNNNN and are shown in italics. For both species, multiple isoforms of the same gene are indicated with a bar. Branch support is the SH-like statistic estimated in phyml. The tree is rooted so as to minimize the number of duplications.
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Fig1: Tep phylogeny. Maximum likelihood amino acid phylogeny of D. melanogaster and M. domestica Teps. D. melanogaster proteins are labeled Tep1 to Tep5. M. domestica Teps are labeled XP_NNNNNNNNN and are shown in italics. For both species, multiple isoforms of the same gene are indicated with a bar. Branch support is the SH-like statistic estimated in phyml. The tree is rooted so as to minimize the number of duplications.

Mentions: In contrast to the signaling pathways, both recognition and effector components of the immune system show substantial increases in copy number and genic diversity in M. domestica compared with D. melanogaster, suggesting the possibility that M. domestica possesses a more robust immune response to diverse pathogens encountered in the pathogen-rich environment in which it lives. In other insects, a variety of cell-surface and secreted proteins involved in recognition of pathogens have been identified, including peptidoglycan recognition proteins and beta-glucan binding proteins (also known as GNBPs in Drosophila), which are upstream of the main signaling pathways [44], and a variety of receptors likely involved in phagocytosis, including Nimrods, thioester-containing proteins (Teps) and scavenger receptors [45,46]. Of these, there are striking expansions in copy number of Nimrods and Teps in particular. The Nimrod gene family is one of the more variable in copy number among the sequenced Drosophila species [47], a trend that is continued in the more divergent comparison to M. domestica (17 Nim-containing proteins in M. domestica and 11 in D. melanogaster; only 8.7% of gene families have a greater degree of expansion in M. domestica). Even more striking is the expansion of the Tep family (FigureĀ 1), which has 19 members in M. domestica and only 6 in D. melanogaster. The Tep1/2 gene family specifically has expanded dramatically in M. domestica: this family has 2 members in D. melanogaster but 16 members in M. domestica, which is the 15th largest species-specific expansion in the M. domestica genome (Additional file 1). In addition, the M. domestica genome contains three lineage-specific genes that encode proteins with Tep-like domains (identified by HMM), but which are not clearly homologous to any characterized D. melanogaster Teps.Figure 1


Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment.

Scott JG, Warren WC, Beukeboom LW, Bopp D, Clark AG, Giers SD, Hediger M, Jones AK, Kasai S, Leichter CA, Li M, Meisel RP, Minx P, Murphy TD, Nelson DR, Reid WR, Rinkevich FD, Robertson HM, Sackton TB, Sattelle DB, Thibaud-Nissen F, Tomlinson C, van de Zande L, Walden KK, Wilson RK, Liu N - Genome Biol. (2014)

Tep phylogeny. Maximum likelihood amino acid phylogeny of D. melanogaster and M. domestica Teps. D. melanogaster proteins are labeled Tep1 to Tep5. M. domestica Teps are labeled XP_NNNNNNNNN and are shown in italics. For both species, multiple isoforms of the same gene are indicated with a bar. Branch support is the SH-like statistic estimated in phyml. The tree is rooted so as to minimize the number of duplications.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4195910&req=5

Fig1: Tep phylogeny. Maximum likelihood amino acid phylogeny of D. melanogaster and M. domestica Teps. D. melanogaster proteins are labeled Tep1 to Tep5. M. domestica Teps are labeled XP_NNNNNNNNN and are shown in italics. For both species, multiple isoforms of the same gene are indicated with a bar. Branch support is the SH-like statistic estimated in phyml. The tree is rooted so as to minimize the number of duplications.
Mentions: In contrast to the signaling pathways, both recognition and effector components of the immune system show substantial increases in copy number and genic diversity in M. domestica compared with D. melanogaster, suggesting the possibility that M. domestica possesses a more robust immune response to diverse pathogens encountered in the pathogen-rich environment in which it lives. In other insects, a variety of cell-surface and secreted proteins involved in recognition of pathogens have been identified, including peptidoglycan recognition proteins and beta-glucan binding proteins (also known as GNBPs in Drosophila), which are upstream of the main signaling pathways [44], and a variety of receptors likely involved in phagocytosis, including Nimrods, thioester-containing proteins (Teps) and scavenger receptors [45,46]. Of these, there are striking expansions in copy number of Nimrods and Teps in particular. The Nimrod gene family is one of the more variable in copy number among the sequenced Drosophila species [47], a trend that is continued in the more divergent comparison to M. domestica (17 Nim-containing proteins in M. domestica and 11 in D. melanogaster; only 8.7% of gene families have a greater degree of expansion in M. domestica). Even more striking is the expansion of the Tep family (FigureĀ 1), which has 19 members in M. domestica and only 6 in D. melanogaster. The Tep1/2 gene family specifically has expanded dramatically in M. domestica: this family has 2 members in D. melanogaster but 16 members in M. domestica, which is the 15th largest species-specific expansion in the M. domestica genome (Additional file 1). In addition, the M. domestica genome contains three lineage-specific genes that encode proteins with Tep-like domains (identified by HMM), but which are not clearly homologous to any characterized D. melanogaster Teps.Figure 1

Bottom Line: 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.Relative to D. melanogaster, M. domestica has also evolved an expanded repertoire of chemoreceptors and odorant binding proteins, many associated with gustation.The genome of this species will also serve as a close out-group to Drosophila in comparative genomic studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY, USA. jgs5@cornell.edu

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus