Tsetse flies use olfactory and gustatory responses, through odorant and gustatory receptors (ORs and GRs), to interact with their environment. Glossina morsitans morsitans genome ORs and GRs were annotated using homologs of these genes in Drosophila melanogaster and an ab initio approach based on OR and GR specific motifs in G. m. morsitans gene models coupled to gene ontology (GO). Phylogenetic relationships among the ORs or GRs and the homologs were determined using Maximum Likelihood estimates. Relative expression levels among the G. m. morsitans ORs or GRs were established using RNA-seq data derived from adult female fly. Overall, 46 and 14 putative G. m. morsitans ORs and GRs respectively were recovered. These were reduced by 12 and 59 ORs and GRs respectively compared to D. melanogaster. Six of the ORs were homologous to a single D. melanogaster OR (DmOr67d) associated with mating deterrence in females. Sweet taste GRs, present in all the other Diptera, were not recovered in G. m. morsitans. The GRs associated with detection of CO2 were conserved in G. m. morsitans relative to D. melanogaster. RNA-sequence data analysis revealed expression of GmmOR15 locus represented over 90% of expression profiles for the ORs. The G. m. morsitans ORs or GRs were phylogenetically closer to those in D. melanogaster than to other insects assessed. We found the chemoreceptor repertoire in G. m. morsitans smaller than other Diptera, and we postulate that this may be related to the restricted diet of blood-meal for both sexes of tsetse flies. However, the clade of some specific receptors has been expanded, indicative of their potential importance in chemoreception in the tsetse.
Trypanosomiasis management has been a longstanding development preoccupation in sub-Saharan Africa, with tsetse fly control constituting the cornerstone in this effort [1]. Since all tsetse species are able to transmit trypanosomes, the critical determinant of transmission is their obligate blood feeding. Tsetse flies select their hosts through visual and olfactory signals, a process that is mediated by olfactory and gustatory receptors. Tsetse flies navigate their environment by detecting and responding to volatiles and non-volatile cues (odors and tastants). Artificial bait technologies, based on tsetse olfactory responses to natural cues and blends of synthetic versions that mimic those of their natural hosts in the field, have successfully been applied in tsetse control because of their relatively high specificity, low cost, community acceptability, and ability to slow down tsetse re-invasion from adjacent areas [2], [3]. These technologies are environment friendly [4], and applicable for riverine and savanna species of tsetse flies [5], [6]. The attractants include various phenolic derivatives [7]–[9], carbon dioxide, acetone, 1-octen-3-ol, and vertebrate host breath, skin and urine extracts [10]–[12]. Interestingly, 1-octen-3-ol is a constituent of the chemical profile from Lantana camara, an invasive plant to which tsetse flies are attracted [13]. The response to olfactory cues has also been exploited in design of tsetse repellents [14], [15]. The repellents include guaiacol (methylphenols), δ-octalactone and methylketones [16]–[18] and 2-methoxy-4-methylphenol [14]. Natural differential responses among tsetse species and even between sexes and allopatric populations of the same species have been observed [18]–[22], which have stimulated research and design to enhance the efficiencies of the existing attractant-based bait technologies, to develop new ones based on repellent blends (‘push’ tactics) from refractory animals, and to integrate these into ‘push-pull’ strategies. Different Glossina species exhibit different olfactory uniqueness' and this may partly account for the observed graduation of preferences for particular hosts. For instance, riverine tsetse species (such as G. fuscipes fuscipes, G. palpalis and G. tachinoides) prefer feeding on reptilian hosts compared to their savanna relatives (G. morsitans morsitans, G. pallidipes) that feed largely on ungulates and other large mammals [6]. Larvipostion pheromones (n-pentadecane and n-dodecane) from exudates of mature larvae are also known to attract and induce gravid G. m. morsitans and G. m. centralis females to aggregate and deposit larvae [23]. Research on response to tastants in tsetse flies are limited, but point to their potential application in tsetse control [10], [24]. In all, responses to odors and tastants in tsetse have established utility in tsetse control that can be augmented with better understanding of the molecular factors that underpin these responses. Molecular factors mediating the olfactory and gustatory responses in the tsetse flies are poorly understood. However, research on other insects indicates that the odors and tastants in the environment are generally detected in peripheral sensory neurons by distinct odorant and gustatory receptors (ORs and GRs) [25]–[28]. These receptors are divergent members of a superfamily characterized by seven transmembrane domains, and share low sequence conservation among them except at the C-terminus region that coincides with the seventh trans-membrane domain [29]. The ORs and GRs are thought to have evolved as parallel chemoreceptors across diverse organisms [26]. Each OR is expressed in olfactory receptor neurons (ORNs) within maxillary palpi and antennae [25], [30]–[32]. The ORs generally have multiple introns and are very divergent with poor structural conservation within and across insect orders and species [33], [34], which potentially reflect diverse olfaction related preferences within the orders and species. However, a canonical co-receptor commonly referred to as Orco remains highly conserved across insect orders [35]–[38], a phenomenon that may be associated with its role in proper tuning of odor specificity and activation necessary for appropriate signal transduction in the neurons [39]. The GRs are generally expressed in gustatory receptor neurons (GRNs) within gustatory organs [40] in response to soluble taste and contact pheromones [41], [42]. However, some GRs are expressed in antennal dendrites and respond to carbon dioxide, potentially implicating them in olfaction [40], [43]. The GRs are more conserved in sequence and structure than the ORs [44], [45] probably due to comparatively smaller search space among cues associated with GRs than ORs. The diversity among the ORs and GRs in tsetse can potentially shed light on the natural differential responses observed among them [12], [17], [18], [20]–[29], with potential application in tsetse control. To improve or develop new approaches of vector management, an understanding of the molecular attributes of GRs and ORs and their potential roles in tsetse ecology is essential. This study was initiated to (1) comparatively annotate and catalogue ORs and GRs in G. m. morsitans (GMOY1. 1), (2) establish evolutionary distance between G. m. morsitans ORs or GRs and those in especially D. melanogaster, and (3) examine relative expression of the ORs and GRs in the G. m. morsitans. The assembly has been estimated to be over 99% complete based on the software Core Eukaryotic Genes Mapping Approach (CEGMA) [46] and manually sequenced BACs data. The assembly is currently undergoing genome-wide manual curation and annotation by the International Glossina Genome Initiative (IGGI) consortium.
Coding sequences (CDS) of ORs and GRs in Drosophila melanogaster were obtained from FlyBase5. 13 [47] and used to isolate their respective homologs in the G. m. morsitans genome (GMOY1. 1) at VectorBase [48] using tBLASTx algorithm [49]. Scaffolds encoding the homologs were searched for and retrieved at a cut-off e-value <1. 0e-05. Whole transcriptome illumina 84 million RNA sequence reads generated from female G. m. morsitans [50] were mapped onto the scaffolds using default settings in CLC Genomics workbench suite Version 4. 8 (CLC Bio, Aarhus, Denmark). Gene loci of putative Glossina homologs were curated in the scaffold sequences flanking the tBLASTx hits, and intron/exons modeled using the RNA-seq mappings. The predicted gene models were viewed and edited using Artemis v13. 2. 12 [51] where, intron/exon boundaries were edited using motifs GT for 5′ donor site, and AG for 3′ acceptor site. The start codon (ATG) for each gene model was fixed at the 5′ end and the reading frame terminated at the first of any of the stop codons (TAA, TGA, or TAG). Sequences shorter than average size of known insect ORs (370 aa) were marked as incomplete if they lacked start or stop codons. Sequences with poorly conserved functional domains were considered as pseudogenes. The homologs were validated through sequence-based searches for presence of ORs or GRs specific 7tm-6-olf-recpt or 7tm-7-olf-recpt [29], [52] domains respectively. The homologs were probed for the domains using DELTA BLAST algorithm [53] against the conserved domains databases (CDD) [54], and presence of alpha helix trans-membrane domains validated using TMHMM server v2. 0 [55]. Additionally, all the putative ORs or GRs were validated, using BLAST2GO analyses [56] against the non-redundant Swiss-Prot database [57]. The curated gene models were assigned annotation identifiers by comparing them with automated transcript feature models obtained from the Glossina community annotation portal at VectorBase [48] and edited using Artemis genome viewer tool [51]. The models without automated prediction matches and identifiers were manually built using the Artemis gene build tool window [51] and given unique temporary annotation identifiers. In this respect, features for gene, exons, mRNA, and CDS were created for such gene models. The Glossina gene models were assigned putative gene names where GmmOR* and GmmGR* were adopted for G. m. morsitans odorant receptors and gustatory receptors respectively (the asterisk (*) being an identifier number). The annotated gene model features were submitted to the VectorBase community annotation portal for G. m. morsitans [48] for integration into genome database; nevertheless, a list of annotated amino acid coding sequences is presented in supplementary Dataset S1, and a list of associated gene identities in Table S2. The G. m. morsitans receptor repertoires were evaluated against those documented for D. melanogaster, Anopheles gambiae, Aedes aegypti, Apis mellifera, Nasonia vitripennis, Camponotus floridanus, Harpegnathos saltator and Tribolium casteneum (references in Table 1). MUltiple Sequence Comparison by Log-Expectation (MUSCLE) tool [58] was used to align GmmORs and GmmGRs with homologs in D. melanogaster, and the alignments edited using Jalview web-server [59]. The secondary structures in the alignments were predicted using JPred program [60]. Phylogenetic cluster inference was done using Maximum Likelihood approach with best fitting Wheelan and Goldman+Freq (WAG+F) model [61], which was chosen as the best ranked from a panel of all amino acid model tests run in MEGA5 [62]. The initial tree was automatically generated and bootstrapped with 500 iterations. The evolutionary rate difference among sites was modeled using a discrete Gamma distribution (5 categories (+G, parameter = 4. 2651) ). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 0. 8705% sites). All positions with less than 95% site coverage were eliminated and branch nodes determination set at very strong. Evolutionary analyses were conducted using the MEGA5 suite [62]. The expression profiles of G. m. morsitans ORs and GRs gene loci were determined using whole transcriptome 84 million illumina RNA-sequence reads [50]. The RNA-seq reads were mapped onto the G. m. morsitans ORs or GRs nucleotide coding sequences (CDS) in CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) via RNA-seq analysis pipeline with default settings. The expression profiles were presented as reads per kilobase of exon model per million mapped reads (RPKM) for each receptor sequence [63].
Numbers of OR and GR gene loci recovered in G. m. morsitans, relative to those published in other insects are summarized in Table 1. Similar to most insects, the G. m. morsitans has more ORs loci than GRs loci, with the exception of D. melanogaster where the numbers are equal. However, the G. m. morsitans ORs are fewer than those documented in all the insects evaluated, including D. melanogaster. A similar trend was exhibited in G. m. morsitans GRs, except in relation to A. mellifera. Annotation of G. m. morsitans ORs and GRs are summarized in Table 2. The lengths of G. m. morsitans ORs varied between 260 and 541 amino acids, while those of G. m. morsitans GRs ranged from 309 to 514 amino acids. The number of exons ranged between two and eight or 12 in GRs and ORs respectively. The predicted genome structures are given in Figure S1. The frequency of detectable trans-membrane domains was also variable, with proteins having six trans–membrane domains representing about one half of all genes. The G. m. morsitans ORs (57%, 26 out of 46) were homologous to nine D. melanogaster ORs. Similarly, most of the G. m morsitans GRs (57%, 8 out of 14) were homologous to three D. melanogaster GRs genes. The remainder of the G. m. morsitans GRs had one-to-one homology with a single D. melanogaster specific homolog. Reciprocal blasts onto non-redundant protein databases for both G. m. morsitans ORs and GRs are summarized in Supplementary material – Table S1). GmmGR3 and GmmGR4 were also homologous to An. gambiae orthologs, while GmmGR5, GmmGR8 and GmmGR13 had homologs to genes in other Drosophila species. The G. m. morsitans ORs pseudogenes were scanty, representing 7% of the ORs genes recovered. Only GmmOR5 had alternative splice variants. The 7tm-6-olfct-rcpt domain was detected in all G. m. morsitans ORs, and the 7tm-7-chem-rcpt domain was detected in five ORs (GmmOR17, GmmOR21, GmmOR24, GmmOR38 and GmmOR39). The 7tm-7-chem-rcpt domain was also detected in all the G. m. morsitans GRs. Phylogenetic relationships between G. m. morsitans ORs and GRs and their counterparts in D. melanogaster are summarized in Figure 1. Most of the G. m. morsitans ORs and GRs clustered with their respective ORs and GRs orthologs with a bootstrap support of over 80%. The G. m. morsitans OR14, OR15 and OR16 were homologous to a drosophila larvae receptor, Or45a. The G. m. morsitans co-receptor (Orco) (GmmOR1) had 100% bootstrap support homology to D. melanogaster homolog, Or63b, and was a single copy in the genome, similar to other insects investigated (data not shown). There was an expanded cluster of ORs in G. m. morsitans (GmmOR41-46), relative to a single D. melanogaster homolog, Or67d (Figure 1A), which also had multiple copies in An. gambiae, Cu. quinquefasciatus, Ae. aegypti, Tribolium casteneum (Data not shown). The G. m. morsitans and D. melanogaster GRs clustered into four groups (Figure 1B). Four G. m. morsitans GRs (GmmGR1-4) clustered with homologs of CO2 receptors, Gr21a and Gr63a in D. melanogaster; GmmGR6-7 and GmmGR14, though distantly, clustered with an unusual splice variant DmelGr28a/28b; GmmGR5,8–12 were homologous to bitter taste-related sensors in D. melanogaster; and GmmGR13 clustered distantly to DmelGr58a/58b homologs, whose functions are unknown. Relative expression profiles of the G. m. morsitans ORs and GRs gene loci are summarized in Figure 2. Among the G. m. morsitans ORs, expression of GmmOR15 was surprisingly most predominant, accounting for more than 90% of the total RNA-sequence data supporting expression of the ORs. GmmOR15 is homologous to Or45a gene in D. melanogaster. About 5% of RNA-sequence data provided supporting evidence for expression of GmmOR2, GmmOR1 (Orco homolog), GmmOR43 and GmmOR9. Expressions of GmmOR8, GmmOR11, GmmOR25, GmmOR31, and GmmOR39 were not detected in the available RNA-sequence dataset (Figure 2A). Amongst the GRs, GmmGR1-4 had the best RNA-sequence data expression support (Figure 2B).
Specific groups of the G. m. morsitans ORs and GRs were clustered within selected scaffolds. Similar clusters of genes performing common and related functions have been observed among chemosensory genes in D. melanogaster [41], [42], [44], and more recently among twelve G. m. morsitans major milk proteins associated with lactation [50]. Since genes within clusters are generally co-regulated and can lead to joint gene expression [29], [34], [64], the individual clusters of ORs and GRs might be under common regulatory mechanisms and in response to common or related stimuli. The ORs and GRs in G. m. morsitans were fewer than those documented in most insects evaluated (Table 1) [65], [66]. Additionally, specific ORs and GRs in D. melanogaster (nine and three ORs and GRs respectively) appear to have been expanded in G. m. morsitans, representing more than half of the chemoreceptors. The factors underlying the apparent reductions and expansions of these receptors in the tsetse are unknown. However, it can be postulated that the obligate blood feeding of the tsetse fly (restricted to vertebrate hosts) relative to D. melanogaster (with expansive fruit species hosts) might have necessitated evolutionary selection for specific chemoreceptor loci relevant to discriminate among limited host choices. We know also that environmental factors can determine host choice, as tsetse have been shown to have an acquired preference to specific hosts encountered early in life [67]. Notably, other blood-feeders, such as mosquitoes also seek a variety of plant sources for sugar as energy source, while tsetse flies derive their energy from the amino acids proline and alanine [68]. The G. m. morsitans OR15 (GmmOR15) accounted for more than 90% of the OR expression data. This OR is homologous to DmelOr45a, whose product has been, associated with an escape response in D. melanogaster larvae [69]. The function of this OR in tsetse was not determined; nonetheless it is notable that the source of RNA sequence data was a reproductively active adult female. Hence, it is possible that the GmmOR15 is in some way associated with larval activity. Similarly, the GmmGR1-4 cluster was most prominent among the GRs homologous to CO2 receptors in D. melanogaster. These GRs may be associated with host seeking and may have a duplicate role in olfaction. These receptors may putatively be associated with attractive responses elicited by the savanna tsetse species, including G. m. morsitans [10]. From the foregoing, it is evident that tsetse seems to prioritize and invest on a select few chemoreceptor genes towards their adaptive behaviors. Indeed, a heavy investment in specific genes is not uncommon in insects [70]–[73]. The G. m. morsitans OR1 (homologous to Orco) was the most conserved amongst the G. m. morsitans ORs, not surprising since such conservation has been observed in other insects [74] probably due to its critical role in modulating responses of the other receptors. In conclusion, when examined against other blood feeders, which also take sugar sources from plants (e. g. An. gambiae and Ae. aegypti), the G. m. morsitans has a reduced repertoire of ORs and GRs genes. There is a complete loss of receptors for sugar, and a heavy investment in some chemoreceptors, such as those associated with detection of CO2. These observations offer opportunities to develop control tools exploiting these unique adaptations.
Tsetse flies navigate their environments using chemosensory receptors, which permit them to locate hosts, mating partners, and resting and larviposition sites. The genome of G. m. morsitans was interrogated for coding genes of odorant receptors (ORs) and gustatory receptors (GRs) that express in antennae and maxillary palp, and detect the volatile and soluble chemical signals. The signals are then transmitted to the central nervous system and translated to phenotypes. Majority of these genes in G. m. morsitans were spread across different scaffolds, but a few were found to occur in clusters, which suggested possible co-regulation of their expression. The number of ORs and GRs were much reduced in the G. m. morsitans genome, including the apparent loss of receptors for sugar when compared to selected Diptera. There was also an apparent numerical expansion of some receptors, presumably to maximize on their restricted blood-meal diet. The annotation of the chemoreceptor package of G. m. morsitans provides a resource for investigating key activities of tsetse flies that could be exploited for their control.
genomics
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comparative genomics
computational biology
evolutionary biology
Odorant and Gustatory Receptors in the Tsetse Fly Glossina morsitans morsitans