Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment
- Jeffrey G Scott1Email author,
- Wesley C Warren2,
- Leo W Beukeboom3,
- Daniel Bopp4,
- Andrew G Clark5,
- Sarah D Giers6,
- Monika Hediger4,
- Andrew K Jones7,
- Shinji Kasai1,
- Cheryl A Leichter1,
- Ming Li8,
- Richard P Meisel9,
- Patrick Minx2,
- Terence D Murphy10,
- David R Nelson11,
- William R Reid8,
- Frank D Rinkevich1,
- Hugh M Robertson6,
- Timothy B Sackton12,
- David B Sattelle13,
- Francoise Thibaud-Nissen14,
- Chad Tomlinson2,
- Louis van de Zande3,
- Kimberly KO Walden6,
- Richard K Wilson2 and
- Nannan Liu8
© Scott et al.; licensee BioMed Central Ltd. 2014
Received: 25 April 2014
Accepted: 10 September 2014
Published: 14 October 2014
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.
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.
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.
House flies, Musca domestica L. (Diptera: Muscidae), are ubiquitous and transmit more than 100 human and animal diseases -, including bacterial infections such as salmonellosis, anthrax, ophthalmia, shigellosis, typhoid fever, tuberculosis, cholera and infantile diarrhea; protozoan infections such as amebic dysentery; helminthic infections such as pinworms, roundworms, hookworms and tapeworms; as well as viral and rickettsial infections. House flies can spread a deadly strain of Escherichia coli and transmit life threatening antibiotic-resistant bacteria ,, which constitute an ever increasing threat in hospitals and other healthcare facilities -. Flies also transmit pathogens responsible for eye diseases such as trachoma and epidemic conjunctivitis, and infect wounds or skin with diseases such as cutaneous diphtheria, mycoses, yaws and leprosy . Fly-transmitted trachoma alone causes 6 million cases of childhood blindness each year . 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 ,. House fly larvae play a vital role in ecosystems as decomposers of animal wastes. This represents a unique niche, relative to other insects that have had their genomes sequenced.
House flies are always found in association with humans and human activities, following the spread of Homo sapiens across the planet . They are also one of the most serious pests at animal production facilities worldwide. Insecticides have been used extensively for controlling house flies for a century and this pest has shown a remarkable ability to rapidly evolve resistance. This led to house flies being one of the primary insects used for studies on insecticide resistance and toxicology.
The house fly has been a model system for studies of insect olfaction , and (Z)-9-tricosene plays an important role in inter-sex communication and mate selection in house flies. New attractants would be valuable for baits in management systems , and could lead to a reduction in insecticide use for house fly control.
Nasonia vitripennis is a parasitoid of the house fly (Nasonia is sold commercially for fly control) and the Nasonia genome has been sequenced . Having the genome of both the parasitoid (Nasonia) and the host (M. domestica) will allow unprecedented insights into the molecular mechanisms of host-parasitoid interaction.
The Diptera clade has radiated into over 120,000 known species since its origin in the late Jurassic. M. domestica is well placed within the Diptera to maximize the utility of sequence data for comparison between existing dipteran genomes . Multiple, deeply divergent comparisons within the order allow identification of lineage effects on rates and patterns of genomic diversity. These comparisons become more powerful in elucidating genome evolution as the phylogenetic context is broadened. Given the well centered position between Drosophila and mosquitoes, the Musca genome is nearly ideal for leveraging analysis and annotation of the mosquito genomes .
M. domestica has a well described linkage map for the five autosomes (I to V) and two sex chromosomes (X and Y) -. In the house fly, male sex is determined by a dominant factor, M, which is located on the Y chromosome in 'standard' populations. Thus, males are XYM and females are XX ,. This is believed to be the ancestral state of sex determination in house flies ,. However, M can be located on one or more of the five autosomes - or even rarely on X ,. The former M factors are referred to as 'autosomal M' and both males and females in carrier populations typically have the XX genotype ,,,. Autosomal M factors act similarly to Y chromosome M factors in determining maleness, by prohibiting the female specific splicing of the transformer (Md-tra, previously F) primary transcript ,. In autosomal M populations from different continents, especially those having males with multiple M factors, a Md-tra variant was found, Md-tra D (previously F D ), which acts as a dominant female determiner. It allows females to be produced even in the presence of multiple copies of M (or a homozygous M) and effectively makes females the heterogametic sex (M/M; Md-tra D /Md-tra + ), and males the homogametic sex (M/M; Md-tra + / Md-tra + ) ,. The genome sequence will accelerate progress in understanding many of these and other aspects of house fly biology.
Results and discussion
Sequencing and assembly
House fly genome assembly scaffold length distribution
250 kb to 1 Mb
100 to 250 kb
10 to 100 kb
5 to 10 kb
2 to 5 kb
Genic characteristics of the house fly genome
Single exon transcripts
We grouped the 14,180 predicted protein-coding genes in M. domestica into 10,427 orthologous groups based on homology to D. melanogaster. Each orthologous group contains at least one M. domestica protein, and can be assigned to one of three categories: single copy ortholog, for groups that contain a single M. domestica protein and a single D. melanogaster protein, conserved paralog, for groups that contain both M. domestica and D. melanogaster proteins, but are not single copy in both species, and lineage-restricted, for groups that contain only M. domestica proteins. Of the 14,180 predicted protein-coding genes, 7,006 (49%) are single copy orthologs of D. melanogaster proteins, 5,240 (37%) are in conserved paralogous groups (mean size in M. domestica: 2.88 proteins), and the remaining 1,934 (14%) are lineage-restricted and lack homologs in D. melanogaster.
The most abundant Gene Ontology (GO) biological processes represented by house fly genes were single-organism process (12.1%), cellular process (12.0%), metabolic process (11.1%) and biological regulation (10.8%; Figure S1A in Additional file 4). The most abundant cellular components were cell (32.6%) and organelle (29.2%; Figure S1B in Additional file 4). The most abundant molecular processes were binding (48.1%) and catalytic activity (28.9%; Figure S1C in Additional file 4). Overall, the distribution of genes within GO classifications was very similar between M. domestica and D. melanogaster (Additional file 5). Within the biological processes classification, the most notable difference was the more than two-fold greater percentage of genes in M. domestica associated with 'growth'. Within the cellular components classification M. domestica had an approximately two-fold greater percentage of genes in the 'membrane', and 'membrane-enclosed lumen' categories (relative to D. melanogaster). M. domestica also had a lower percentage of genes in the 'cell' category, relative to D. melanogaster. There were no remarkable differences between M. domestica and D. melanogaster in the percentage of genes in the molecular functions categories (Additional file 5).
We identified 771 putative immune-related genes in the house fly, of which 416 have direct homology (see Materials and methods) to known or putative D. melanogaster immune-related proteins, and the remaining 355 are identified based on hidden Markov model (HMM) queries. As in other insects, these genes encode proteins with several functions: recognition proteins that identify pathogen-associated molecular patterns, proteins that belong to signaling pathways that activate the transcriptional response to infection, and effector molecules that kill pathogens.
Previous work, primarily in Drosophila, has identified four primary signaling pathways involved in the systemic transcriptional response to bacterial and fungal infection: the Toll, imd, JAK/STAT, and JNK pathways ,. The M. domestica genome possess the full complement of signal transduction or signal modulation components of these pathways, and the vast majority are conserved as single copy orthologs between M. domestica and D. melanogaster. It appears likely, therefore, that immune signaling in M. domestica is substantially similar to immune signaling in D. melanogaster.
In M. domestica, similar to recognition proteins, the effector molecule repertoire is also significantly expanded. M. domestica shares four antimicrobial families with D. melanogaster, the attacins, diptericins, cecropins, and defensins (D. melanogaster also possesses one drosocin, one metchnikowin, and seven drosomycins that are not identifiable in the M. domestica genome), three of which have expanded relative to D. melanogaster (10 attacins in M. domestica, 4 in D. melanogaster; 12 cecropins in M. domestica, 5 in D. melanogaster (including andropin); 5 defensins in M. domestica, 1 in D. melanogaster; 2 diptericins in M. domestica, 2 in D. melanogaster). Even including the 9 antimicrobial peptides in Drosophila-specific families, M. domestica has a significantly enlarged antimicrobial peptide (AMP) repertoire (29 versus 19). AMP gene families are known to evolve very rapidly , and it is likely that novel effectors remain to be discovered in M. domestica (as in mosquitos , bees , and wasps ,), further increasing the potential diversity of the house fly AMP response.
A total of 33 glutathione S-transferase (GST) genes and 3 splice variants were predicted from the M. domestica genome (Additional file 9). This is similar to the number present in D. melanogaster, which has 36 GST genes and 11 splice variants . An unrooted phylogenetic analysis of the GSTs for M. domestica and D. melanogaster showed that the M. domestica GST genes were distributed among the different classes of cytosolic GSTs present in the D. melanogaster genome: epsilon, omega, theta, sigma, and zeta (Additional file 10). An additional four microsomal GST genes were predicted from the M. domestica genome, which is similar to the number of microsomal GST genes present in D. melanogaster (three genes with a total of four isoforms).
In the M. domestica genome, a total of 92 genes were predicted to have esterase activities, including phosphodiesterase, acetylcholinesterase, thioesterase, carboxylesterase, metallophosphoesterase, neuropathy target esterase and palmitoyl-protein thioesterase (Additional file 5). Based on the chemical reactions they catalyze, these enzymes were divided into four categories, containing a total of 39 carboxylic-ester hydrolases (EC 3.1.1), 10 thioester hydrolases (EC 3.1.2), three phosphoric-monoester hydrolases (EC 3.1.3) and 40 phosphoric-diester hydrolases (EC 3.1.4) .
Cys-loop ligand-gated ion channels
The house fly cysLGIC superfamily also includes Rdl , GRD and LCCH3, which form ion channels gated by ?-aminobutyric acid (GABA) , a glutamate-gated chloride channel (GluCl) , two histamine-gated chloride channels (HisCl1 and HisCl2) , and a pH-sensitive chloride channel (Figure 3) . The remaining cysLGICs have yet to be functionally characterized. M. domestica is the only other insect reported to possess a putative ortholog of D. melanogaster cysLGIC, NtR. Insect cysLGICs are of importance as they are targets of widely used insecticides , such as phenylpyrazoles (which act on GABA receptors and GluCls), spinosyns and neonicotinoids (which act on nAChRs). The cysLGIC sequence information from diverse species, including agricultural pests, disease vectors and pollinating insects -, provides a valuable starting point for understanding the interactions of insecticides with their targets at the molecular level, as well as enhancing our understanding of mechanisms causing insecticide resistance, and may prove instructive in the future design and development of improved insecticides with enhanced specificity for pest species.
The olfactory and gustatory abilities of insects depend on many chemoreceptors and associated proteins encoded by at least four major gene families . The odorant binding proteins (OBPs) are small, globular, secreted proteins that transport hydrophobic odorants to the receptors in sensory neuron membranes within sensory sensilla, primarily on the antennae, but also on the maxillary palps and other chemosensory organs . The odorant receptors (ORs) are a relatively recently evolved family within the insect chemosensory superfamily of ligand-gated ion channels that mediate much of olfaction in insects . The gustatory receptors (GRs) mediate much of gustation, especially perception of sugars and bitter tasting compounds, but as the basal family of highly divergent receptors within the superfamily, also mediate some aspects of olfaction, such as perception of carbon dioxide . The ionotropic receptors (IRs) are a greatly expanded and divergent family of chemoreceptors that evolved from the ionotropic glutamate receptor superfamily in basal animals, and while some function in olfaction, many are involved in gustation .
As the obvious comparison for the M. domestica repertoire, D. melanogaster has 52 genes encoding OBPs , 60 genes encoding 62 ORs and 60 genes encoding 68 GRs via alternative splicing of some loci , and 65 genes encoding IRs . We find that the M. domestica genome encodes at least 87 OBPs, has 85 genes encoding 86 ORs, 79 genes encoding 103 GRs, and 110 IRs (Additional files 12, 13, 14, 15, and 16). Detailed examination of the relationships of these gene families in these two flies (Additional files 17, 18, 19, and 20) reveals the expected patterns of birth-and-death gene family evolution typical of environmentally relevant genes. As expected, M. domestica shares the highly conserved members of these families, such as the OrCo protein that functions with each specific OR to make a functional olfactory receptor, and the apparently equivalent IR8a/25a proteins, along with the conserved suites of sugar and carbon dioxide receptors, and some highly conserved bitter taste receptors. In general, however, while there are roughly equal numbers of gene losses and pseudogenes in each species, M. domestica has duplicated and retained more genes in each family. These gene subfamily expansions are particularly prominent in the candidate gustatory receptors, especially those implicated in perception of bitter tasting compounds. For example, M. domestica has a large, mostly tandem array of 26 genes, one of which is alternatively spliced to encode 11 receptors, that are related to 8 D. melanogaster GRs implicated in bitter taste that are now spread around that genome. The expansions in the IR family are also primarily in receptors implicated in gustation. M. domestica also has large expansions of ORs related to Or45a and Or67d in D. melanogaster, receptors involved in repulsion from aversive chemicals in larvae and in perception of a male-produced pheromone, respectively.
In summary, M. domestica has evolved an expanded repertoire of chemoreceptors and associated proteins compared with D. melanogaster. This expansion is mostly associated with gustation, specifically perception of bitter tasting compounds. It may be that the more diverse and potentially toxic food sources and larval habitats of M. domestica have led to retention and specialization of gene duplicates in these receptor gene subfamilies. Unfortunately, the ligand specificity of most candidate bitter taste receptors in Drosophila have proven difficult to resolve, so it is not yet possible to infer likely ligands for these novel receptors in M. domestica.
Sex determination, sex-biased gene expression and the evolution of sex-biased genes
Genes with sexually dimorphic (sex-biased) expression, much like other sexually dimorphic traits, tend to evolve faster than genes with equal (unbiased) expression in males and females ,. Among genes with sex-biased expression, genes expressed in reproductive tissues evolve fastest, particularly those expressed primarily in male-limited organs . The faster evolution of genes with sex-biased expression is likely driven by a combination of positive Darwinian selection and relaxed purifying selection ,. Genes with higher expression in males (male-biased) are also more likely than unbiased genes to not have identifiable homologs in comparisons between Drosophila species ,, suggesting that genes with male-biased functions are more dispensable or that their protein coding sequences evolve too fast for homolog identification .
Sex-biased expression of house fly genes and homology with D. melanogaster genes
To test the hypothesis that genes with sex-biased expression experience more evolutionary turnover than unbiased genes, we used the ortholog calls described above to divide house fly genes into those with at least one D. melanogaster homolog (conserved) and those that are lineage-specific. Not all M. domestica genes tested for sex-biased expression were included in the test of homologous genes in D. melanogaster (and vice versa), because of how the data were handled. House fly genes with sex-biased expression are less likely to be conserved than genes with unbiased expression (P?<?0.01, Fisher's exact test (FET)) (Table 3). Genes with male-biased expression are less likely to be conserved than unbiased genes (P?<?0.005, FET), whereas female-biased genes are as conserved as unbiased genes (P?=?0.729, FET) (Table 3). While male-biased house fly genes have a lower frequency of homology matches to D. melanogaster than female-biased genes, this difference is not significant (P?=?0.091, FET). These results support the hypothesis that genes with male-biased expression are gained/lost from the genome at a faster rate than other genes, and/or that genes with male-biased expression have faster evolving protein-coding sequences that evade homology detection.
Sex-biased expression of house fly genes and duplication status
Five actin genes were found in house fly (LOC101901018, LOC101887443, LOC101890414, LOC101895248, LOC101888968), one less than found in D. melanogaster. The sequences were highly similar at the amino acid level (95.5 to 99.5%; Martinez-NW pairwise alignments) and the nucleotide level (84.4 to 96.8%). Like D. melanogaster each sequence was 1,131 nucleotides in length. The high degree of similarity between these genes suggests that the use of one of these genes as an internal standard for quantitative PCR should be carefully scrutinized to avoid detection of multiple actin genes. The deduced amino acid sequences of LOC101888968 and LOC101895248 were 100% identical to D. melanogaster actin 5c and 88 F, respectively. Other orthologs could not be unambiguously identified.
MicroRNA and microRNA machinery
After mapping all of the miRbase sequences against the M. domestica genome, a total of 69 microRNAs (miRNAs) along with their hairpin precursors were predicted to be present in the M. domestica genome (Additional file 22). Seven miRNAs had two copies and two had three copies, making a total of at least 81 miRNA loci in the M. domestica genome. Within the multiple copy miRNAs, two miRNAs, miR-1-5p and miR-996-5p, had the same hairpin precursors, but were located in two distinct locations of the genome, suggesting a duplication event. In addition to the predicted miRNA, 25 isoforms of 11 genes were predicted to be involved in the transporting, processing and function of miRNAs, so-called miRNA machinery  (Additional file 23). These genes include Drosha, DGCR (partner of Drosha), ran-like GTPase, exportin-5, Dicer, multiple argonaute proteins, including one ago-1-like gene with four isoforms, two ago-2-like genes, one with two isoforms and another ago-2-like gene with five isoforms, and one ago-3-like gene, and two RISC-loading genes. Similar to other dipteran species, no sid-1 homolog, which is involved in systemic miRNA, was identified in the M. domestica genome . However, multiple genes putatively involved in the uptake of exogenous double-stranded RNA were identified; including two eater genes, and one nibbler gene (Additional file 23). Although the biological function of these miRNAs are currently unknown, the availability of bioinformatics information will provide a valuable tool for future studies targeting on the gene regulation in physiological processes  of house flies.
We have sequenced and analyzed the genome of the M. domestica using DNA from female flies. This represents the first genome sequence of an insect that lives in intimate association with abundant animal pathogens. The sequenced genome size is 691 Mb and contains 15,345 genes. Compared with D. melanogaster, the genome contains a rich resource of shared and novel protein coding genes and a significantly higher amount of repetitive elements.
In comparison to D. melanogaster, the house fly genome has a larger number of genes associated with immune response, detoxification and chemosensation. Relative to D. melanogaster there are substantial increases in copy number and diversity of both the recognition and effector components of the immune system in the house fly genome, consistent with life in a pathogen-rich environment. For detoxification genes, there are 146 P450 genes (plus 11 pseudogenes) in M. domestica, representing a significant increase relative to D. melanogaster (or G. morsitans) and suggesting the presence of enhanced detoxification capacity 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.
The availability of the house fly genome should accelerate the pace of research on this important vector of human and animal diseases. 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, host parasitoid interactions, and for exploring the basic biology of this important pest. The genome of this species will also serve as a close out-group to G. morsitans in comparative genomic studies.
Materials and methods
Genome and transcriptomes
DNA was extracted  from individual unmated adult females of the M. domestica aabys strain  and used for genome sequencing. The aabys strain was selected because it was inbred (to reduce polymorphisms and thus facilitate the genome assembly), is an XY strain, and because it is a widely disseminated and commonly used strain, particularly for linkage analyses. A total sequence coverage of approximately 90× was generated from fragment and jumping libraries then assembled using the ALLPATHS-LG assembler . Contaminating contigs, adaptors, ambiguous bases as N's in the sequence and all contigs 200 bp and smaller were removed. The final M. domestica 2.0.2 genome sequence is available under the GenBank accession number AQPM00000000.1 and NCBI assembly accession GCA_000371365.1. All genome sequences utilized in de novo assembly of M. domestica were submitted to the NCBI short read archive (SRA) under accession numbers SRX217932-217940.
RNA was isolated from individual last instar larvae (n?=?1; accession SRX208995), individual 1-day-old adult males (n?=?2; accessions SRX208993 and SRX208994) and individual unmated 1-day-old adult females (n?=?2; accessions SRX208996 and SRX208997) as described previously . Poly(A)?+?RNA was isolated as a starting input for the Ovation® RNASeq System V2 (NuGEN, San Carlos, CA USA). A check of quality was measured with the Agilent Bioanalyzer. From samples that passed our quality control (minimum RNA integrity number (RIN) score of 7), a non-normalized cDNA library was constructed using a modified version of the Ovation® RNASeq System V2  that generates strand specificity, an important factor in alignment biases seen with non-directional RNA-seq data. We sequenced each cDNA library (0.125 lane) on an Illumina HiSeq 2000 instrument (approximately 36 Gb per lane) at 100 bp length. These data provided sufficient sequence coverage of the estimated exon content (approximately 29 Mb) of a 691 Mb assembled house fly genome.
The pipeline used for the annotation of house fly is fully documented in the NCBI handbook  and is briefly described here. Prior to gene annotation 52% of the assembly was masked with WindowMasker , a word-based algorithm that identifies repeats de novo. By comparison, masking with the RepeatMasker library would have resulted in only 2.15% of the genome being masked. The annotation process was initiated by the alignment to the masked genome of publicly available house fly transcripts and RNA-seq from project SRP015949 with Splign , and Diptera proteins by ProSplign. Overlapping alignments with compatible frames were assembled into chains and extended or filled-in as needed by the ab initio prediction component of Gnomon to form complete models . The resulting models were then evaluated and retained or discarded based on multiple criteria, including evidence support and homology to existing proteins. Following manual checks we predicted a total house fly gene count of 15,349, consisting of 14,180 protein-coding genes (with 17,508 transcripts), 1,165 non-coding genes and 4 pseudogenes. The number of genes is comparable to D. melanogaster (15,771) . A total of 3,985 transcripts were filled-in or extended by ab initio prediction for 5% of their length or more, and 1,375 models were marked partial. The mean number of exons per transcript were estimated to be 4.9.
In total, 17,508 protein sequences were searched against Swiss-Prot with the BLASTp algorithm . The E-value cutoff was set at 10?5 and taking the best 20 hits for annotation. Blast2GO , was used to predict the functions of the sequences and assign GO terms. Simplification of the annotation into functional categories was also done by Blast2GO using GO slim. Proteins were summarized at level 2 into three main GO categories (biological process, cellular component, and molecular function) and 33 subcategories.
Defining homology to D. melanogaster
To define homology between D. melanogaster and M. domestica proteins, we started with an all-against-all BLASTp, using standard parameters and an E-value cutoff of 1e-5. We then filtered hits to remove all hits with similarity below 30% and at least 70% alignment coverage (dropping to 40% if the aligned region is at least 100 amino acids long). After filtering, we converted E-values to scores by taking the negative log10 (capped at 200), and then for each query computed a minimum score to keep by subtracting 10 from the minimum of the maximum score to the other species or the average of the top 5 hits. After removing hits below the minimum score for each query, we clustered proteins into groups using MCL  with the following parameters: ?we 2 --force-connected?=?y -scheme 7. These are considered homologous groups. This procedure is tuned to be conservative about missing true orthologs at the cost of inflating group size by linking sets of reciprocal best hits into a single group.
To resolve relationships among groups that contain more than one D. melanogaster or M. domestica member, we aligned members of each cluster using mafft (with the --auto option) , trimmed the resulting alignments with trimal (default options) , and then computed trees with phyml  using default options. After computing trees for each paralogous group, we used the SDI algorithm implemented in TreeBest  and RIO  to resolve speciation and duplication events. We split groups that could be completely parsed into smaller orthologous groups, but retained as large families cases with complicated histories, which implied lineage-specific losses at the root of the tree. In many cases these likely resulted from low-confidence basal nodes. For all single copy orthologous gene pairs between M. domestica and D. melanogaster, we produced protein alignments using mafft  with the --auto flag and otherwise default parameters. Rates of protein divergence were calculated for each alignment with PAML version 4.4d .
Two complementary computational approaches were used to define the repertoire of immune-related genes in M. domestica. The first relied on the well-annotated D. melanogaster genome. We curated a list of immune-related D. melanogaster proteins from the literature (updated from ), and assumed an immune function for proteins in M. domestica that are homologous (as defined by the method described above) to proteins with immune function in D. melanogaster. To supplement the homology-based annotations, our second approach applied a HMM originally developed to characterize the mosquito immune system . Using curated alignments of putative immune-related proteins and domains from D. melanogaster and two mosquitoes available at ImmunoDB, plus a NIM domain alignment , we built HMMs using HMMER , and then computed the likelihood of containing each domain for each M. domestica predicted protein. After correcting for the number of domains tested, we retained all calls with an E-value <0.01, assigning genes to the class with the lowest E-value in cases where a single protein hit multiple domains. The classes included are: several antimicrobial peptides (attacins, cecropins, defensins, diptericins), CLIP-domain serine proteases (?A, ?B, ?C-, ?D, and -E), serpins, C-type lectins (CTLs) and galectins, beta-glucan binding proteins, peptidoglycan recognition proteins, fibrinogen-related proteins (FREPs), peroxidases, lysozymes, MD2-like receptors, Nimrods, prophenoloxidases, scavenger receptors (A, B, and C), thioester-containing proteins, Tolls, spaetzle-like proteins, and Rel-domain proteins. In some cases (for example, SrcA, galectin, FREPs, CLIP-A, CTLs, peroxidases) there is little evidence for an immune role in D. melanogaster, but we included them in our analysis given the evidence for an immune role in other metazoans. However, it is important to note that similarity to an HMM cannot guarantee an immune function, as many immune-related proteins in insects share domains with non-immune functions (that is, serine proteases).
Primary metabolism of xenobiotics is most commonly carried out by cytochrome P450s, esterases/hydrolases and/or GSTs. To identify these genes two approaches were taken. TBLASTn searches  were carried out using all the known sequences of insect P450s, GSTs and esterases. We also searched the annotated genome for appropriately named sequences.
Cys-loop ligand-gated ion channels and actin
Putative M. domestica cys-loop ligand-gated ion channel subunits were identified by searching the annotated genome with TBLASTn  using protein sequences of every member of the D. melanogaster cys-loop ligand-gated ion channel superfamily. The neighbor-joining method , available with the Clustal X program , was used to construct a phylogenetic tree, which was then viewed using TreeView . Actin sequences were identified using the same approach.
The GR family was manually annotated using methods employed for other insect genomes . Briefly, TBLASTn searches were performed using all D. melanogaster GRs as queries, and gene models were manually assembled in TextWrangler . Additional details are provided in Additional file 16.
Sex determination, sex-biased gene expression and the evolution of sex-biased genes
Md-tra D females were collected from seven populations in different countries and different continents: Trabzon (Turkey), Faverges (France), Santa Fé (Spain), Tansania, North Carolina (USA), Osaka (Japan) and Ipswich (Australia).
RNA-seq reads of two biological replicates each of adult males and females were aligned to the reference genome using TopHat2 (v2.0.8b)  with the default parameters. We tested for differential expression between the male and female samples using Cuffdiff version 2.1.1  with the default parameters and a false discovery rate of 0.05.
microRNA and microRNA machinery
The mature miRNAs from the miRbase database (release 20)  were tested against the M. domestica supercontigs using miRdeep2, version 220.127.116.11 ,. The known D. melanogaster miRNAs were used as the reference mature miRNA sets -. The miRNA machinery was primarily predicted from the Gnomon annotated M. domestica genome. Additional gene prediction for genes putatively involved in double-stranded RNA uptake was predicted by BLASTp comparison  to known genes in the D. melanogaster genome (v. dmel_r5.9_FB2008_06 ).
JGS, NL, and AGC conceived of the study. CAL prepared the genomic DNA. FDR prepared the RNA. WCW, PM, CT and RKW prepared the sequencing libraries, directed the sequencing and assembled the genome. Annotation of the genome was by TM and FT-N. SK carried out the GO analyses. TBS manually annotated and analyzed the immune-related genes. WZR, ML, NL, DN and JGS manually annotated and analyzed the detoxification genes. AKJ and DBS manually annotated and analyzed the LGIC genes. HMR, SDG and KKOW manually annotated and analyzed the chemoreceptors and odorant binding protein genes. RPM analyzed the sex-biased genes. JGS and SK annotated the actin genes. LB, DB, LvdZ and MH carried out the analysis of Md-tra. WRR, ML and NL manually annotated and analyzed the miRNA genes. All authors read and approved the final manuscript.
Fisher's exact test
hidden Markov model
nicotinic acetylcholine receptor
odorant binding protein
We thank the production sequencing group of The Genome Institute at Washington University for library construction, sequencing and data curation. This work was supported by NIH-NHGRI grant 5U54HG00307907 to RKW, Hatch Project NYC-139416 to JGS and multistate project S-1030 to JGS.
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