De novo genome assembly, annotation, and characterization of chemosensory genes in the camel ked (Hippobosca camelina)

De novo genome assembly, annotation, and characterization of chemosensory genes in the camel ked (Hippobosca camelina) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article De novo genome assembly, annotation, and characterization of chemosensory genes in the camel ked (Hippobosca camelina) Fredrick Kebaso, Souleymane Diallo, Caleb Kibet, Suhaila Hashim, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6505113/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 16 Jul, 2025 Read the published version in BMC Genomics → Version 1 posted 10 You are reading this latest preprint version Abstract Background Hippobosca camelina (camel ked) is an obligate hematophagous ectoparasite that infests camels. Hematophagy inflicts painful bites leading to myiasis, anemia and pathogen transmission such as Candidatus Anaplasma camelii . A genome assembly for this biting flies is currently unavailable, limiting understanding of its genetics, particularly the chemosensory system. Results The genome size for Hippobosca camelina female is 135.6 Mb with 17.08 % repeated regions, an N50 of 1.2 Mb , a total of 2,182 contigs, a GC content of 33.5 % and compleasm (Busco) completion rate of 95.38% with the diptera_odb10 lineage (S:95.83%, 3148, D:0.30%, 10, F:0.30%, 10, I:0.00%, 0, M:3.56%, 117, N:3285) and Hippobosca camelina male had a genome size of 133.5 Mb with 15.38% being repeats, an N50 of 419.6 Kb , 2,318 contigs, GC content of 33.5% , and compleasm (Busco) completion rate of 94.70% with diptera_odb10 lineage (S:94.70%, 3111, D:0.49%, 16, F:0.85%, 28, I:0.00%, 0, M:3.96%, 130, N:3285). A total of 14,240 putative genes for H. camelina male and 13,496 putative genes for H. camelina female annotated were identified as orthologous to genes in selected dipterans that included Drosophila melanogaster, Glossina morsitans morsitans, Glossina fuscipes, Glossina brevipalpis and Anopheles gambiae. Chemosensory genes recovered included 4 Chemosensory specific proteins (CSPs), 18 Ionotropic receptors (IRs), 7 Gustatory receptors (GRs), 5 Odorant receptors (ORs), 9 Odorant binding proteins (OBPs) and 1 Sensory Neuron Membrane Protein (SNMP). Conclusion This study generated two genomes for Hippoboscacamelina. Both are smaller in size compared to Melophugus ovinus (1) and Glossina morsitans (2). The Hippobosca genomes have a lower repeat content compared to G. morsitans and M. ovinus, a phenomenon that may explain the reduced genome size. A total of 44 chemosensory genes for H. camelina were annotated. The obligate parasitic lifestyle, limited movement, and narrow host specificity in Hippobosca camelina could be attributed to reduced chemosensory system genes in the six known families of chemosensory genes as reported in this study. Hippobosca Chemosensory genes Genomic analysis Hematophagy Comparative genomics Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Background Hippoboscid flies, or keds, are obligate hematophagous or blood-sucking ectoparasites that invade birds, mammals, and rarely humans( 3 ). They are dipterans that belong to the superfamily of the Hippoboscoidea along with the Glossinidae family. The current taxonomic classification of Hippobosca species is based on morphological traits, particularly species-specific patterns of colouration on the scutellum ( 4 ). Genomic studies provide insight into the genome structure and functional genes of organisms. This has provided useful information on the behavioural ecology of many insects of veterinary importance ( 1 , 5 ). Additionally, genomic studies have established a molecular basis for decades-old ecological observations, such as the preference for specific colours in trap designs for the deer ked ( 6 ). The integration of genomics with field ecology holds great promise for developing innovative and effective tools in vector control, capitalizing on the genetic basis of insect behaviour, and leveraging the identified receptors for targeted interventions against disease vectors ( 7 – 10 ). However, the Hippobosca genome is absent from existing databases, limiting the understanding of vector biology, which is necessary to design control strategies for Hippobosca camelina . Annotation of chemosensory genes in Hippobosca camelina underpins the design of eco-friendly traps, baits, and vector control strategies. As obligate blood-feeders, they potentially vector several infectious pathogens such as protozoa, bacteria, helminths, trypanosomes, and viruses to their hosts ( 11 , 12 ). Although the role of Hippobosca species as disease vectors is still under-explored, there is evidence of the existence of epizootic pathogens in keds: Trypanosoma melophagium , T. vivax , T. evansi , and Candidatus anaplasma camelii in Hippobosca camelina , ( 11 ). Furthermore, high infestation by these blood-feeding parasites impairs the hosts' health, exposing them to alopecia, anaemia, skin lesions, stress, sickness, and death if not treated ( 13 ). Hence, there is a need to study camel ked's vector competence and capability to determine the pathogen transmission potential to uninfected hosts, and the role of keds as vectors. Additionally, for obligate hematophagous ectoparasites like Hippoboscid flies (keds) and Glossina sp , the olfactory system is critical for host detection, mate location, predator evasion, and navigating ecological niches. Furthermore, vector control strategies have taken advantage of insect chemical sensing systems to develop several olfactory-based tools for vector management. For example, this system has been exploited in Glossina (tsetse fly species), a close species of Hippobosca keds, to design traps and odor baits, which have played a vital role in combating African Trypanosomiasis AT in tropical areas ( 14 , 15 ). Despite their biological and epidemiological significance, the chemosensory mechanisms of Hippobosca keds remain poorly understood. This knowledge gap has limited the development of targeted vector management strategies, particularly in regions where these parasites contribute to the spread of vector-borne diseases in livestock and wildlife. To date, the most studied species in the Hippoboscidae family includes M. ovinus (Sheep ked) and H. equina , and only M. ovinus , transmitting Anaplasma ovis and Rickettsiae in sheep and wild ruminants has its genome sequenced ( 1 ) However, molecular evidence and information on these two species on their biology, epidemiology, and pathogen transmission ability is scanty ( 16 ). As for Hippobosca camelina , mainly feeding on camel, little is known about the chemosensory system and no information is available on their genetic makeup limiting our understanding of the cellular and molecular basis of their host detection. In the current study, we aimed to assemble the genomes of Hippobosca camelina species and identify the putative chemosensory genes that support their superb chemical sensing ability. Results and Discussion Hippobosca camelina whole genome assembly Using nanopore technology, we sequenced the genome of an individual male and female of H. camelina . The assembled draft genomes showed a relatively equivalent size for male (133.5 Mb) and female (135.6 Mb) with greater than 94% completeness relative to the Dipteran lineage (Fig. 1 ,A). This is 50% less than the well-annotated Glossina morsitans morsitans genome with 366 Mb ( 2 ) and slightly smaller than the sheep ked ( Melophagus ovinus ) with 188 Mb ( 17 ). The reduction in the genome size would be partially attributed to the reduced repeats in H. camelina female with 17.08 %, and H. camelina male with 15.38% repeats, compared to 27.08% of Melophagus ovinus ( 17 ) and 34.95% of G. morsitans ( 2 ), among other genome attributes. The most abundant repeat elements were simple repeats, (Fig. 1 ,C) followed by low-complexity repeats for both genomes (Supplementary Table 2 and Table 3) showing the detailed repeat element counts and Nucleotide base pairs covered by each repeat element. The GC content is 33.5% for both Keds relatively equal to 33% of G. morsitans ( 2 ). The Hippobosca camelina male and female genomes had contig N50 of 419.6 kb and 1.2 Mb, respectively. The low contig N50 implies low genome contiguity of the final assembly, consequently leading to fragmented assemblies with over 2,000 contigs for both genomes, (Fig. 1 , A). However, the genome quality completeness exceeded 94% for both genomes relative to the dipteran lineage; H. camelina female (S:95.83%, 3148, D:0.30%, 10, F:0.30%, 10, I:0.00%, 0, M:3.56%, 117, N:3285), (Fig. 1 ,B). H. camelina male (S:94.70%, 3111, D:0.49%, 16, F:0.85%, 28, I:0.00%, 0, M:3.96%, 130, N:3285), (Fig. 1 ,A). Although the genome is not 100% complete, the high completion rate suggests that most core conserved genes are faithfully represented in the assembled genome. A greater number of hypothetical genes totalling up to 14,240 genes for H. camelina male and 13,496 genes for H. camelina female, were found to be orthologous to genes from selected dipterans including Drosophila melanogaster, Glossina morsitans morsitans , G. fuscipes, G. brevipalpis , and Anopheles gambiae . This is in comparison to M. ovinus , which had 9,505 genes ( 17 ) and the genome of G. morsitans is estimated to contain 12,308 protein-encoding genes based on automated and manual annotations. Of this, 9,172 Glossina genes (74%) have a Dipteran ortholog ( 2 ). These variations in the number of genes predicted and ortholog assignments can be attributed to the fragmented genome of Hippobosca camelina , consequently leading to fragmented gene predictions. Additionally, Hippobosca genome ab initio predictions might have generated false positives, while other genes could be non-functional despite displaying high similarity and orthology indices. Olfactory structure of H. camelina H. camelina possesses a reduced olfactory apparatus, with diminished antennal structures (Fig. 2 A) compared to other dipteran flies, which have been shown to rely heavily on olfaction for locating food and mates ( 18 ). Our preliminary scanning electron micrographs showed a reduced antennal surface area and sensillum number diversity (Fig. 2 C). Given its close association with camel hosts, the reduced olfactory apparatus may indicate a shift toward contact-based host detection rather than long-range olfactory host-seeking. To pave the way for deeper insights in understanding olfactory adaptations in H. camelina we focused on characterizing for the first time the chemosensory genes repertoire in male and female of camel ked. (A) Head structure, (B) Antennal pit without antennal extension, (C) Scanned image of the antennal pit showing reduced number of olfactory sensillum, (D) Forked structure protrude from the base of the antenna, we named it equivalent of arista. i) Chemosensory Specific Proteins (CSPs) Chemosensory specific proteins (CSPs) are soluble hydrophobic proteins, majorly involved in Carbon II Oxide detection, transmitting chemical signals, chemoperception which encompasses olfactory cues and taste detection, in early stages of larval growth, brood (immature stages of the bee colony, such as eggs, larvae, and pupae) pheromone transportation ( 19 ) CSPs contain a highly conserved four cysteine signature across dipterans. They are uniquely identified with the presence of a signal peptide and alpha helices joined by disulphide bonds. They have an average length of 130 aa ( 20 ) In this study, we identified 4 CSP genes for both H. camelina female and male. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamCSP1, HcamCSP2, HcamCSP3, and HcamCSP4 exhibited > 99% sequence similarity and had identical lengths (number of amino acids) across their respective homologs in the male and female genomes. All the 4 CSP genes had four conserved cysteine signatures with the sequence features C 1 -X 6 -C 2 -X 19 -C 3 -X 2 -C 4, (X represents any amino acid other than cysteine), (Fig. 3 ). All four CSPs contained the Signal Peptide (Sec/SPI) with the prediction probabilities > 0.85 for HcamCSP1, HcamCSP2, and HcamCSP3. HcamCSP4 had a lower prediction probability of 0.5826. The cleavage positions for the CSPs were predicted as: HcamCSP1 at position 20/21, HcamCSP2 at position 18/19, HcamCSP3 at position 17/18, and HcamCSP4 at position 29/30. The amino acid length ranged between 113 aa and 162 aa, with an average of 136 aa. HcamCSP2, HcamCSP3 and HcamCSP4 had 2 exons each while HcamCSP1 had a single exon, (Table 1 and Supplementary Table 4). Notably, Hippobosca camelina and Glossina morsitans share a comparable number of CSP genes, with G. morsitans having 5 CSP genes ( 19 ) while M. ovinus has 3 CSP genes ( 17 ). A phylogenetic tree was generated to infer the relationships between the annotated CSPs with homologs from Glossina morsitans , Glossina brevipalpis , Glossina fuscipes , and Anopheles gambiae . HcamCSP4 clustered closely with GmmCSP5 and GfucCSP5, indicating a potential shared ancestry and functional conservation. Similarly, HcamCSP3 forms a distinct clade with GbreCSP4, GfucCSP4, and GmmCSP4, suggesting diversification within this gene family. HcamCSP2 is positioned near GbreCSP2, GfucCSP2, and GmmCSP2, while HcamCSP1 aligns closely with GfucCSP3 and GmmCSP3, (Fig. 4 ). This suggests that H. camelina CSPs are evolutionarily linked to their Glossina and Anopheles homologs, highlighting conserved roles in chemosensory functions with species-specific adaptations that could be critical for host recognition and survival in H. camelina . ii) Ionotropic Receptors (IRs) Insect ionotropic receptors (IRs) are a broad class of ligand-gated ion channels that play an important role in chemosensation, specifically in the detection of acids, amines, and other volatile chemicals. They are evolutionarily related to ionotropic glutamate receptors (iGluRs) and facilitate direct ion flow when ligands are bound. They are largely found in olfactory sensory neurons, particularly in the coeloconic sensilla, especially in Drosophila melanogaster , but they also contribute to gustation and other sensory modalities ( 21 , 22 ). We identified 18 IRs in the H. camelina male genome, and 17 IRs were recovered in female. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamIR8, HcamIR18, HcamIR4, HcamIR15a, HcamIR15b, HcamIR15c, HcamIR2, HcamIR3, HcamIR6, HcamIR7, HcamIR10, and HcamIR16 exhibited > 99% sequence similarity and with relatively identical lengths (number of amino acids) across their respective homologs in the male and female genomes. HcamIR14, HcamIR17, HcamIR12, and HcamIR5 were identified in the H. camelina female genome while HcamIR11, HcamIR1, HcamIR9 and HcamIR13 were identified in the male genome. The amino acid length ranged between 601 aa and 1181 aa with an average of 832 aa. The number of exons ranged between 5 and 16, (Supplementary Table 5). The retention of relatively equal gene numbers of both CSP and IRs (Table 1 ) would perhaps explain the obligate hematophagy or blood-sucking lifestyle common in these keds. A phylogenetic analysis of Hippobosca camelina revealed distinct clustering patterns with orthologs from Drosophila melanogaster , Anopheles gambiae , and Glossina morsitans morsitans . HcamIR1 and HcamIR2 were closely related to AgamIR176, AgamIR180, and GmmIr47a, suggesting conserved roles in odor detection. Similarly, HcamIR4 clustered with DmelIr31a and DmelIr56a, while HcamIR3 aligned with AgamIR133 and AgamIR195, indicating potential involvement in chemical signal transduction. HcamIR5, HcamIR6, and HcamIR7 grouped with AgamIR7x, DmelIr67a, and AgamNMDAR2, respectively, indicating expanded diversity. Notably, HcamIR13 through HcamIR18 clustered with AgamIr168 in one clade, (Fig. 5 ). These findings may suggest that H. camelina chemosensory genes are evolutionarily conserved yet exhibit functional diversification, this may provide insights into their roles in host-seeking and survival behaviors. iii) Gustatory Receptors (GRs) Gustatory Receptors (GRs), facilitate gustation, detection of nonvolatile chemicals (liquids or solids) or contact chemoreception. Additionally, Gustatory Receptor Neurons (GRNs) in Drosophila detect volatile compounds like N,N-diethyl-meta-toluamide (DEET) and coumarin by responding robustly to their vapors, revealing a dual role in both taste and olfactory signaling. This volatile sensitivity enhances the chemical coding capacity of GRNs, enabling flies to finely assess environmental cues for behavior guidance ( 23 ). They belong to a superfamily identified by the presence of seven transmembrane domains (7tm_7), which exhibit low sequence conservation, typically ranging from 7–50% similarity, except for the C-terminus region, spanning 33 amino acid residues, which aligns with the seventh transmembrane domain ( 24 ). These genes respond to soluble tastes (sweet and bitter) and contact pheromones. They detect nonvolatile chemicals (liquids or solids) and facilitate contact chemoreception ( 25 ). H. camelina female had 6 GR genes and the male ked had 7 GR genes. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamGR6, HcamGR7, HcamGR3, HcamGR1, HcamGR5, and HcamGR4 exhibited > 99% sequence similarity and had identical lengths (number of amino acids) across their respective homologs in the male and female genomes. HcamGR2 was only identified in the male genome. The amino acid lengths ranged from 357 to 486 aa, with an average of 433 amino acids. The number of transmembrane domains varied between 5 and 9. The exon numbers ranged between 3 and 7, (Table 6 ) . This number of H. camelina GR genes ( 7 ) is relatively lower than the 11 GR genes identified in M. ovinus and significantly fewer than the 14 GR genes reported in Glossina m. morsitans , (Table 1 ). This would perhaps explain the adaptability to the narrow host range and strict host specificity among Hippobosca ( 26 ) and M. ovinus ( 27 ) compared to G. m. morsitans , which parasitizes a wider host range ( 28 – 30 ). A phylogenetic analysis of the 7 GRs annotated for H. camelina was performed to infer the evolutionary relationship among Drosophila melanogaster , Glossina fuscipes , Anopheles gambiae , Glossina brevipalpis , and Glossina morsitans . HcamGR4 clustered closely with GbreGr6 and AgamGr60, suggesting a shared ancestry and potential functional similarity in taste perception. Similarly, HcamGR3 was nested within a clade containing DmelGr8a and GfucGr9, highlighting its divergence from other GRs and potential specialization within this gene family. HcamGR6 aligned with DmelGr64a pointing to putative roles in sugar feeding. HcamGR7 formed a unique association with GfucGr5, indicating lineage-specific adaptations. HcamGR5 grouped closely with DmelGr98a and AgamGr13, reflecting evolutionary conservation in gustatory function. HcamGR1 aligned with AgamGr24 and DmelGr59e, suggesting a potential role in broad-spectrum taste perception, (Fig. 6 ). These findings underscore the complex evolutionary trajectories and functional diversification of GR genes in H. camelina , contributing to its ecological adaptation. iv) Odorant Receptors (ORs) Odorant Receptors (ORs), detect volatile and non-volatile chemo signals. Odorants propagate into the sensilla through pores and diffuse into the dendrites, facilitated by the OBPs, particularly the hydrophobic odour molecules ( 21 ). Insect ORs are characterised by a reversed N-terminal topology, an average length of 400 amino acids, and a seven-transmembrane domain (7tm_6). They function in complexes with Orco, a non-conventional co-receptor, to form functional ion channels that confer specificity to a repertoire of odorants ( 31 ). H. camelina female had 5 ORs and H. camelina male had 5 OR genes. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamOr1, HcamOrco, HcamOr4a, HcamOr4b, HcamOr3, and HcamOr2 exhibited 100% sequence similarity and identical lengths (number of amino acids) across their respective homologs in the male and female genomes. The amino acid length ranged between 363 aa and 476 aa. The transmembrane domains varied between 3 and 7, (Supplementary Table 7). The reduced number of ORs further supports the absence of antennal extension which houses the sensilla with the olfactory sensory organs where ORs are expressed (Fig. 2 B). The decrease in OR numbers in H. camelina compared to the 46 ORs found in G. morsitans ( 32 ) may partially explain the obligate parasitism and lifestyle, restricted movement, and narrow host specificity of Hippobosca camelina keds. A phylogenetic analysis of the OR genes, including Orco receptors from; Drosophila melanogaster , Glossina morsitans , Anopheles gambiae and Hippobosca camelina , showed that Orco sequences cluster together in a single clade reflecting their high conservation across species, (Fig. 7 ). These co-receptors are essential for forming functional ion channels that provide specificity to a range of odorants responsible for detecting environmental odors. Orco genes across different species exhibit high similarity (greater than 70%), whereas OR genes within the same species show low similarity ( 21 ). HcamOr4a and HcamOr4b clustered with GmmOR31 and DmelOr22c in one clade. HcamOr3 formed a single clade with GmmOr37 while HcamOr2 clustered with DmelOr64a, (Fig. 7 ). v) Odorant Binding Proteins (OBPs) Odorant Binding Proteins (OBPs), bind to pheromones and are actively involved in the early stages of olfactory molecular recognition and signal transduction by transducing host odorants across the sensillum lymph to the relevant odorant receptor with high specificity. OBPs are characterised by the presence of a six-cysteine signature, that confers odorant binding specificity by forming disulphide bridges and unique 3D tertiary protein structure ( 33 ). They range between 15-20KDa in size with an alpha helix pattern, presence of a signal peptide and an average length of 150aa ( 33 ). H. camelina female had 9 OBPs and H. camelina male had 8 OBPs. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamOBP6, HcamOBP5, HcamOBP4, HcamOBP3, HcamOBP2, HcamOBP8, and HcamOBP1 had 100% sequence similarity and identical lengths (number of amino acids) across their respective homologs in the male and female genomes. HcamOBP7 was only found in the male genome and HcamOBP9 was only found in the female genome. HcamOBP2 to HcamOBP8 had a six conserved cysteine signature with the sequence features C 1 -X 24 − 29 -C 2 -X 3 -C 3 -X 37 − 42 -C 4 -X 8 − 10 -C 5− X 8 -C 6 , (X represents any amino acid except cysteine), and were therefore classified in the “Classic OBP” subfamily (Fig. 8 ). HcamOBP1 had four cysteines conserved and was classified as a “Minus-C OBP” subfamily gene (Fig. 8 ). The signal peptide (Sec/SPI) was predicted in HcamOBP2, HcamOBP3, HcamOBP4, HcamOBP5, HcamOBP6, HcamOBP8, and HcamOBP9, all with a probability > 0.95. The predicted cleavage sites for these proteins were as follows: HcamOBP2 (positions 23/24), HcamOBP3 (19/20), HcamOBP4 (18/19), HcamOBP5 (17/18), HcamOBP6 (17/18), and HcamOBP8 (20/21). The amino acid length ranged between 103 aa and 162 aa with an average of 146 aa (Supplementary Table 8). The nine OBP genes retrieved for H. camelina , (Table 1 ) is far less than G. morsitan’s 32 OBPs ( 34 ). This drop in the number of insect pheromone/odorant-binding genes in Hippobosca may explain the obligate and high host specificity lifestyle of this keds. Additionally, the limited ORs, despite the diverse OBPs, indicate a specialized olfactory mechanism, potentially focusing on key environmental odorants crucial for survival and ecological interactions. This finding underscores the complexity of olfactory processing in these species, where receptor diversity does not directly parallel the variety in odorant binding capabilities ( 35 ). Phylogenetic analysis showed that HcamOBP5 and HcamOBP6 group within a conserved clade containing AgamOBP54 and DmelObp57b, suggesting functional parallels in odour detection. Similarly, HcamOBP9 and HcamOBP8 cluster closely together, indicating a shared evolutionary origin or related function. These observations suggest that H. camelina OBPs retain core roles in olfactory processes while also exhibiting species-specific divergence. Several H. camelina OBPs including HcamOBP4 and HcamOBP3, form unique sub-branches within clades that include OBPs from the other species, this would indicate adaptations to specific ecological niches. For instance, HcamOBP4 clusters with DmelObp19d, suggesting potential specialization in recognizing odorants or pheromones. Additionally, HcamOBP1 groups with conserved genes, GmmOBP5 and AgamOBP33, reflect their evolutionary importance and potential functional similarity in chemical signaling across insect species (Fig. 9 ). This phylogenetic analysis demonstrates that Hcam OBP genes exhibit a mix of conservation and divergence. While they cluster with OBPs from other dipterans, reflecting their shared evolutionary origins, their distinct positioning in some clades suggests adaptations to the specific ecological context of Hippobosca camelina . Further functional studies could confirm whether these genes are involved in host detection or other olfactory-driven behaviors specific to this parasitic fly. vi) Sensory Neuron Membrane Proteins (SNMPs) Sensory Neuron Membrane Proteins (SNMPs), these molecules belong to the CD36 superfamily, which is categorized as lipid receptors and transporters. They participate in a wide range of functions, such as the recognition and conveyance of lipids, lipophilic substances, and lipoproteins. Their structure comprises two transmembrane domains and a substantial ectodomain responsible for interacting with ligands. Both H. camelina male and female had only 1 SNMP gene predicted. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that both HcamSNMP1 genes had 100% sequence similarity and identical lengths (number of amino acids). The SNMP gene had 565 amino acids with 9 exons, (Supplementary Table 9). In contrast, most dipterans contain 2 SNMP genes, (Table 1 ). Interestingly, a similar study involving the sheep ked ( 1 ) did not document any SNMP gene, this may suggest possible continuous evolutionary events that may have led to the loss of the other gene. The phylogenetic analysis of SNMPs in Hippobosca camelina revealed distinct evolutionary relationships with homologs from Glossina species and Drosophila melanogaster , (Fig. 10 ). The analysis showed that the HcamSNMP1 is closely associated with DmelSnmp2, forming a well-supported clade that diverges from the main lineage containing DmelSnmp1 and the Glossina SNMP1 group. The close clustering of HcamSNMP1 with DmelSnmp2 suggests a potential functional divergence or specialization within this gene family. In contrast, the Glossina SNMP1 genes (GmmSNMP1, GfucSNMP1, and GbreSNMP1) form a separate, cohesive clade, indicating evolutionary divergence between H. camelina and Glossina SNMP1 genes. These findings highlight possible lineage-specific adaptations in H. camelina SNMP, which may play a critical role in chemosensory processes, such as host detection and olfactory signalling. Table 1 Comparison of Chemosensory Gene Numbers Across H. camelina, Melophagus ovinus , and Glossina morsitans . Chemosensory gene family Hippobosca camelina Melophagus ovinus Glossina Morsitans Chemosensory Specific Proteins (CSPs) 4 3 5 Ionotropic Receptors (Irs) 18 6 30 Gustatory Receptors (GRs)​ 7 11 14 Odorant Receptors (ORs) 5 2 46 Odorant Binding Proteins (OBP​s) 9 3 32 Sensory Neuron Membrane Proteins (SNMPs) ​ 1 0 2 The comparison includes gene counts for Chemosensory Specific Proteins (CSPs), Ionotropic Receptors (I R s), Gustatory Receptors (GRs), Odorant Receptors (ORs), Odorant Binding Proteins (OBPs), and Sensory Neuron Membrane Proteins (SNMPs), illustrating the differences in chemosensory gene numbers across these species and sexes. Conclusion This study generated two genomes for Hippobosca camelina female and Hippobosca camelina male. Both of these are smaller in size compared to Melophugus ovinus ( 1 ) and Glossina morsitans ( 2 ). The Hippobosca genomes have a lower repeat content compared to G. morsitans and M. ovinus , a phenomenon that may explain the reduced genome size. A total of forty-four chemosensory genes were annotated for Hippobosca camelina ked. The obligate parasitic lifestyle, limited movement, and narrow host specificity in Hippobosca camelina could be attributed to the reduced chemosensory system genes across the six known families of chemosensory genes as reported in this study. Materials and Methods Field data collection, DNA isolation and sequencing Male and Female keds were collected from the Laisamis area, Marsabit County, Kenya. The samples were hand-picked and kept in perforated water bottles to prevent them from suffocating. They were shipped to the International Centre of Insect Physiology and Ecology ( icipe ), Molecular Biology and Bioinformatics Unit (MBBU) laboratories, Kenya and stored in a -80 degrees celsius freezer before processing. DNA was extracted from the thoracic muscle using the Protein Precipitate Solution (PPS) method and eluted using 40uL of elution buffer from Qiagen's DNA extraction kit. Nucleic acids were run on a 2% agarose gel to check their integrity. Library Preparation and Sequencing The sequencing library was prepared using the Ligation Sequencing Kit (SQK-LSK109) using 1 g (or 100–200 fmol) of gDNA. The process began with size selection of the DNA, followed by an end-prep and nick repair step. During this stage, the DNA ends were repaired and prepared for adapter attachment. The next step involved the ligation of sequencing adapters, using components provided in the kit, to the prepared DNA ends. The ligation reaction included Ligation Buffer (LNB), NEBNext Quick T4 DNA Ligase, and Adapter Mix (AMX). The reaction mixture was incubated to facilitate the attachment of the adapters. After ligation, the library was cleaned up using AMPure XP beads to remove excess adapters and other reaction components. The cleaned library was eluted in Elution Buffer (EB) and quantified using a Qubit fluorometer. The final prepared library was loaded onto a SpotON Flow Cell using the appropriate amount of Sequencing Buffer (SQB) and Loading Beads (LB), as per the MinION device requirements. Base calling was performed using Dorado version 7.2.13. Genome Assembly and Quality assessment Adapters still attached to the Oxford Nanopore (ONT) reads were removed using chopper version v0.8.0 ( 36 ). Flye version 2.9.4( 37 ) a long-read assembler was employed to assemble the reads. For the male ked genome, Pilon version 1.24( 38 ) was used to polish the genome using high-quality, > Q30, Illumina short reads obtained from a previous experiment involving a camel male ked. The short Illumina reads were first mapped to the assembled genome using bwa2 version 0.7.18 ( 39 ) and 99.9% of the reads mapped to the genome. This was necessary to ensure the two species were not cryptic. The improvement involved filling gaps, and correcting single base differences, indels, and insertions. Compleasm version 0.2.6 ( 40 ) was used to assess the Busco completeness of the assembled genome using Dipteran lineages_odb10 ( 41 ). The assessment involved the evaluation of various metrics, including conserved genes, contig and scaffold N50, largest and smallest contigs. Genome annotation and Chemosensory gene retrieval and analysis RepeatModeler version 2.0.4, a de novo transposable element (TE) family identification and modelling package, was used to model de novo repeat element boundaries and family relationships from the assembled genome. It utilized three other repeat finding programs (RECON, Repeat Scout, and LtrHarvest/Ltr_retriever) to construct a high-quality library of the TE family’s library compatible with RepeatMasker. RepeatMasker program version 4.1.4 ( 42 ) was used to soft mask the assembled genome using the repeat library generated by RepeatModeler. Braker version 3.0.8 ( 23 , 43 – 51 ), a fully automated ab-initio gene predictor that incorporates GeneMark-ES/ET( 52 ) and AUGUSTUS( 53 ) in novel eukaryotic genome gene prediction, was used to predict the intron-exon boundaries, start, and stop codons from the generated assembly. Hints were prepared using whole genome proteins from Glossina morsitans morsitans, Glossina fuscipes, Glossina brevipalpis, Anopheles gambiae , and Drosophila melanogaster . Braker was then run using the genome and the prepared hints, producing high-quality gene structures. The predicted genes were subjected to a quality check using Compleasm version 0.2.6( 40 ) in reference to Metazoan_odb10, Arthropoda_odb10, Insecta_odb10, and Dipteran lineages_odb10( 41 ) lineage databases. For functional assignment, Orthofinder version 2.5 ( 54 , 55 ), a precise and all-encompassing platform for comparative genomics. All the predicted genes were assigned to different orthogroups. A total of 9 close species were used, including Anopheles gambiae , Glossina morsitans morsitans, Glossina fuscipes, Glossina brevipalpis , and Drosophila melanogaster , to identify their homologs in the predicted genes. These generated orthogroups contained orthologous genes. SeqKit version 2.5.0 ( 56 ), in combination with basic bash commands, was used to filter out predicted chemosensory gene homologs of interest from the orthogroups and these were subjected to further tests to confirm whether they are true genes. Confirmation of the predicted chemosensory genes The putative genes were subjected to further analysis and tests to confirm whether they are true genes. This included (i) Reverse blasting to vector base database( 57 ) using BlastP online version integrated in VectorBase with an e-value of 0.001. (ii) Functional gene domain presence confirmation by blasting against the NCBI Conserved Domain Database (NCBI CDD) at an e-value of 0.001, and (iii) Amino acid alignment of the gene sequences to confirm the positions of the conserved residues and motifs using Muscle tool within Mega( 58 ) and visualized the alignment with Jalview version 2.10.5 ( 59 ). Finally, Phylogenetic analysis using RaxML version 1.2.2( 60 ) with 1000 bootstraps. SignalP 6.0( 61 ) was used to predict the presence of the signal peptide and the amino acid cleavage sites for chemosensory-specific proteins and the odorant binding proteins. Manual annotation Artemis version 18.2.0 ( 62 ), a genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the sequence context, and its six-frame translation, was used to visualize the predicted genes. Artemis allowed inspection of the intron-exon junctions to ensure they contained the right residues, followed the intron-exon rules, and corrected any other feature requiring manual intervention. The intron donor splice site was checked for the presence of GT, and the acceptor site for the presence of AG. Additionally, we confirmed the presence of ATG at the 5’ of the gene (start codon) and either TAG, TAA, or TGA at the 3’ of the gene (stop codon). Phylogenetic clustering of chemosensory genes MUSCLE tool version 5 ( 63 ) was used to perform multiple sequence alignment with 100 iterations for all the putative chemosensory gene sequences (amino acids) of Hippobosca camelina , per individual chemosensory gene family. These sequences were aligned alongside gene models from well-characterized chemosensory genes in Drosophila melanogaster, Glossina fuscipes, Glossina morsitans morsitans, Glossina brevipalpis , and Anopheles gambiae . The resulting alignments were automatically edited using Trimal version 1.4.1 ( 64 ) tool with the strict-plus option. The edited alignment was used to construct a maximum likelihood phylogenetic tree with 1000 bootstraps and LG + FC + G8m as the best-fitting model as implemented in RAxML-NG v1.2.0 ( 60 ). The resulting phylogenetic tree was viewed and edited using the iTOl tree viewer version 5 ( 65 ). Abbreviations CSP chemosensory-specific protein IR Ionotropic receptor GR Gustatory receptor OR Odorant receptors OBP Odorant binding protein SNMP Sensory Neuron Membrane Protein DNA Deoxyribonucleic Acid RNA Ribonucleic Acid LNB Ligation Buffer AMX Adapter Mix ONT Oxford Nanopore CDD Conserved Domain Database BMZ German Federal Ministry for Economic Cooperation and Development GIZ Deutsche Gesellschaft für Internationale Zusammenarbeit FIA Fund for International Agricultural Research Declarations Authors’ contribution Fredrick Kebaso - Data analysis and manuscript writing Souleymane Diallo – Manuscript review Caleb Kibet -Manuscript review Suhaila Hashim - Manuscript review JohnMark O Makwatta and Dennis Getange – sample collection, DNA Extraction, and manuscript review Domelevo Entfellner, Jean-Baka – Genome sequencing and manuscript review Merid Getahun – Provided the scanned image of the head region of the Hippobosca camelina and Manuscript review Daniel Masiga – Manuscript review All authors read and approved the manuscript Funding This study was funded by The German Federal Ministry for Economic Cooperation and Development (BMZ) commissioned and administered through the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) Fund for International Agricultural Research (FIA), grant number 81235250 Availability of data and materials The codes and scripts used in this study can be accessed at: (https://github.com/fredrickkebaso/Hippobosca-camelina-Genome-and-Chemosensory-genes). The assembled genomes are available at NCBI - Genbank with the following accessions: Hippoboscas camelina male genome assembly: GCA_041146595.1 Hippoboscas camelina female genome assembly: GCA_041146635.1 The raw data used in this study is available in the NCBI Sequence Read Archive with the accessions specified below: Hippobosca camelina female Nanopore Raw genomic DNA sequences: SRX25529404 Hippobosca camelina male Nanopore Raw genomic DNA sequences: SRX25529403 The chemosensory genes characterised in this study can be accessed in the NCBI-GenBank database using gene accessions listed in the Supplementary tables (Table 4, Table 5, Table 6, Table 7, Table 8, and Table 9). Ethics approval and consent to participate The study was approved by the International Centre of Insect Physiology and Ecology’s Institutional Animal Care and Use Committee (IACUC) ( icipe - IACUC ref no. IcipeACUC2018-003-2023). 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6505113","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":453782978,"identity":"03c35b52-f1e5-4f5c-bb41-1c8e2be3de19","order_by":0,"name":"Fredrick Kebaso","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0UlEQVRIiWNgGAWjYBAC9gYgkWDAwMDPzMBwgCgtPAfAWgwYJJtJ0sLAYMBgQJx6kBaxw88+PCj4I298nPnh4YIKBjnz/gUEtEinGc8AOsxw22E2g8MzzjAYy9x4gF+LvXSCMcgvjNsO8zAc5m1jSJwhQcCJPNLpn0Fa7Dc3g7T8I0pLDtiWxA3MIC0NQC38DQS1FAO1GCfPAPvlmISxhAR+HSCHbWb88UfOtr//8OPPBTU2chL8BByGAoAJAGiFRAJpWoCAJFtGwSgYBaNgJAAAxwk9g7bXV4YAAAAASUVORK5CYII=","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":true,"prefix":"","firstName":"Fredrick","middleName":"","lastName":"Kebaso","suffix":""},{"id":453782979,"identity":"9c6f6886-5828-4f38-a510-4d13b9d91926","order_by":1,"name":"Souleymane Diallo","email":"","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":false,"prefix":"","firstName":"Souleymane","middleName":"","lastName":"Diallo","suffix":""},{"id":453782982,"identity":"5e779c01-f154-4dba-9b6b-6827e31a97bf","order_by":2,"name":"Caleb Kibet","email":"","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":false,"prefix":"","firstName":"Caleb","middleName":"","lastName":"Kibet","suffix":""},{"id":453782983,"identity":"7c499ca5-0d72-4157-a3d2-0c827a25b7bf","order_by":3,"name":"Suhaila Hashim","email":"","orcid":"","institution":"Pwani Univerisity","correspondingAuthor":false,"prefix":"","firstName":"Suhaila","middleName":"","lastName":"Hashim","suffix":""},{"id":453782984,"identity":"594363f5-3f2f-491c-aa5c-fd546caf50dd","order_by":4,"name":"JohnMark Makwatta","email":"","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":false,"prefix":"","firstName":"JohnMark","middleName":"","lastName":"Makwatta","suffix":""},{"id":453782985,"identity":"d85d4625-05bd-4e59-8b2b-31b471023ef9","order_by":5,"name":"Merid Getahun","email":"","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":false,"prefix":"","firstName":"Merid","middleName":"","lastName":"Getahun","suffix":""},{"id":453782986,"identity":"bd6d18a9-542e-4c29-8d75-62b6def25e7b","order_by":6,"name":"Dennis Getange","email":"","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":false,"prefix":"","firstName":"Dennis","middleName":"","lastName":"Getange","suffix":""},{"id":453782989,"identity":"7ad3a402-95d6-4ce5-bc65-affb07efe95f","order_by":7,"name":"Jean-Baka Domelevo Entfellner","email":"","orcid":"","institution":"International Livestock Research Institute","correspondingAuthor":false,"prefix":"","firstName":"Jean-Baka","middleName":"Domelevo","lastName":"Entfellner","suffix":""},{"id":453782990,"identity":"9b91ae81-76ba-46e5-a890-30ae8ae3e280","order_by":8,"name":"Daniel Masiga","email":"","orcid":"","institution":"International Centre of Insect Physiology and Ecology","correspondingAuthor":false,"prefix":"","firstName":"Daniel","middleName":"","lastName":"Masiga","suffix":""}],"badges":[],"createdAt":"2025-04-22 14:08:19","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6505113/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6505113/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12864-025-11833-1","type":"published","date":"2025-07-16T16:05:43+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":82551025,"identity":"b6fe9971-2f60-412f-8c05-ea843583166f","added_by":"auto","created_at":"2025-05-12 20:14:32","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":546795,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eQuality of the assembled draft genome.\u003c/strong\u003e \u003cstrong\u003eA\u003c/strong\u003e. The metrics column shows the quality assessment of the assembled genome of H. camelinamale and female, \u003cstrong\u003eB\u003c/strong\u003e. BUSCO Completeness Analysis Across Different Lineages for H. camelina genomes, illustrating the percentages of single-copy (S), duplicated (D), fragmented (F), and missing (M) BUSCO genes for the lineage diptera_odb10. \u003cstrong\u003eC\u003c/strong\u003e. Scatter Plot of repeat elements in H. camelina Male and Female including retroelements, DNA transposons, rolling circles, unclassified sequences, small RNA, satellites, simple repeats, and low-complexity regions.\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/de868ab9812737da726a9dc9.png"},{"id":82551278,"identity":"73bb6ab4-28a8-4106-a404-4745ecc5f415","added_by":"auto","created_at":"2025-05-12 20:22:32","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":733318,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eMorphological characteristics of the head region of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eHippobosca camelina\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e(A) Head structure, (B) Antennal pit without antennal extension, (C) Scanned image of the antennal pit showing reduced number of olfactory sensillum, (D) Forked structure protrude from the base of the antenna, we named it equivalent of arista.\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/d47682fea0a376ea7c4ba865.png"},{"id":82551024,"identity":"e517548c-4d15-4d31-80fd-6d771ebd1c2d","added_by":"auto","created_at":"2025-05-12 20:14:32","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":500369,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eMultiple amino acid sequence alignment of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eH. camelina\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e CSPs.\u003c/strong\u003e The four conserved cysteine residues are labelled (\u003cstrong\u003eC1 to C4\u003c/strong\u003e) and highlighted with a red background and a black border. Amino acids that are 100% identical in all sequences are also shown with different colours.\u003c/p\u003e\n\u003cp\u003eA phylogenetic tree was generated to infer the relationships between the annotated CSPs with homologs from \u003cem\u003eGlossina morsitans\u003c/em\u003e, \u003cem\u003eGlossina brevipalpis\u003c/em\u003e, \u003cem\u003eGlossina fuscipes\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e. HcamCSP4 clustered closely with GmmCSP5 and GfucCSP5, indicating a potential shared ancestry and functional conservation. Similarly, HcamCSP3 forms a distinct clade with GbreCSP4, GfucCSP4, and GmmCSP4, suggesting diversification within this gene family. HcamCSP2 is positioned near GbreCSP2, GfucCSP2, and GmmCSP2, while HcamCSP1 aligns closely with GfucCSP3 and GmmCSP3, (Figure 4). This suggests that \u003cem\u003eH. camelina\u003c/em\u003e CSPs are evolutionarily linked to their \u003cem\u003eGlossina\u003c/em\u003e and \u003cem\u003eAnopheles \u003c/em\u003ehomologs, highlighting conserved roles in chemosensory functions with species-specific adaptations that could be critical for host recognition and survival in \u003cem\u003eH. camelina\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/05ffc3d612bfff28d9a27619.png"},{"id":82551027,"identity":"75fb5134-45fc-499f-81ea-c7fb7fc5a8e0","added_by":"auto","created_at":"2025-05-12 20:14:32","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":242356,"visible":true,"origin":"","legend":"\u003cp\u003eApproximate maximum likelihood phylogenetic tree for the annotated \u003cem\u003eHippobosca camelina\u003c/em\u003e chemosensory protein (CSP) sequences. The analysis also included CSP gene sequences from four closely related insect species: \u003cem\u003eGlossina brevipalpis\u003c/em\u003e, \u003cem\u003eGlossina fuscipes\u003c/em\u003e, \u003cem\u003eGlossina morsitans\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/ef60376b6329a80f52862fb4.png"},{"id":82551030,"identity":"d6427bf3-7bfc-40e6-8bb2-388280f99c86","added_by":"auto","created_at":"2025-05-12 20:14:32","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":601513,"visible":true,"origin":"","legend":"\u003cp\u003eApproximate maximum likelihood phylogenetic tree for the annotated \u003cem\u003eHippobosca camelina\u003c/em\u003e Ionotropic receptor (IR) sequences. The analysis also included IR gene sequences from three closely related insect species: \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina m. morsitans\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/3a2835c6d96a8b740446b3e2.png"},{"id":82551032,"identity":"7d61b0d2-3baf-4179-9078-df96bdc800e6","added_by":"auto","created_at":"2025-05-12 20:14:32","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":671266,"visible":true,"origin":"","legend":"\u003cp\u003eApproximate maximum likelihood phylogenetic tree for the annotated \u003cem\u003eHippobosca camelina\u003c/em\u003e Gustatory receptors (GRs) sequences. The analysis also included GR gene sequences from four closely related insect species: \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina brevipalpis\u003c/em\u003e, \u003cem\u003eGlossina fuscipes\u003c/em\u003e, \u003cem\u003eGlossina morsitans\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"floatimage6.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/8aaf28148b475d6f7a719ccd.png"},{"id":82551294,"identity":"835ee363-8d02-4cc2-9f11-91d580c9150e","added_by":"auto","created_at":"2025-05-12 20:22:38","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":716574,"visible":true,"origin":"","legend":"\u003cp\u003eApproximate maximum likelihood phylogenetic tree for the annotated \u003cem\u003eHippobosca camelina\u003c/em\u003e Odorant receptors (ORs) sequences. The analysis also included OR gene sequences from three closely related insect species: \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina morsitans\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e. The orco-co-receptor sequences clustered in one clade confirming the high similarity indices among the orco sequences from different species.\u003c/p\u003e","description":"","filename":"floatimage7.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/3e664f5be3b584fa0e5c764f.png"},{"id":82551591,"identity":"45edb50f-b602-4738-ac8c-f1a44bb2b7bc","added_by":"auto","created_at":"2025-05-12 20:30:32","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":1060353,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eMultiple amino acid sequence alignment of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eH. camelina\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e OBPs.\u003c/strong\u003e The six conserved cysteine residues are labelled (\u003cstrong\u003eC1 to C6\u003c/strong\u003e) and highlighted with a blue background and a black border.\u003c/p\u003e","description":"","filename":"floatimage8.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/75c1f9924371ec46f5df9e6c.png"},{"id":82551282,"identity":"7cddc820-aaa9-4f04-8b32-c106cdb5c56c","added_by":"auto","created_at":"2025-05-12 20:22:32","extension":"jpeg","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":1480895,"visible":true,"origin":"","legend":"\u003cp\u003eApproximate maximum likelihood phylogenetic tree for the annotated \u003cem\u003eHippobosca camelina\u003c/em\u003e Odorant Binding Proteins (OBP) sequences. The analysis also included OBP gene sequences from three closely related insect species: \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina morsitans\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"floatimage9.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/89df4b2f65521e58ca636f4c.jpeg"},{"id":82551041,"identity":"f3571568-aec3-4336-ac3e-ee12088d455b","added_by":"auto","created_at":"2025-05-12 20:14:32","extension":"png","order_by":10,"title":"Figure 10","display":"","copyAsset":false,"role":"figure","size":108836,"visible":true,"origin":"","legend":"\u003cp\u003eApproximate maximum likelihood phylogenetic tree for the annotated \u003cem\u003eHippobosca camelina\u003c/em\u003e Sensory Neuron Membrane Protein (SNMP) sequence. The analysis also included SNMPs gene sequences from four closely related insect species: \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina brevipalpis\u003c/em\u003e, \u003cem\u003eGlossina fuscipes\u003c/em\u003e, and \u003cem\u003eGlossina morsitans\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"floatimage10.png","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/33a97e47a5b95765493d9da5.png"},{"id":87220382,"identity":"06475f7a-c117-4862-920a-17e194a28a8f","added_by":"auto","created_at":"2025-07-21 16:12:19","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":7920684,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/ace610fd-ca9d-440e-a8fb-0d5b7e514753.pdf"},{"id":82551590,"identity":"aaf80f66-55b4-4f38-9d8c-e1e99e01fe5c","added_by":"auto","created_at":"2025-05-12 20:30:32","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":33967,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementarymaterial.docx","url":"https://assets-eu.researchsquare.com/files/rs-6505113/v1/80634669b688b47dfc03b953.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"De novo genome assembly, annotation, and characterization of chemosensory genes in the camel ked (Hippobosca camelina)","fulltext":[{"header":"Background","content":"\u003cp\u003eHippoboscid flies, or keds, are obligate hematophagous or blood-sucking ectoparasites that invade birds, mammals, and rarely humans(\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e). They are dipterans that belong to the superfamily of the Hippoboscoidea along with the Glossinidae family. The current taxonomic classification of \u003cem\u003eHippobosca\u003c/em\u003e species is based on morphological traits, particularly species-specific patterns of colouration on the scutellum (\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e). Genomic studies provide insight into the genome structure and functional genes of organisms. This has provided useful information on the behavioural ecology of many insects of veterinary importance (\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e). Additionally, genomic studies have established a molecular basis for decades-old ecological observations, such as the preference for specific colours in trap designs for the deer ked (\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e). The integration of genomics with field ecology holds great promise for developing innovative and effective tools in vector control, capitalizing on the genetic basis of insect behaviour, and leveraging the identified receptors for targeted interventions against disease vectors (\u003cspan additionalcitationids=\"CR8 CR9\" citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e). However, the \u003cem\u003eHippobosca\u003c/em\u003e genome is absent from existing databases, limiting the understanding of vector biology, which is necessary to design control strategies for \u003cem\u003eHippobosca camelina\u003c/em\u003e. Annotation of chemosensory genes in \u003cem\u003eHippobosca camelina\u003c/em\u003e underpins the design of eco-friendly traps, baits, and vector control strategies.\u003c/p\u003e \u003cp\u003eAs obligate blood-feeders, they potentially vector several infectious pathogens such as protozoa, bacteria, helminths, trypanosomes, and viruses to their hosts (\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e). Although the role of \u003cem\u003eHippobosca\u003c/em\u003e species as disease vectors is still under-explored, there is evidence of the existence of epizootic pathogens in keds: \u003cem\u003eTrypanosoma melophagium\u003c/em\u003e, \u003cem\u003eT. vivax\u003c/em\u003e, \u003cem\u003eT. evansi\u003c/em\u003e, and \u003cem\u003eCandidatus anaplasma camelii\u003c/em\u003e in \u003cem\u003eHippobosca camelina\u003c/em\u003e, (\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eFurthermore, high infestation by these blood-feeding parasites impairs the hosts' health, exposing them to alopecia, anaemia, skin lesions, stress, sickness, and death if not treated (\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e). Hence, there is a need to study camel ked's vector competence and capability to determine the pathogen transmission potential to uninfected hosts, and the role of keds as vectors.\u003c/p\u003e \u003cp\u003eAdditionally, for obligate hematophagous ectoparasites like Hippoboscid flies (keds) and \u003cem\u003eGlossina sp\u003c/em\u003e, the olfactory system is critical for host detection, mate location, predator evasion, and navigating ecological niches. Furthermore, vector control strategies have taken advantage of insect chemical sensing systems to develop several olfactory-based tools for vector management. For example, this system has been exploited in \u003cem\u003eGlossina\u003c/em\u003e (tsetse fly species), a close species of Hippobosca keds, to design traps and odor baits, which have played a vital role in combating African Trypanosomiasis AT in tropical areas (\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e, \u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eDespite their biological and epidemiological significance, the chemosensory mechanisms of \u003cem\u003eHippobosca\u003c/em\u003e keds remain poorly understood. This knowledge gap has limited the development of targeted vector management strategies, particularly in regions where these parasites contribute to the spread of vector-borne diseases in livestock and wildlife. To date, the most studied species in the \u003cem\u003eHippoboscidae\u003c/em\u003e family includes \u003cem\u003eM. ovinus\u003c/em\u003e (Sheep ked) and \u003cem\u003eH. equina\u003c/em\u003e, and only \u003cem\u003eM. ovinus\u003c/em\u003e, transmitting \u003cem\u003eAnaplasma ovis\u003c/em\u003e and \u003cem\u003eRickettsiae\u003c/em\u003e in sheep and wild ruminants has its genome sequenced (\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e) However, molecular evidence and information on these two species on their biology, epidemiology, and pathogen transmission ability is scanty (\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eAs for \u003cem\u003eHippobosca camelina\u003c/em\u003e, mainly feeding on camel, little is known about the chemosensory system and no information is available on their genetic makeup limiting our understanding of the cellular and molecular basis of their host detection. In the current study, we aimed to assemble the genomes of \u003cem\u003eHippobosca camelina\u003c/em\u003e species and identify the putative chemosensory genes that support their superb chemical sensing ability.\u003c/p\u003e"},{"header":"Results and Discussion","content":"\u003cp\u003e \u003cul\u003e \u003cli\u003e \u003cp\u003e \u003cb\u003eHippobosca\u003c/b\u003e \u003cb\u003ecamelina whole genome assembly\u003c/b\u003e\u003c/p\u003e \u003c/li\u003e \u003c/ul\u003e \u003c/p\u003e \u003cp\u003eUsing nanopore technology, we sequenced the genome of an individual male and female of \u003cem\u003eH. camelina\u003c/em\u003e. The assembled draft genomes showed a relatively equivalent size for male (133.5 Mb) and female (135.6 Mb) with greater than 94% completeness relative to the Dipteran lineage (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e,A). This is 50% less than the well-annotated \u003cem\u003eGlossina morsitans morsitans\u003c/em\u003e genome with 366 Mb (\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e) and slightly smaller than the sheep ked (\u003cem\u003eMelophagus ovinus\u003c/em\u003e) with 188 Mb (\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e). The reduction in the genome size would be partially attributed to the reduced repeats in \u003cem\u003eH. camelina\u003c/em\u003e female with 17.08 %, and\u003cem\u003eH. camelina\u003c/em\u003e male with 15.38% repeats, compared to 27.08% of \u003cem\u003eMelophagus ovinus\u003c/em\u003e (\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e) and 34.95% of \u003cem\u003eG. morsitans\u003c/em\u003e (\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e), among other genome attributes. The most abundant repeat elements were simple repeats, (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e,C) followed by low-complexity repeats for both genomes (Supplementary Table\u0026nbsp;2 and Table\u0026nbsp;3) showing the detailed repeat element counts and Nucleotide base pairs covered by each repeat element. The GC content is 33.5% for both Keds relatively equal to 33% of \u003cem\u003eG. morsitans\u003c/em\u003e (\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe \u003cem\u003eHippobosca camelina\u003c/em\u003e male and female genomes had contig N50 of 419.6 kb and 1.2 Mb, respectively. The low contig N50 implies low genome contiguity of the final assembly, consequently leading to fragmented assemblies with over 2,000 contigs for both genomes, (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e, A). However, the genome quality completeness exceeded 94% for both genomes relative to the dipteran lineage; \u003cem\u003eH. camelina\u003c/em\u003e female (S:95.83%, 3148, D:0.30%, 10, F:0.30%, 10, I:0.00%, 0, M:3.56%, 117, N:3285), (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e,B). \u003cem\u003eH. camelina\u003c/em\u003e male (S:94.70%, 3111, D:0.49%, 16, F:0.85%, 28, I:0.00%, 0, M:3.96%, 130, N:3285), (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e,A). Although the genome is not 100% complete, the high completion rate suggests that most core conserved genes are faithfully represented in the assembled genome.\u003c/p\u003e \u003cp\u003eA greater number of hypothetical genes totalling up to 14,240 genes for \u003cem\u003eH. camelina\u003c/em\u003e male and 13,496 genes for \u003cem\u003eH. camelina\u003c/em\u003e female, were found to be orthologous to genes from selected dipterans including Drosophila melanogaster, \u003cem\u003eGlossina morsitans morsitans\u003c/em\u003e, \u003cem\u003eG. fuscipes, G. brevipalpis\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e. This is in comparison to \u003cem\u003eM. ovinus\u003c/em\u003e, which had 9,505 genes (\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e) and the genome of \u003cem\u003eG. morsitans\u003c/em\u003e is estimated to contain 12,308 protein-encoding genes based on automated and manual annotations. Of this, 9,172 \u003cem\u003eGlossina\u003c/em\u003e genes (74%) have a Dipteran ortholog (\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e). These variations in the number of genes predicted and ortholog assignments can be attributed to the fragmented genome of \u003cem\u003eHippobosca camelina\u003c/em\u003e, consequently leading to fragmented gene predictions. Additionally, \u003cem\u003eHippobosca\u003c/em\u003e genome ab initio predictions might have generated false positives, while other genes could be non-functional despite displaying high similarity and orthology indices.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eOlfactory structure of \u003cem\u003eH. camelina\u003c/em\u003e\u003c/h2\u003e \u003cp\u003e \u003cem\u003eH. camelina\u003c/em\u003e possesses a reduced olfactory apparatus, with diminished antennal structures (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA) compared to other dipteran flies, which have been shown to rely heavily on olfaction for locating food and mates (\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e). Our preliminary scanning electron micrographs showed a reduced antennal surface area and sensillum number diversity (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC). Given its close association with camel hosts, the reduced olfactory apparatus may indicate a shift toward contact-based host detection rather than long-range olfactory host-seeking. To pave the way for deeper insights in understanding olfactory adaptations in \u003cem\u003eH. camelina\u003c/em\u003e we focused on characterizing for the first time the chemosensory genes repertoire in male and female of camel ked.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e(A) Head structure, (B) Antennal pit without antennal extension, (C) Scanned image of the antennal pit showing reduced number of olfactory sensillum, (D) Forked structure protrude from the base of the antenna, we named it equivalent of arista.\u003c/p\u003e \u003cp\u003e \u003col\u003e \u003cspan\u003e \u003cli\u003e \u003cp\u003e \u003cb\u003ei) Chemosensory Specific Proteins (CSPs)\u003c/b\u003e \u003c/p\u003e \u003c/li\u003e \u003c/span\u003e \u003c/ol\u003e \u003c/p\u003e \u003cp\u003eChemosensory specific proteins (CSPs) are soluble hydrophobic proteins, majorly involved in Carbon II Oxide detection, transmitting chemical signals, chemoperception which encompasses olfactory cues and taste detection, in early stages of larval growth, brood (immature stages of the bee colony, such as eggs, larvae, and pupae) pheromone transportation (\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e) CSPs contain a highly conserved four cysteine signature across dipterans. They are uniquely identified with the presence of a signal peptide and alpha helices joined by disulphide bonds. They have an average length of 130 aa (\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e)\u003c/p\u003e \u003cp\u003eIn this study, we identified 4 CSP genes for both \u003cem\u003eH. camelina\u003c/em\u003e female and male. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamCSP1, HcamCSP2, HcamCSP3, and HcamCSP4 exhibited\u0026thinsp;\u0026gt;\u0026thinsp;99% sequence similarity and had identical lengths (number of amino acids) across their respective homologs in the male and female genomes. All the 4 CSP genes had four conserved cysteine signatures with the sequence features C\u003csub\u003e1\u003c/sub\u003e-X\u003csub\u003e6\u003c/sub\u003e-C\u003csub\u003e2\u003c/sub\u003e-X\u003csub\u003e19\u003c/sub\u003e-C\u003csub\u003e3\u003c/sub\u003e-X\u003csub\u003e2\u003c/sub\u003e-C\u003csub\u003e4,\u003c/sub\u003e (X represents any amino acid other than cysteine), (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). All four CSPs contained the Signal Peptide (Sec/SPI) with the prediction probabilities\u0026thinsp;\u0026gt;\u0026thinsp;0.85 for HcamCSP1, HcamCSP2, and HcamCSP3. HcamCSP4 had a lower prediction probability of 0.5826. The cleavage positions for the CSPs were predicted as: HcamCSP1 at position 20/21, HcamCSP2 at position 18/19, HcamCSP3 at position 17/18, and HcamCSP4 at position 29/30. The amino acid length ranged between 113 aa and 162 aa, with an average of 136 aa. HcamCSP2, HcamCSP3 and HcamCSP4 had 2 exons each while HcamCSP1 had a single exon, (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e and Supplementary Table\u0026nbsp;4).\u003c/p\u003e \u003cp\u003eNotably, \u003cem\u003eHippobosca camelina\u003c/em\u003e and \u003cem\u003eGlossina morsitans\u003c/em\u003e share a comparable number of CSP genes, with \u003cem\u003eG. morsitans\u003c/em\u003e having 5 CSP genes (\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e) while \u003cem\u003eM. ovinus\u003c/em\u003e has 3 CSP genes (\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eA phylogenetic tree was generated to infer the relationships between the annotated CSPs with homologs from \u003cem\u003eGlossina morsitans\u003c/em\u003e, \u003cem\u003eGlossina brevipalpis\u003c/em\u003e, \u003cem\u003eGlossina fuscipes\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e. HcamCSP4 clustered closely with GmmCSP5 and GfucCSP5, indicating a potential shared ancestry and functional conservation. Similarly, HcamCSP3 forms a distinct clade with GbreCSP4, GfucCSP4, and GmmCSP4, suggesting diversification within this gene family. HcamCSP2 is positioned near GbreCSP2, GfucCSP2, and GmmCSP2, while HcamCSP1 aligns closely with GfucCSP3 and GmmCSP3, (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). This suggests that \u003cem\u003eH. camelina\u003c/em\u003e CSPs are evolutionarily linked to their \u003cem\u003eGlossina\u003c/em\u003e and \u003cem\u003eAnopheles\u003c/em\u003e homologs, highlighting conserved roles in chemosensory functions with species-specific adaptations that could be critical for host recognition and survival in \u003cem\u003eH. camelina\u003c/em\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eii) Ionotropic Receptors (IRs)\u003c/h3\u003e\n\u003cp\u003eInsect ionotropic receptors (IRs) are a broad class of ligand-gated ion channels that play an important role in chemosensation, specifically in the detection of acids, amines, and other volatile chemicals. They are evolutionarily related to ionotropic glutamate receptors (iGluRs) and facilitate direct ion flow when ligands are bound. They are largely found in olfactory sensory neurons, particularly in the coeloconic sensilla, especially in \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, but they also contribute to gustation and other sensory modalities (\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e, \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eWe identified 18 IRs in the \u003cem\u003eH. camelina\u003c/em\u003e male genome, and 17 IRs were recovered in female. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamIR8, HcamIR18, HcamIR4, HcamIR15a, HcamIR15b, HcamIR15c, HcamIR2, HcamIR3, HcamIR6, HcamIR7, HcamIR10, and HcamIR16 exhibited\u0026thinsp;\u0026gt;\u0026thinsp;99% sequence similarity and with relatively identical lengths (number of amino acids) across their respective homologs in the male and female genomes. HcamIR14, HcamIR17, HcamIR12, and HcamIR5 were identified in the \u003cem\u003eH. camelina\u003c/em\u003e female genome while HcamIR11, HcamIR1, HcamIR9 and HcamIR13 were identified in the male genome. The amino acid length ranged between 601 aa and 1181 aa with an average of 832 aa. The number of exons ranged between 5 and 16, (Supplementary Table\u0026nbsp;5). The retention of relatively equal gene numbers of both CSP and IRs (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e) would perhaps explain the obligate hematophagy or blood-sucking lifestyle common in these keds.\u003c/p\u003e \u003cp\u003eA phylogenetic analysis of \u003cem\u003eHippobosca camelina\u003c/em\u003e revealed distinct clustering patterns with orthologs from \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eAnopheles gambiae\u003c/em\u003e, and \u003cem\u003eGlossina morsitans morsitans\u003c/em\u003e. HcamIR1 and HcamIR2 were closely related to AgamIR176, AgamIR180, and GmmIr47a, suggesting conserved roles in odor detection. Similarly, HcamIR4 clustered with DmelIr31a and DmelIr56a, while HcamIR3 aligned with AgamIR133 and AgamIR195, indicating potential involvement in chemical signal transduction. HcamIR5, HcamIR6, and HcamIR7 grouped with AgamIR7x, DmelIr67a, and AgamNMDAR2, respectively, indicating expanded diversity. Notably, HcamIR13 through HcamIR18 clustered with AgamIr168 in one clade, (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e). These findings may suggest that \u003cem\u003eH. camelina\u003c/em\u003e chemosensory genes are evolutionarily conserved yet exhibit functional diversification, this may provide insights into their roles in host-seeking and survival behaviors.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e\n\u003ch3\u003eiii) Gustatory Receptors (GRs)\u003c/h3\u003e\n\u003cp\u003eGustatory Receptors (GRs), facilitate gustation, detection of nonvolatile chemicals (liquids or solids) or contact chemoreception. Additionally, Gustatory Receptor Neurons (GRNs) in Drosophila detect volatile compounds like N,N-diethyl-meta-toluamide (DEET) and coumarin by responding robustly to their vapors, revealing a dual role in both taste and olfactory signaling. This volatile sensitivity enhances the chemical coding capacity of GRNs, enabling flies to finely assess environmental cues for behavior guidance (\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e). They belong to a superfamily identified by the presence of seven transmembrane domains (7tm_7), which exhibit low sequence conservation, typically ranging from 7\u0026ndash;50% similarity, except for the C-terminus region, spanning 33 amino acid residues, which aligns with the seventh transmembrane domain (\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e). These genes respond to soluble tastes (sweet and bitter) and contact pheromones. They detect nonvolatile chemicals (liquids or solids) and facilitate contact chemoreception (\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cem\u003eH. camelina\u003c/em\u003e female had 6 GR genes and the male ked had \u003cb\u003e7\u003c/b\u003e GR genes. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamGR6, HcamGR7, HcamGR3, HcamGR1, HcamGR5, and HcamGR4 exhibited\u0026thinsp;\u0026gt;\u0026thinsp;99% sequence similarity and had identical lengths (number of amino acids) across their respective homologs in the male and female genomes. HcamGR2 was only identified in the male genome. The amino acid lengths ranged from 357 to 486 aa, with an average of 433 amino acids. The number of transmembrane domains varied between 5 and 9. The exon numbers ranged between 3 and 7, (Table\u0026nbsp;6\u003cem\u003e)\u003c/em\u003e. This number of \u003cem\u003eH. camelina\u003c/em\u003e GR genes (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e) is relatively lower than the 11 GR genes identified in \u003cem\u003eM. ovinus\u003c/em\u003e and significantly fewer than the 14 GR genes reported in \u003cem\u003eGlossina m. morsitans\u003c/em\u003e, (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). This would perhaps explain the adaptability to the narrow host range and strict host specificity among \u003cem\u003eHippobosca\u003c/em\u003e (\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e) and \u003cem\u003eM. ovinus\u003c/em\u003e (\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e) compared to \u003cem\u003eG. m. morsitans\u003c/em\u003e, which parasitizes a wider host range (\u003cspan additionalcitationids=\"CR29\" citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eA phylogenetic analysis of the 7 GRs annotated for \u003cem\u003eH. camelina\u003c/em\u003e was performed to infer the evolutionary relationship among \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina fuscipes\u003c/em\u003e, \u003cem\u003eAnopheles gambiae\u003c/em\u003e, \u003cem\u003eGlossina brevipalpis\u003c/em\u003e, and \u003cem\u003eGlossina morsitans\u003c/em\u003e. HcamGR4 clustered closely with GbreGr6 and AgamGr60, suggesting a shared ancestry and potential functional similarity in taste perception. Similarly, HcamGR3 was nested within a clade containing DmelGr8a and GfucGr9, highlighting its divergence from other GRs and potential specialization within this gene family. HcamGR6 aligned with DmelGr64a pointing to putative roles in sugar feeding. HcamGR7 formed a unique association with GfucGr5, indicating lineage-specific adaptations. HcamGR5 grouped closely with DmelGr98a and AgamGr13, reflecting evolutionary conservation in gustatory function. HcamGR1 aligned with AgamGr24 and DmelGr59e, suggesting a potential role in broad-spectrum taste perception, (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). These findings underscore the complex evolutionary trajectories and functional diversification of GR genes in \u003cem\u003eH. camelina\u003c/em\u003e, contributing to its ecological adaptation.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e\n\u003ch3\u003eiv) Odorant Receptors (ORs)\u003c/h3\u003e\n\u003cp\u003eOdorant Receptors (ORs), detect volatile and non-volatile chemo signals. Odorants propagate into the sensilla through pores and diffuse into the dendrites, facilitated by the OBPs, particularly the hydrophobic odour molecules (\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e). Insect ORs are characterised by a reversed N-terminal topology, an average length of 400 amino acids, and a seven-transmembrane domain (7tm_6). They function in complexes with Orco, a non-conventional co-receptor, to form functional ion channels that confer specificity to a repertoire of odorants (\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cem\u003eH. camelina\u003c/em\u003e female had 5 ORs and \u003cem\u003eH. camelina\u003c/em\u003e male had 5 OR genes. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamOr1, HcamOrco, HcamOr4a, HcamOr4b, HcamOr3, and HcamOr2 exhibited 100% sequence similarity and identical lengths (number of amino acids) across their respective homologs in the male and female genomes. The amino acid length ranged between 363 aa and 476 aa. The transmembrane domains varied between 3 and 7, (Supplementary Table\u0026nbsp;7). The reduced number of ORs further supports the absence of antennal extension which houses the sensilla with the olfactory sensory organs where ORs are expressed (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB). The decrease in OR numbers in \u003cem\u003eH. camelina\u003c/em\u003e compared to the 46 ORs found in \u003cem\u003eG. morsitans\u003c/em\u003e(\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e) may partially explain the obligate parasitism and lifestyle, restricted movement, and narrow host specificity of \u003cem\u003eHippobosca camelina\u003c/em\u003e keds.\u003c/p\u003e \u003cp\u003eA phylogenetic analysis of the OR genes, including Orco receptors from; \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, \u003cem\u003eGlossina morsitans\u003c/em\u003e, \u003cem\u003eAnopheles gambiae\u003c/em\u003e and \u003cem\u003eHippobosca camelina\u003c/em\u003e, showed that Orco sequences cluster together in a single clade reflecting their high conservation across species, (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). These co-receptors are essential for forming functional ion channels that provide specificity to a range of odorants responsible for detecting environmental odors. Orco genes across different species exhibit high similarity (greater than 70%), whereas OR genes within the same species show low similarity (\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e). HcamOr4a and HcamOr4b clustered with GmmOR31 and DmelOr22c in one clade. HcamOr3 formed a single clade with GmmOr37 while HcamOr2 clustered with DmelOr64a, (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003ev) Odorant Binding Proteins (OBPs)\u003c/h2\u003e \u003cp\u003eOdorant Binding Proteins (OBPs), bind to pheromones and are actively involved in the early stages of olfactory molecular recognition and signal transduction by transducing host odorants across the sensillum lymph to the relevant odorant receptor with high specificity. OBPs are characterised by the presence of a six-cysteine signature, that confers odorant binding specificity by forming disulphide bridges and unique 3D tertiary protein structure (\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e). They range between 15-20KDa in size with an alpha helix pattern, presence of a signal peptide and an average length of 150aa (\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cem\u003eH. camelina\u003c/em\u003e female had 9 OBPs and \u003cem\u003eH. camelina\u003c/em\u003e male had 8 OBPs. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that HcamOBP6, HcamOBP5, HcamOBP4, HcamOBP3, HcamOBP2, HcamOBP8, and HcamOBP1 had 100% sequence similarity and identical lengths (number of amino acids) across their respective homologs in the male and female genomes. HcamOBP7 was only found in the male genome and HcamOBP9 was only found in the female genome. HcamOBP2 to HcamOBP8 had a six conserved cysteine signature with the sequence features \u003cb\u003eC\u003c/b\u003e\u003csub\u003e\u003cb\u003e1\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-X\u003c/b\u003e\u003csub\u003e\u003cb\u003e24\u0026thinsp;\u0026minus;\u0026thinsp;29\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-C\u003c/b\u003e\u003csub\u003e\u003cb\u003e2\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-X\u003c/b\u003e\u003csub\u003e\u003cb\u003e3\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-C\u003c/b\u003e\u003csub\u003e\u003cb\u003e3\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-X\u003c/b\u003e\u003csub\u003e\u003cb\u003e37\u0026thinsp;\u0026minus;\u0026thinsp;42\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-C\u003c/b\u003e\u003csub\u003e\u003cb\u003e4\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-X\u003c/b\u003e\u003csub\u003e\u003cb\u003e8\u0026thinsp;\u0026minus;\u0026thinsp;10\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-C\u003c/b\u003e\u003csub\u003e\u003cb\u003e5\u0026minus;\u003c/b\u003e\u003c/sub\u003e\u003cb\u003eX\u003c/b\u003e\u003csub\u003e\u003cb\u003e8\u003c/b\u003e\u003c/sub\u003e\u003cb\u003e-C\u003c/b\u003e\u003csub\u003e\u003cb\u003e6\u003c/b\u003e,\u003c/sub\u003e (X represents any amino acid except cysteine), and were therefore classified in the \u0026ldquo;Classic OBP\u0026rdquo; subfamily (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003e). HcamOBP1 had four cysteines conserved and was classified as a \u0026ldquo;Minus-C OBP\u0026rdquo; subfamily gene (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e8\u003c/span\u003e). The signal peptide (Sec/SPI) was predicted in HcamOBP2, HcamOBP3, HcamOBP4, HcamOBP5, HcamOBP6, HcamOBP8, and HcamOBP9, all with a probability\u0026thinsp;\u0026gt;\u0026thinsp;0.95. The predicted cleavage sites for these proteins were as follows: HcamOBP2 (positions 23/24), HcamOBP3 (19/20), HcamOBP4 (18/19), HcamOBP5 (17/18), HcamOBP6 (17/18), and HcamOBP8 (20/21). The amino acid length ranged between 103 aa and 162 aa with an average of 146 aa (Supplementary Table\u0026nbsp;8). The nine OBP genes retrieved for \u003cem\u003eH. camelina\u003c/em\u003e, (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e\u003cem\u003e)\u003c/em\u003e is far less than \u003cem\u003eG. morsitan\u0026rsquo;s\u003c/em\u003e 32 OBPs (\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e). This drop in the number of insect pheromone/odorant-binding genes in \u003cem\u003eHippobosca\u003c/em\u003e may explain the obligate and high host specificity lifestyle of this keds. Additionally, the limited ORs, despite the diverse OBPs, indicate a specialized olfactory mechanism, potentially focusing on key environmental odorants crucial for survival and ecological interactions. This finding underscores the complexity of olfactory processing in these species, where receptor diversity does not directly parallel the variety in odorant binding capabilities (\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003ePhylogenetic analysis showed that HcamOBP5 and HcamOBP6 group within a conserved clade containing AgamOBP54 and DmelObp57b, suggesting functional parallels in odour detection. Similarly, HcamOBP9 and HcamOBP8 cluster closely together, indicating a shared evolutionary origin or related function. These observations suggest that \u003cem\u003eH. camelina\u003c/em\u003e OBPs retain core roles in olfactory processes while also exhibiting species-specific divergence. Several \u003cem\u003eH. camelina\u003c/em\u003e OBPs including HcamOBP4 and HcamOBP3, form unique sub-branches within clades that include OBPs from the other species, this would indicate adaptations to specific ecological niches. For instance, HcamOBP4 clusters with DmelObp19d, suggesting potential specialization in recognizing odorants or pheromones. Additionally, HcamOBP1 groups with conserved genes, GmmOBP5 and AgamOBP33, reflect their evolutionary importance and potential functional similarity in chemical signaling across insect species (Fig.\u0026nbsp;\u003cspan refid=\"Fig9\" class=\"InternalRef\"\u003e9\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThis phylogenetic analysis demonstrates that Hcam OBP genes exhibit a mix of conservation and divergence. While they cluster with OBPs from other dipterans, reflecting their shared evolutionary origins, their distinct positioning in some clades suggests adaptations to the specific ecological context of \u003cem\u003eHippobosca camelina\u003c/em\u003e. Further functional studies could confirm whether these genes are involved in host detection or other olfactory-driven behaviors specific to this parasitic fly.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003evi) Sensory Neuron Membrane Proteins (SNMPs)\u003c/h3\u003e\n\u003cp\u003eSensory Neuron Membrane Proteins (SNMPs), these molecules belong to the CD36 superfamily, which is categorized as lipid receptors and transporters. They participate in a wide range of functions, such as the recognition and conveyance of lipids, lipophilic substances, and lipoproteins. Their structure comprises two transmembrane domains and a substantial ectodomain responsible for interacting with ligands. Both \u003cem\u003eH. camelina\u003c/em\u003e male and female had only 1 SNMP gene predicted. A consensus analysis involving pairwise sequence alignment and length comparison between homologs of both sexes revealed that both HcamSNMP1 genes had 100% sequence similarity and identical lengths (number of amino acids). The SNMP gene had 565 amino acids with 9 exons, (Supplementary Table\u0026nbsp;9). In contrast, most dipterans contain 2 SNMP genes, (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Interestingly, a similar study involving the sheep ked (\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e) did not document any SNMP gene, this may suggest possible continuous evolutionary events that may have led to the loss of the other gene. The phylogenetic analysis of SNMPs in \u003cem\u003eHippobosca camelina\u003c/em\u003e revealed distinct evolutionary relationships with homologs from \u003cem\u003eGlossina\u003c/em\u003e species and \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, (Fig.\u0026nbsp;\u003cspan refid=\"Fig10\" class=\"InternalRef\"\u003e10\u003c/span\u003e). The analysis showed that the HcamSNMP1 is closely associated with DmelSnmp2, forming a well-supported clade that diverges from the main lineage containing DmelSnmp1 and the \u003cem\u003eGlossina\u003c/em\u003e SNMP1 group. The close clustering of HcamSNMP1 with DmelSnmp2 suggests a potential functional divergence or specialization within this gene family. In contrast, the Glossina SNMP1 genes (GmmSNMP1, GfucSNMP1, and GbreSNMP1) form a separate, cohesive clade, indicating evolutionary divergence between \u003cem\u003eH. camelina\u003c/em\u003e and \u003cem\u003eGlossina\u003c/em\u003e SNMP1 genes. These findings highlight possible lineage-specific adaptations in \u003cem\u003eH. camelina\u003c/em\u003e SNMP, which may play a critical role in chemosensory processes, such as host detection and olfactory signalling.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eComparison of Chemosensory Gene Numbers Across \u003cem\u003eH. camelina, Melophagus ovinus\u003c/em\u003e, and \u003cem\u003eGlossina morsitans\u003c/em\u003e.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eChemosensory gene family\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eHippobosca\u003c/em\u003e\u003c/p\u003e \u003cp\u003e\u003cem\u003ecamelina\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cem\u003eMelophagus ovinus\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003e\u003cem\u003eGlossina Morsitans\u003c/em\u003e\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eChemosensory Specific Proteins (CSPs)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eIonotropic Receptors (Irs)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGustatory Receptors (GRs)​\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOdorant Receptors (ORs)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e46\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOdorant Binding Proteins (OBP​s)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e32\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSensory Neuron Membrane Proteins (SNMPs) ​\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e \u003cp\u003e0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe comparison includes gene counts for Chemosensory Specific Proteins (CSPs), Ionotropic Receptors (I\u003cem\u003eR\u003c/em\u003es), Gustatory Receptors (GRs), Odorant Receptors (ORs), Odorant Binding Proteins (OBPs), and Sensory Neuron Membrane Proteins (SNMPs), illustrating the differences in chemosensory gene numbers across these species and sexes.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis study generated two genomes for \u003cem\u003eHippobosca camelina\u003c/em\u003e female and \u003cem\u003eHippobosca camelina\u003c/em\u003e male. Both of these are smaller in size compared to \u003cem\u003eMelophugus ovinus\u003c/em\u003e (\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e) and \u003cem\u003eGlossina morsitans\u003c/em\u003e (\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e). The \u003cem\u003eHippobosca\u003c/em\u003e genomes have a lower repeat content compared to \u003cem\u003eG. morsitans\u003c/em\u003e and \u003cem\u003eM. ovinus\u003c/em\u003e, a phenomenon that may explain the reduced genome size.\u003c/p\u003e \u003cp\u003eA total of forty-four chemosensory genes were annotated for \u003cem\u003eHippobosca camelina\u003c/em\u003e ked. The obligate parasitic lifestyle, limited movement, and narrow host specificity in \u003cem\u003eHippobosca camelina\u003c/em\u003e could be attributed to the reduced chemosensory system genes across the six known families of chemosensory genes as reported in this study.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eField data collection, DNA isolation and sequencing\u003c/h2\u003e \u003cp\u003eMale and Female keds were collected from the Laisamis area, Marsabit County, Kenya. The samples were hand-picked and kept in perforated water bottles to prevent them from suffocating. They were shipped to the International Centre of Insect Physiology and Ecology (\u003cem\u003eicipe\u003c/em\u003e), Molecular Biology and Bioinformatics Unit (MBBU) laboratories, Kenya and stored in a -80 degrees celsius freezer before processing. DNA was extracted from the thoracic muscle using the Protein Precipitate Solution (PPS) method and eluted using 40uL of elution buffer from Qiagen's DNA extraction kit. Nucleic acids were run on a 2% agarose gel to check their integrity.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eLibrary Preparation and Sequencing\u003c/h2\u003e \u003cp\u003eThe sequencing library was prepared using the Ligation Sequencing Kit (SQK-LSK109) using 1 g (or 100\u0026ndash;200 fmol) of gDNA. The process began with size selection of the DNA, followed by an end-prep and nick repair step. During this stage, the DNA ends were repaired and prepared for adapter attachment. The next step involved the ligation of sequencing adapters, using components provided in the kit, to the prepared DNA ends. The ligation reaction included Ligation Buffer (LNB), NEBNext Quick T4 DNA Ligase, and Adapter Mix (AMX). The reaction mixture was incubated to facilitate the attachment of the adapters. After ligation, the library was cleaned up using AMPure XP beads to remove excess adapters and other reaction components. The cleaned library was eluted in Elution Buffer (EB) and quantified using a Qubit fluorometer. The final prepared library was loaded onto a SpotON Flow Cell using the appropriate amount of Sequencing Buffer (SQB) and Loading Beads (LB), as per the MinION device requirements. Base calling was performed using Dorado version 7.2.13.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eGenome Assembly and Quality assessment\u003c/h2\u003e \u003cp\u003eAdapters still attached to the Oxford Nanopore (ONT) reads were removed using chopper version v0.8.0 (\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e). Flye version 2.9.4(\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e) a long-read assembler was employed to assemble the reads. For the male ked genome, Pilon version 1.24(\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e) was used to polish the genome using high-quality, \u0026gt; Q30, Illumina short reads obtained from a previous experiment involving a camel male ked. The short Illumina reads were first mapped to the assembled genome using bwa2 version\u003c/p\u003e \u003cp\u003e0.7.18 (\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e) and 99.9% of the reads mapped to the genome. This was necessary to ensure the two species were not cryptic. The improvement involved filling gaps, and correcting single base differences, indels, and insertions.\u003c/p\u003e \u003cp\u003eCompleasm version 0.2.6 (\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e) was used to assess the Busco completeness of the assembled genome using Dipteran lineages_odb10 (\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e). The assessment involved the evaluation of various metrics, including conserved genes, contig and scaffold N50, largest and smallest contigs.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eGenome annotation and Chemosensory gene retrieval and analysis\u003c/h2\u003e \u003cp\u003eRepeatModeler version 2.0.4, a de novo transposable element (TE) family identification and modelling package, was used to model de novo repeat element boundaries and family relationships from the assembled genome. It utilized three other repeat finding programs (RECON, Repeat Scout, and LtrHarvest/Ltr_retriever) to construct a high-quality library of the TE family\u0026rsquo;s library compatible with RepeatMasker. RepeatMasker program version 4.1.4 (\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e) was used to soft mask the assembled genome using the repeat library generated by RepeatModeler.\u003c/p\u003e \u003cp\u003eBraker version 3.0.8 (\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e, \u003cspan additionalcitationids=\"CR44 CR45 CR46 CR47 CR48 CR49 CR50\" citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e), a fully automated \u003cem\u003eab-initio\u003c/em\u003e gene predictor that incorporates GeneMark-ES/ET(\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e) and AUGUSTUS(\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e) in novel eukaryotic genome gene prediction, was used to predict the intron-exon boundaries, start, and stop codons from the generated assembly. Hints were prepared using whole genome proteins from \u003cem\u003eGlossina morsitans morsitans, Glossina fuscipes, Glossina brevipalpis, Anopheles gambiae\u003c/em\u003e, and \u003cem\u003eDrosophila melanogaster\u003c/em\u003e. Braker was then run using the genome and the prepared hints, producing high-quality gene structures. The predicted genes were subjected to a quality check using Compleasm version 0.2.6(\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e) in reference to Metazoan_odb10, Arthropoda_odb10, Insecta_odb10, and Dipteran lineages_odb10(\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e) lineage databases. For functional assignment, Orthofinder version 2.5 (\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e, \u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e), a precise and all-encompassing platform for comparative genomics. All the predicted genes were assigned to different orthogroups. A total of 9 close species were used, including \u003cem\u003eAnopheles gambiae\u003c/em\u003e, \u003cem\u003eGlossina morsitans morsitans, Glossina fuscipes, Glossina brevipalpis\u003c/em\u003e, and \u003cem\u003eDrosophila melanogaster\u003c/em\u003e, to identify their homologs in the predicted genes. These generated orthogroups contained orthologous genes. SeqKit version 2.5.0 (\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e), in combination with basic bash commands, was used to filter out predicted chemosensory gene homologs of interest from the orthogroups and these were subjected to further tests to confirm whether they are true genes.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003eConfirmation of the predicted chemosensory genes\u003c/h2\u003e \u003cp\u003eThe putative genes were subjected to further analysis and tests to confirm whether they are true genes. This included (i) Reverse blasting to vector base database(\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e) using BlastP online version integrated in VectorBase with an e-value of 0.001. (ii) Functional gene domain presence confirmation by blasting against the NCBI Conserved Domain Database (NCBI CDD) at an e-value of 0.001, and (iii) Amino acid alignment of the gene sequences to confirm the positions of the conserved residues and motifs using Muscle tool within Mega(\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e) and visualized the alignment with Jalview version 2.10.5 (\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e). Finally, Phylogenetic analysis using RaxML version 1.2.2(\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e) with 1000 bootstraps. SignalP 6.0(\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e) was used to predict the presence of the signal peptide and the amino acid cleavage sites for chemosensory-specific proteins and the odorant binding proteins.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eManual annotation\u003c/h2\u003e \u003cp\u003eArtemis version 18.2.0 (\u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e), a genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the sequence context, and its six-frame translation, was used to visualize the predicted genes. Artemis allowed inspection of the intron-exon junctions to ensure they contained the right residues, followed the intron-exon rules, and corrected any other feature requiring manual intervention. The intron donor splice site was checked for the presence of GT, and the acceptor site for the presence of AG. Additionally, we confirmed the presence of ATG at the 5\u0026rsquo; of the gene (start codon) and either TAG, TAA, or TGA at the 3\u0026rsquo; of the gene (stop codon).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003ePhylogenetic clustering of chemosensory genes\u003c/h2\u003e \u003cp\u003eMUSCLE tool version 5 (\u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e) was used to perform multiple sequence alignment with 100 iterations for all the putative chemosensory gene sequences (amino acids) of \u003cem\u003eHippobosca camelina\u003c/em\u003e, per individual chemosensory gene family. These sequences were aligned alongside gene models from well-characterized chemosensory genes in \u003cem\u003eDrosophila melanogaster, Glossina fuscipes, Glossina morsitans morsitans, Glossina brevipalpis\u003c/em\u003e, and \u003cem\u003eAnopheles gambiae\u003c/em\u003e. The resulting alignments were automatically edited using Trimal version 1.4.1 (\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e) tool with the strict-plus option. The edited alignment was used to construct a maximum likelihood phylogenetic tree with 1000 bootstraps and LG\u0026thinsp;+\u0026thinsp;FC\u0026thinsp;+\u0026thinsp;G8m as the best-fitting model as implemented in RAxML-NG v1.2.0 (\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e). The resulting phylogenetic tree was viewed and edited using the iTOl tree viewer version 5 (\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e).\u003c/p\u003e \u003c/div\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eCSP\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;chemosensory-specific protein\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eIR\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Ionotropic receptor\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eGR\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Gustatory receptor\u003c/p\u003e\n\u003cp\u003eOR\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Odorant receptors\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eOBP\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Odorant binding protein\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eSNMP\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Sensory Neuron Membrane Protein\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eDNA\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Deoxyribonucleic Acid\u003c/p\u003e\n\u003cp\u003eRNA\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Ribonucleic Acid\u003c/p\u003e\n\u003cp\u003eLNB\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Ligation Buffer\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAMX\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Adapter Mix\u003c/p\u003e\n\u003cp\u003eONT\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Oxford Nanopore\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eCDD\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Conserved Domain Database\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eBMZ\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;German Federal Ministry for Economic Cooperation and Development\u003c/p\u003e\n\u003cp\u003eGIZ\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Deutsche Gesellschaft für Internationale Zusammenarbeit\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eFIA \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Fund for International Agricultural Research\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAuthors\u0026rsquo; contribution\u003c/strong\u003e\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003eFredrick Kebaso - Data analysis and manuscript writing\u003c/li\u003e\n \u003cli\u003eSouleymane Diallo \u0026ndash; Manuscript review\u003c/li\u003e\n \u003cli\u003eCaleb Kibet -Manuscript review\u003c/li\u003e\n \u003cli\u003eSuhaila Hashim - Manuscript review\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eJohnMark O Makwatta and Dennis Getange \u0026ndash; sample collection, DNA Extraction, and manuscript review\u003c/li\u003e\n \u003cli\u003eDomelevo Entfellner, Jean-Baka \u0026ndash; Genome sequencing and manuscript review\u003c/li\u003e\n \u003cli\u003eMerid Getahun \u0026ndash; Provided the scanned image of the head region of the \u003cem\u003eHippobosca camelina\u003c/em\u003e and Manuscript review\u003c/li\u003e\n \u003cli\u003eDaniel Masiga \u0026ndash; Manuscript review\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eAll authors read and approved the manuscript\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was funded by The German Federal Ministry for Economic Cooperation and Development (BMZ) commissioned and administered through the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) Fund for International Agricultural Research (FIA), grant number 81235250\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe codes and scripts used in this study can be accessed at:\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e(https://github.com/fredrickkebaso/Hippobosca-camelina-Genome-and-Chemosensory-genes).\u003c/p\u003e\n\u003cp\u003eThe assembled genomes are available at NCBI - Genbank with the following accessions:\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003e\u003cem\u003eHippoboscas camelina\u003c/em\u003e male genome assembly: GCA_041146595.1\u003c/li\u003e\n \u003cli\u003e\u003cem\u003eHippoboscas camelina\u003c/em\u003e female genome assembly: GCA_041146635.1\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eThe raw data used in this study is available in the NCBI Sequence Read Archive with the accessions specified below:\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003e\u003cem\u003eHippobosca camelina\u003c/em\u003e female Nanopore Raw genomic DNA sequences: SRX25529404\u003c/li\u003e\n \u003cli\u003e\u003cem\u003eHippobosca camelina\u003c/em\u003e male Nanopore Raw genomic DNA sequences: SRX25529403\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eThe chemosensory genes characterised in this study can be accessed in the NCBI-GenBank database using gene accessions listed in the Supplementary tables (Table 4, Table 5, Table 6, Table 7, Table 8, and Table 9).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe study was approved by the International Centre of Insect Physiology and Ecology\u0026rsquo;s Institutional Animal Care and Use Committee (IACUC) (\u003cem\u003eicipe\u003c/em\u003e- IACUC ref no. IcipeACUC2018-003-2023).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting Interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eZhang Q, Zhou Q, Han S, Li Y, Wang Y, He H. The genome of sheep ked (Melophagus ovinus) reveals potential mechanisms underlying reproduction and narrower ecological niches. BMC Genomics. 2023;24(1).\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWatanabe J, Hattori M, Berriman M, Lehane MJ, Hall N, Solano P et al. Genome sequence of the tsetse fly (Glossina morsitans): Vector of African trypanosomiasis. 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Nucleic Acids Res. 2021;49(W1):W293\u0026ndash;6.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Hippobosca, Chemosensory genes, Genomic analysis, Hematophagy, Comparative genomics","lastPublishedDoi":"10.21203/rs.3.rs-6505113/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6505113/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cem\u003e\u003cstrong\u003eBackground\u003c/strong\u003e\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003e\u003cem\u003eHippobosca camelina \u003c/em\u003e(camel ked)\u003cem\u003e \u003c/em\u003eis an obligate hematophagous ectoparasite that infests camels. Hematophagy inflicts painful bites leading to myiasis, anemia and pathogen transmission such as \u003cem\u003eCandidatus Anaplasma camelii\u003c/em\u003e. A genome assembly for this biting flies is currently unavailable, limiting understanding of its genetics, particularly the chemosensory system.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003e\u003cstrong\u003eResults\u003c/strong\u003e\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eThe genome size for \u003cem\u003eHippobosca camelina \u003c/em\u003efemale is \u003cstrong\u003e135.6 Mb \u003c/strong\u003ewith \u003cstrong\u003e17.08 %\u003c/strong\u003e \u0026nbsp;repeated regions, an N50 of \u003cstrong\u003e1.2 Mb\u003c/strong\u003e, a total of \u003cstrong\u003e2,182\u003c/strong\u003e contigs, a GC content of \u003cstrong\u003e33.5 %\u003c/strong\u003e and compleasm (Busco) completion rate of 95.38% with the diptera_odb10 lineage (S:95.83%, 3148, D:0.30%, 10, F:0.30%, 10, I:0.00%, 0, M:3.56%, 117, N:3285) and \u003cem\u003eHippobosca camelina \u003c/em\u003emale had a genome size of \u003cstrong\u003e133.5 Mb \u003c/strong\u003ewith \u003cstrong\u003e15.38% \u003c/strong\u003ebeing repeats, an N50 \u003cstrong\u003eof 419.6 Kb\u003c/strong\u003e, 2,318 contigs, GC content of \u003cstrong\u003e33.5%\u003c/strong\u003e, and compleasm (Busco) completion rate of 94.70% \u0026nbsp;with diptera_odb10 lineage (S:94.70%, 3111, D:0.49%, 16, F:0.85%, 28, I:0.00%, 0, M:3.96%, 130, N:3285). \u003cstrong\u003e\u0026nbsp;\u003c/strong\u003eA total of \u003cstrong\u003e14,240\u003c/strong\u003e putative genes for \u003cem\u003eH. camelina \u003c/em\u003emale and \u003cstrong\u003e13,496 \u003c/strong\u003eputative genes for \u003cem\u003eH. camelina\u003c/em\u003e female annotated were identified as orthologous to genes in selected dipterans that included \u003cem\u003eDrosophila melanogaster, Glossina morsitans morsitans, Glossina fuscipes, Glossina brevipalpis \u003c/em\u003eand\u003cem\u003e Anopheles gambiae. \u003c/em\u003eChemosensory genes recovered included \u003cstrong\u003e4\u003c/strong\u003eChemosensory specific proteins (CSPs), \u003cstrong\u003e18\u003c/strong\u003e Ionotropic receptors (IRs), \u003cstrong\u003e7 \u003c/strong\u003eGustatory receptors (GRs), \u003cstrong\u003e5 \u003c/strong\u003eOdorant receptors (ORs), \u003cstrong\u003e9 \u003c/strong\u003eOdorant binding proteins (OBPs) and \u003cstrong\u003e1\u003c/strong\u003e Sensory Neuron Membrane Protein (SNMP).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study generated two genomes for \u003cem\u003eHippoboscacamelina. \u003c/em\u003eBoth are smaller in size compared to \u003cem\u003eMelophugus ovinus\u003c/em\u003e (1) and \u003cem\u003eGlossina morsitans \u003c/em\u003e(2). The \u003cem\u003eHippobosca\u003c/em\u003e genomes have a lower repeat content compared to \u003cem\u003eG. morsitans\u003c/em\u003e and \u003cem\u003eM. ovinus,\u003c/em\u003e a phenomenon that may explain the reduced genome size. A total of 44 chemosensory genes for \u003cem\u003eH. camelina \u003c/em\u003ewere annotated. The obligate parasitic lifestyle, limited movement, and narrow host specificity in \u003cem\u003eHippobosca camelina\u003c/em\u003e could be attributed to reduced chemosensory system genes in the six known families of chemosensory genes as reported in this study.\u003c/p\u003e","manuscriptTitle":"De novo genome assembly, annotation, and characterization of chemosensory genes in the camel ked (Hippobosca camelina)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-05-12 20:14:27","doi":"10.21203/rs.3.rs-6505113/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-06-04T05:03:43+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-06-01T15:44:08+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"297027495131290035114350346013131424674","date":"2025-05-22T17:19:45+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-05-19T18:17:58+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"53826528644897055532496443029046113884","date":"2025-05-07T10:17:48+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-05-07T09:28:15+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-05-07T09:09:05+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-05-06T08:00:59+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-05-05T20:13:04+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-05-05T15:21:41+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"7d281b67-09bc-41f7-a6fd-0f10c54fb40b","owner":[],"postedDate":"May 12th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-07-22T17:09:28+00:00","versionOfRecord":{"articleIdentity":"rs-6505113","link":"https://doi.org/10.1186/s12864-025-11833-1","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2025-07-16 16:05:43","publishedOnDateReadable":"July 16th, 2025"},"versionCreatedAt":"2025-05-12 20:14:27","video":"","vorDoi":"10.1186/s12864-025-11833-1","vorDoiUrl":"https://doi.org/10.1186/s12864-025-11833-1","workflowStages":[]},"version":"v1","identity":"rs-6505113","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6505113","identity":"rs-6505113","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}