- Research article
- Open Access
The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii
BMC Genomics volume 17, Article number: 648 (2016)
Drosophila suzukii differs from other melanogaster group members in their proclivity for laying eggs in fresh fruit rather than in fermenting fruits. Olfaction and gustation play a critical role during insect niche formation, and these senses are largely mediated by two important receptor families: olfactory and gustatory receptors (Ors and Grs). Earlier work from our laboratory has revealed how the olfactory landscape of D. suzukii is dominated by volatiles derived from its unique niche. Signaling and reception evolve in synchrony, since the interaction of ligands and receptors together mediate the chemosensory behavior. Here, we manually annotated the Ors and Grs in D. suzukii and two close relatives, D. biarmipes and D. takahashii, and compared these repertoires to those in other melanogaster group drosophilids to identify candidate chemoreceptors associated with D. suzukii’s unusual niche utilization.
Our comprehensive annotations of the chemosensory genomes in three species, and comparative analysis with other melanogaster group members provide insights into the evolution of chemosensation in the pestiferous D. suzukii. We annotated a total of 71 Or genes in D. suzukii, with nine of those being pseudogenes (12.7 %). Alternative splicing of two genes brings the total to 62 genes encoding 66 Ors. Duplications of Or23a and Or67a expanded D. suzukii’s Or repertoire, while pseudogenization of Or74a, Or85a, and Or98b reduced the number of functional Ors to roughly the same as other annotated species in the melanogaster group. Seventy-one intact Gr genes and three pseudogenes were annotated in D. suzukii. Alternative splicing in three genes brings the total number of Grs to 81. We identified signatures of positive selection in two Ors and three Grs at nodes leading to D. suzukii, while three copies in the largest expanded Or lineage, Or67a, also showed signs of positive selection at the external nodes.
Our analysis of D. suzukii’s chemoreceptor repertoires in the context of nine melanogaster group drosophilids, including two of its closest relatives (D. biarmipes and D. takahashii), revealed several candidate receptors associated with the adaptation of D. suzukii to its unique ecological niche.
Chemoreception, broadly encompassing olfaction and gustation, is essential to a number of insect life history traits such as host detection and discrimination, mate location, and predator avoidance. Chemoreception in insects is largely mediated by two divergent protein families, olfactory receptors (Ors) and gustatory receptors (Grs). A third family described in 2009 by Benton et al.  as the ionotropic receptors (Irs) has been implicated in multiple sensory modalities, including chemosensation . Insect chemoreceptors (Ors and Grs) are seven transmembrane proteins expressed on the surface of chemosensory neurons housed in hair-like structures called sensilla [3, 4]. The genome of Drosophila melanogaster contains 60 Ors encoding 62 proteins through alternative splicing [4, 5], and each Or is expressed in a specific sub-set of olfactory receptor neurons (ORNs), with very few exceptions. All ORNs expressing the same Or merge into a single glomerulus . While the basic principles and mechanisms of olfaction remain conserved across phyla [3, 7, 8], insect Ors have little homology to Caenorhabditis elegans or vertebrates, and the membrane topology is quite distinct . Moreover, all canonical Ors are co-expressed with a single noncanonical olfactory receptor co-receptor (Orco), and together appear to define the response characteristic of an ORN . The sense of taste in D. melanogaster is defined by 60 Grs encoding 68 proteins through alternative splicing . In contrast to Ors, there is no clear evidence for a non-canonical co-receptor, and the membrane topology remains poorly defined .
The number of chemoreceptors often varies widely among insects, broadly reflecting their environment and function . For example, the tsetse fly, Glossina morsitans, is estimated to have 40–46 Ors and 11–14 Grs [12, 13], while the red flour beetle, Tribolium castaneum, has 259 Ors and 220 Grs  (Tribolium Genome Sequencing Consortium 2008), and the honey bee, Apis mellifera, has 163 Ors and only 10 functional Grs . The largest chemoreceptor repertoires (over 350 Ors) are reported in eusocial insects, such as ants . In Drosophila, Or repertoires reflect the niche specialization patterns, such that a restricted spectrum of host/diet choice can be correlated with changes in chemoreceptor repertoire, such as specific losses and/or duplications in a set of receptors [17–21]. These changes can be further correlated with structural changes to the peripheral olfactory apparatus such as an altered number of specialized sensilla/ORNs [22–24]. Since, signaling and reception evolve in synchrony and in parsimony , an overall understanding of both these aspects will provide insights into the chemosensory basis of host utilization.
The recent (Drosophila 12 Genomes Consortium, Drosophila modENCODE Project) sequencing and subsequent annotation of multiple Drosophila spp. provides us with an excellent opportunity to connect the natural history of drosophilids  with the evolutionary history of chemosensation . Recently, a member of the melanogaster group, Drosophila suzukii (Matsumura), has gained immense attention due to its invasion of the western hemisphere from its original endemic zone of South East Asia and emergence as a serious economic pest. A reduction in the yield of berry and soft fruit crops in newly invaded areas of North America and Europe are reported to reach as high as 80 % in the absence of any management practices, although a current and comprehensive economic assessment is lacking [28, 29].
Among the Drosophilidae, comprising over 1,500 known species , D. suzukii is one of only a few Drosophila with a highly evolved serrated ovipositor  that enables gravid females to pierce the skin of fresh fruits and lay their eggs inside the flesh. Though D. suzukii has been recognized as a pest of cherries in Japan since 1931, they were found infesting strawberries and cranberries in California, USA in 2008 . They have since been discovered in at least a dozen states in the USA, as well as areas of Canada, Mexico, Italy, Spain and France [28, 29, 32]. We recently conducted a comprehensive analysis of the suite of volatile organic chemicals (VOCs) that define the unique olfactory landscape of D. suzukii, and compared it with that of D. melanogaster . We demonstrated that D. suzukii’s unique attraction to fresh fruits may be associated with the distinctive volatile repertoire originating from the host fruit-fly associated yeast complex. Recent studies are providing exciting insights into the complex interactions of D. Suzukii with yeast and fruits .
Here, we explored the role of olfaction and gustation in D. suzukii’s unique ecological niche. We first manually annotated the Ors and Grs in the recently sequenced D. suzukii genomes [35, 36], and two closely related species, D. biarmipes and D. takahashii (Drosophila modENCODE Project), herein collectively referred to as the suzukii-takahashii clade. The latter two species occur in geographically overlapping regions with D. suzukii  but are mostly saprophytic and do not have the pointed ovipositor that enables them to lay eggs in fresh fruits . We then compared these repertoires to those in six other previously annotated melanogaster group Drosophila [5, 19, 37]. Following our earlier comprehensive analysis of ligand repertoires for D. suzukii , we present the associated chemoreceptor repertoire that together defines D. suzukii’s unique ability to exploit diverse niches, and in turn pose a serious threat to fruit crops. This study further adds to ongoing efforts in understanding the chemosensory basis of host and mate finding in D. suzukii [33, 34, 38–40].
Manual curation of Or and Gr repertoires
D. suzukii gene models were manually curated based on the D. melanogaster Or and Gr annotations in FlyBase version FB2015_03 . In short, D. melanogaster peptide sequences were used to screen the D. suzukii genome scaffolds using tBLASTn analysis in SpottedWingFlyBase v1.0 (last accessed on 4 September, 2015) . To help predict start and stop codons, and exon-intron boundaries, scaffold regions containing putative chemoreceptors were aligned with their homologous D. melanogaster coding sequences (CDS) in MultAlin . Where exon-intron boundaries were ambiguous, intron donor and accepter sites were evaluated using the splice site prediction tool  on the Berkeley Drosophila Genome Project web site (http://www.fruitfly.org/seq_tools/splice.html). Complementary strands were generated using the Reverse Compliment tool in the Sequence Manipulation Suite  (http://www.bioinformatics.org/sms/rev_comp.html), and coding sequences were translated using the ExPASy translate tool . The D. suzukii Or and Gr annotations were then used to screen the D. biarmipes (Dbia_2.0, GCA_000233415.2) and D. takahashii (Dtak_2.0, GCA_000224235.2) genome assemblies with the methods described for D. suzukii using the BLAST tools on the National Center for Biotechnology Information (NCBI) web server. The D. biarmipes and D. takahashii genome assemblies were generated and made publicly available by the Drosophila ModENCODE project and the Baylor College of Medicine-Human Genome Sequencing Center (BCM-HGSC).
Gap filling and sequence validation
We filled gaps in the genome scaffolds that prevented the building of complete gene models using the sequence read archive (SRA) databases in NCBI. In those gene models where this method failed, PCR and capillary sequencing were used to fill the gaps.
Validation of duplications
Two approaches were used to evaluate duplications. When possible, tandem repeats were confirmed by amplifying and sequencing a region spanning the proximal ends of the duplicates. However, when the copies were greater than ~4,000 nucleotides apart or on a different scaffold we sequenced the individual genes.
Validation of pseudogenes
Predicted pseudogenes were resequenced to confirm the predictions from the initial tBLASTn analysis for D. suzukii, D. takahashii and D. biarmipes.
Genomic DNA (gDNA) for resequencing was extracted from the strains used for genome sequencing that are presently available at the UC San Diego Drosophila Stock Center: D. suzukii (stock # 14023–0311.03), D. biarmipes (stock # 14023–0361.10) and D. takahashii (stock # 14022–0311.13). A cetyltrimethylammonium bromide (CTAB) protocol  was modified for the extraction of genomic DNA from insects. Ten adult flies (5 males and 5 females) were ground with a pestle in 1.5 ml microcentrifuge tubes containing 200 μl 2 % CTAB solution (100 mM Tris HCl pH 8.0, 10 mM EDTA, 1.4 M NaCl, and 2 % CTAB). Samples were incubated for 5 min at 65 °C, followed by the addition of 200 μl chloroform and mixing by inverting 10 times. Samples were then centrifuged for 5 min at 13,000 x g. The aqueous phase was removed and placed in a new tube containing 200 μl isopropanol, mixed by inverting 10 times, and centrifuged for 5 min at 13,000 x g. The supernatant was poured off, 500 μl of 70 % ethanol was added, and the sample was centrifuged for 5 min at 13,000 x g. The supernatant was removed and the pellet was allowed to dry at room temperature for 15 min. DNA was resuspended in 50 μl deionized water, and all samples were normalized to 50 ng/μl using a Nanodrop ND-2000 (ThermoScientific, USA).
Primers flanking the gaps were designed using the Primer3plus program . PCR was carried out in 50 μl reaction volumes using GoTaq® reagents (Promega). Each reaction contained a final concentration of 0.2 μM of each primer, 1.0 units of Taq polymerase and 2 ng/μl of genomic DNA. The thermal cycle included an initial denaturation of 94 °C for 2 min, 35 cycles of 94 °C for 1 min, 58 °C for 1 min, and 72 °C for 2 min, with a final extension time of 5 min at 72 °C. PCR products were visualized with agarose gel electrophoresis using SYBR® Safe gel stain (ThermoScientific). PCR products were cleaned-up using the Wizard® SV Gel and PCR Clean-Up System (Promega). Sequencing was performed using the ABI 3730xl (Life Technologies) and BigDye® chemistry (Life Technologies) at the University of Notre Dame Genomics Core Facility. Genes with sequence gaps filled using the SRA databases or by PCR and sequencing were suffixed with “fixSRA” or “fixPCR”, respectively. Nucleotides that were fixed based on SRA or PCR are in bold or underlined, respectively (Additional file 1: Table S1-S6).
Ors and Grs were named based on homology to D. melanogaster using standard Drosophila community gene nomenclature . Each gene was prefixed with ‘D’ and the first three letters of the specific epithet (Dsuz, Dbia or Dtak), and named based on a combination of phylogenetic and reciprocal BLASTp analyses with the D. melanogaster annotated protein database in FlyBase version FB2015_03 . Duplications were suffixed with a unique numeral (e.g. DsuzOr23a-1 and DsuzOr23a-2). Splice variants were predicted solely on genomic sequence (no transcript evidence) and suffixed using the capital letter designation in accordance with the homologous splice variant in FlyBase for D. melanogaster (e.g. DmelOr69aA and DsuzOr69aA). However, where novel splice variants were predicted, splice variants were designated based on their order on the scaffold rather than homology to D. melanogaster.
Pseudogenes were suffixed with ‘P’, and are defined here as genes with a mutated start codon, premature stop codon, or frameshift mutation leading to loss of ≥20 % of the original protein and ≥1 transmembrane domain  compared to the D. melanogaster homolog. The number of transmembrane domains was predicted using the topology prediction program, OCTOPUS . Pseudogenes that were not excessively degraded were reconstructed for phylogenetic analysis by repairing mutated start codons, exon-intron boundaries or frameshift mutations to a functional state based on an intact homolog in the suzukii or takahashii subgroup. Repaired nucleotides are in lowercase in Table S1. All genes other than pseudogenes and partial gene models are assumed to be functional and are referred to here as intact. We refer to a lineage as lost when pseudogenizations or deletions (no apparent vestiges) resulted in the absence of at least one intact gene in one of 47 Gr or 54 Or orthologous groups (OGs) present in the melanogaster group as defined by Almeida et al. 2014  (see Additional file 2: Table S3 and S4).
Comparisons were made to the previously annotated chemoreceptor repertoires of D. melanogaster , D. ananassae, D. erecta, D. sechellia, D. simulans, and D. yakuba [19, 37]. To better characterize lineages that were lost in the suzukii-takahashii clade, we screened the genomes of six additional Drosophila genome assemblies (D. bipectinata, D. elegans, D. eugracilis, D. ficusphila, D. kikkawai, and D. rhopaloa), generated and made publicly available by the BCM-HGSC, using the methods described above. Evolutionary inferences were based on phylogeny reconstruction by Chiu et al. , while divergence times were based on earlier estimates . Reconciliation of gene trees with the species tree for the expanded lineages was performed using the parsimony-based method in NOTUNG v188.8.131.52 . Gene trees were estimated using Mega version 6  where the maximum likelihood approach with the Jones, Taylor, Thornton (JTT) substitution model , a Gamma distribution (+G) with five discrete categories, and complete deletion of gaps was implemented. The edge weight thresholds were 0.9 and based on bootstrap support following 500 iterations, while the loss and duplication costs were 1.0 and 1.5, respectively. No branches were collapsed for NOTUNG analysis.
Measures of divergence
Two proxies were used to describe divergence, the percent of identical amino acids in a peptide sequence alignment to D. melanogaster (%ID) and the ratio of nonsynonymous (dN) to synonymous (dS) substitution rates (dN/dS). %ID was calculated using Clustal Omega  on the European Bioinformatics Institute (EMBL-EBI) web server . Nonsynonymous and synonymous substitution rates were calculated using the Nei and Gojobori method  implemented in SNAP v2.1.1  (http://www.hiv.lanl.gov/content/sequence/SNAP/SNAP.html). D. melanogaster was used as an outgroup for dN and dS calculations for all three species (i.e. suzukii-melanogaster, biarmipes-melanogaster, and takahashii-melanogaster). Differences were determined using paired (between species) and unpaired (Ors vs Grs) Wilcoxon Signed-Rank tests with the MASS package  in the R statistical environment.
Tests for positive selection
Positive selection acting on a small proportion of sites is often hard to detect using the ratio of nonsynonymous to synonymous substitution rates across the entire length of a gene (dN/dS). Therefore, we used the adaptive branch-site random effects likelihood (aBSREL) approach  to identify signatures of diversifying selection at the codon level within a phylogenetic framework comprised of 9 species in the melanogaster group: D. ananassae, D. biarmipes, D. erecta, D. melanogaster, D. sechellia, D. simulans, D. suzukii, D. takahashii and D. yakuba. Or sequences for D. ananassae, D. erecta, D. sechellia, D. simulans and D. yakuba were from Guo and Kim  while Gr sequences were kindly provided by Michael Ritchie (University of St Andrews, UK). Only functional genes were used in the positive selection analysis.
Peptide sequences of homologous chemoreceptors (gene sets) were aligned in MAFFT v7 using the Blosum62 scoring matrix, a gap penalty of 1.53, and the G-INS-1 refinement method . Each alignment was visually inspected and manually edited, when necessary, and used to estimate a phylogeny for each homologous gene set. The maximum likelihood approach with the Jones, Taylor, Thornton (JTT) substitution model  and a Gamma distribution (+G) with five discrete categories, and complete deletion of gaps was implemented in Mega version 6 . Codon alignments were generated using PAL2NAL . The aBSREL method  was implemented in HyPhy , where all internal and external nodes were tested for signatures of diversifying selection using likelihood ratio tests (LRTs). The Holm-Bonferroni method was used to control the familywise error rate for multiple tests within a gene set , whereas the Benjamini-Hochberg false discovery rate method was used for corrections across all gene sets . Chemoreceptors showing positive selection based on the aBSREL method were further tested by using the stringent M1–M2 models of the codeml program in PAML . Values >0.95 from Bayes empirical Bayes (BEB) method were considered sites under diversifying selection .
Phylogenies were estimated for Ors and Grs to help reconstruct evolutionary events and to assist in the naming of the genes. Peptide sequences of D. suzukii, D. biarmipes, D. takahashii and D. melanogaster ≥ 360 aa (Ors) or ≥ 340 (Grs) in length were multiply aligned using MUSCLE v3.8.31 . Maximum likelihood trees were inferred using the PROTGAMMA model of protein substitution, JTT matrix, and 500 bootstrap replications in RAxML v.8 . RAxML analysis was conducted on the CIPRES Science Gateway and XSEDE . Figures were prepared using the FigTree program for visualization and annotation of phylogenetic trees . The Or and Gr trees were rooted with Orco and Gr21a, respectively. The aligned peptide sequences files (Phylip) and phylogenetic tree files (Nexus) for both the OR and Gr families are in the additional files (Additional files 3, 4, 5 and 6)
Scanning electron microscopy (SEM)
Freshly emerged D. suzukii were placed in acetone for at least 24 h until they could be processed by scanning electron microscopy (SEM). After undergoing critical point drying, flies were mounted both dorsally and ventrally on carbon tape attached to an aluminum stub mount, and coated with 4 μM of iridium using a Cressington 208 HR sputter coater (Cressington Scientific Instruments, Watford, UK) in conjunction with the Cressington MTM 20 thickness monitor. Images were taken with a FEI-Magellan 400 FESEM (FEI, Hillsboro, OR, USA).
Chemosensory organs and receptor repertoires
Scanning Electron Microscopy (SEM) of the olfactory organs in D. suzukii revealed striking morphological similarity to the well-defined D. melanogaster structures (Fig. 1) [71, 72]. Maxillary palps were adorned with a single class of olfactory sensilla, basiconic (Fig. 1c, d), whereas an additional two types, trichodea and coeloconic, are seen on the antenna (Fig. 1e). One unusual feature we noted in the large basiconic class was the presence of two distinct pore patterns. The single pattern reported earlier in D. melanogaster (Fig. 1f; circle) [71, 72] was observed in D. suzukii, but we also noted an additional unique pore pattern (Fig. 1f; circle).
Next, we annotated the Ors and Grs from the genome assemblies of D. suzukii and two closely related members, D. biarmipes and D. takahashii. A summary of the Or and Gr repertoires, along with those previously annotated in D. melanogaster, are reported in Table 1. Phylogenetic relationships among the Ors in these four species are represented in Fig. 2, illustrating several clade specific and species specific expansions. The total number of Or loci ranged from 64 in D. biarmipes to 71 in D. suzukii and D. takahashii. However, pseudogenizations reduced the number of functional Or genes to 62, 60, and 70 in D. suzukii, D. biarmipes and D. takahashii, respectively. We predicted alternative splicing in two Or genes (Or46a and Or69a) in all three species, the same genes with splice variants in D. melanogaster . Or46a encodes two splice variants that are moderately conserved, with percent identity of D. suzukii to D. melanogaster ranging from 80.7 to 83.4 % (Additional file 1: Table S1). Conversely, Or69a is predicted to encode four to seven splice variants in the suzukii-takahashii clade, compared to only two isoforms in D. melanogaster. The number of functional genes in D. suzukii and D. biarmipes is roughly the same as D. melanogaster, whereas D. takahashii, with 70 genes, is more than the 66 predicted in D. ananassae, the largest Or repertoire among the melanogaster group Drosophila annotated prior to this study.
We predicted a total of 74 Gr genes in D. suzukii, of which 71 are functional and three are pseudogenes, while 74 intact genes and no pseudogenes were predicted in D. biarmipes, and 88 genes were predicted in D. takahashii of which six are pseudogenes (Table 1). Phylogenetic relationships among the Grs in four species showed several unique expansions (Fig. 3). In D. suzukii, three genes encode 13 splice variants, bringing the total to 81 functional Grs (Table 1). D. suzukii’s repertoire of Grs is nearly identical to D. biarmipes, which has 74 genes encoding 83 Grs. While these two Gr repertoires are larger than any other Drosophila annotated thus far, D. takahashii’s repertoire is even larger with 82 intact genes encoding 91 Grs (Table 1).
The number of introns in Ors and Grs was consistent with those in D. melanogaster, with the exception of Gr85a. D. suzukii, D. biarmipes and D. takahashii each have two copies of Gr85a, and Gr85a-1 has one intron while Gr85a-2 has two introns. Furthermore, the peptide sequences are notably shorter (374–381 aa) than Gr85a in D. melanogaster (397 aa). The functional state of Or42a in both D. suzukii and D. biarmipes was initially unclear due to an unusually long first intron. Or42a resides on two different scaffolds in both species where it is fragmented in the 1st intron. Attempts to amplify and sequence the gene region were unsuccessful. Or42a in D. takahashii has a large first intron (2511 nucleotides) compared to D. ananassae (66 nucleotides) and D. melanogaster (185 nucleotides), so next we examined Or42a in other melanogaster group genomes and found that the first intron is also large in D. kikkawai (4,475), and on two different scaffolds in the D. eugracilis assembly. Consequently, failure to amplify the gene could have been due to the size of the amplicon. Screening of the SRA from transcriptome sequencing by Chiu et al. , however, shows that Or42a is being transcribed in D. suzukii; therefore, we considered Or42a intact in D. suzukii and D. biarmipes.
Expansions and losses
Gene tree reconciliation revealed complex birth-and-death evolutionary patterns, wherein the suzukii and takahashii subfamilies (Fig. 4a and b; shaded box) underwent changes in copy numbers in a subset of Ors and Grs as they diverged from their common ancestor (CA1 in Fig. 4a). The later split of D. suzukii and D. biarmipes from CA2 was accompanied by similar changes. Three Or lineages, Or74a, Or85a and Or98b were lost in D. suzukii but were functional in D. biarmipes and D. takahashii, while Or33c was lost in D. biarmipes, and none were lost in D. takahashii (Fig. 4). Based on previous annotations, and the screening of five additional melanogaster group genomes, the loss of Or74a is unique to D. suzukii, while Or85a was lost independently in D. ananassae and D. suzukii.
The two largest expansions in the D. suzukii and D. takahashii Or lineages were Or23a and Or67a (Fig. 4b; Additional file 7: Figure S1). D. suzukii and D. takahashii have four and five copies of Or23a, respectively, while D. biarmipes has only one (Fig. 4b). Four intact and one Or67a pseudogene were found in D. suzukii, while four intact copies were found in D. biarmipes, and six copies plus a pseudogene were found in D. takahashii (Fig. 4b). The Gr lineages showed by far the largest expansions in the suzukii-takahashii clade compared to all of the annotated melanogaster group Drosophila. Four lineages were expanded in D. suzukii, two in D. biarmipes, and six in D. takahashii (Fig. 4a and b; Additional file 7: Figure S1). One lineage, Gr59cd, was expanded in all three members of the suzukii-takahashii clade, whereas Gr36a-c was uniquely expanded in the D. suzukii and D. biarmipes. The only other shared expansion was between D. suzukii and D. takahashii for Gr59ab. The largest number of unique expansions in the suzukii-takahashii clade was in D. takahashii and includes Gr22a-f, Gr64a, Gr64f and Gr98b-d. Interestingly, no Gr lineages were lost in any of the three species annotated in the present study.
Next, we used the parsimony-based gene tree reconciliation method in NOTUNG v184.108.40.206  to analyze the two largest expanded lineages in both Ors and Grs. Among the Ors, Or23a duplicated several times, and the common ancestor to the suzukii-takahashii clade probably had three copies, indicating that D. biarmipes lost two copies while D. suzukii and D. takahashii gained one and two copies, respectively (Additional file 7: Figure S1). The expansion of the Or67a lineage was already present prior to the suzukii-takahashii split, except for one later duplication in D. takahashii (Fig. S1). The two largest expanded Gr lineages were Gr59a and Gr59d in all three species. The Gr59a duplication pattern was comparable to Or67a, whereas Gr59d showed by far the most complex pattern of evolution resulting in 27 total copies in the three species (Fig. S1).
Having annotated the genomes of three species that include the pest, D. suzukii, we estimated divergence and selection in the chemosensory receptor families using the percent of identical amino acids to homologous D. melanogaster peptide sequences (%ID) and the ratio of nonsynonymous (dN) to synonymous (dS) substitution rates (dN/dS) (Table 2). The dN/dS ratios in Ors ranged from 0.0125 in DsuzOrco to 0.3670 in DbiaOr19a (mean of three species = 0.111), while the %IDs ranged from 44.72 % in DbiaOr67a-2 to 98.77 % in DsuzOrco (mean = 81.9 %). The %ID of Grs ranged from 33.06 % in DbiaGr59a-3 to 99.55 % in Gr21a (mean = 74.8 %). The Gr dN/dS ratios ranged from 0.002 in Gr21a to 0.370 in Gr10b (mean = 0.138). These low dN/dS values imply that both chemoreceptor families have evolved under strong purifying selection. These values are larger than the reported genome wide estimates of 0.095 for X chromosome genes and 0.090 for autosomal genes ,. Differences in the means between species, based on paired Wilcoxon Signed-Rank tests, are shown in Table 2. Comparisons between dN, dS, and dN/dS of Ors and Grs using unpaired tests showed that Grs are more divergent than Ors in all three species (Table 3).
Genes with the highest and lowest dN/dS values in D. suzukii provide insights into highly divergent or conserved functions. Among the most conserved Ors, Orco tops the list, followed by Or47a, Or92a, Or42b and Or24a, and whereas Gr21a, Gr28a, Gr28bB, Gr63a and Gr64c were the most conserved Grs. Most divergent Ors were Or19a, Or23a, Or69aA, Or65a and Or33a and the Grs included Gr10b, Gr93d, Gr92a, Gr85a and Gr22c (Additional file 2: Tables S1 and S2). This trend was comparable in D. takahashii and D. biarmipes.
Next we tested for the signatures of positive selection acting on a small proportion of sites that are often difficult to detect using the dN/dS ratio across the entire gene. The adaptive branch-site random effects likelihood (aBSREL) approach  on homologous gene sets revealed two Ors and three Grs showing evidence of positive selection the suzukii-takahashii clade in the phylogenetic framework comprising nine melanogaster group drosophilids (Fig. 5; Additional file 2, Table S5). The number of tests for each gene set ranged from a small set of 11 (singletons with losses in some lineages) to as many as 43 for a gene with large expansion across spp. (Gr59d). A total of five lineages showed signatures of positive selection, four of those being at internal nodes and one being at an external node (Fig. 5). In all cases, the percentage of sites exhibiting signatures of positive selection (ω2%) was small, ranging from 1.1 % to 7.2 % (Fig. 5). Selection at the remaining sites (ω1) ranged from very high purifying selection (ω1 < 0.01) to neutral selection (ω1 = 1).
In the suzukii-takahashii clade, positive selection was detected in Or2a, Gr5a and Gr97a along branches leading to both the suzukii and takahashii subgroups, while Gr58a showed signatures of positive selection along the branch leading to the suzukii subgroup (Fig. 5). In Or2a, positive selection was found at a very small percentage of codons (1.9 %), while the remaining sites exhibit signatures of purifying selection (ω1 = 0.225) (Fig. 5). Strong purifying selection (ω1 < 0.01) was evident at 96.4 % of Gr5a, while 3.6 % of the codons showed evidence of positive selection (ω2 = 11; p = 0.024). Gr58a also exhibited strong purifying selection (ω1 < 0.01) at the majority of sites (92.8 %), while the remaining 7.2 % exhibited signatures of positive selection (; p = 0.031). The vast proportion of Gr97a (98.6 %) shows no signs of selection pressure (ω1 = 1.0) while 1.6 % of the sites show evidence for positive selection (p = 0.004).
Next, the two largest expanded Or and Gr lineages were subjected to aBSREL analysis by restricting the phylogeny to the three species in the takahashii-suzukii clade. Only the Or67a lineage had genes with signatures of positive selection, of which two genes were in D. takahashii (DtakOr67a-4 and DtakOr67a-4) and one in D. suzukii (DsuzOr67a-3) (Fig. 6a). These results were independently confirmed using the branch-site test in PAML that further identified codons under positive selection (Fig. 6b).
Finally, we would like to state that the reason for reporting the less stringent p-values from Holm-Bonferroni corrections within gene sets was to extract candidates with some (any) evidence of positive selection.
Peripheral olfactory structures in D. melanogaster have been studied over the years and have revealed stereotypic pattern of sensillary organization [6, 71, 73]. These studies laid a solid foundation to the functional mapping of sensilla [74, 75]. More advanced molecular techniques have correlated the morphological and functional sensillary patterns with that of chemosensory gene expression [76, 77]. A broadly conserved pattern emerged in our D. suzukii SEM studies as compared to D. melanogaster. Limited single sensillum recordings (SSR) from D. suzukii antennal basiconic (ab) sensilla in combination with high resolution gas chromatography (GC-SSR) suggested a high conservation in response profile from the ab1 sensilla as compared to D. melanogaster, whereas other two large sensilla (ab2 and ab3) had significantly altered physiological profiles . This could be due to the alteration in Or sequences and/or expression profiles.
Unlike vertebrates and many insects, in which there has been extensive variation in the number of genes in the chemoreceptor families, the size of the Or and Gr repertoires in Drosophila have changed little during the last ~70 million years  despite their extensive distribution and diverse life history traits  that range from primitive sap and slime feeding (virilis-repleta) to more recent adaptations in the melanogaster group that utilize decaying and fermenting fruits . Of ~30 Drosophila genomes that have been sequenced, the melanogaster group is the most represented. Furthermore, this group has been well characterized in terms of chemosensory repertoire annotation.
A number of previous studies have described a balanced birth-and-death process of evolution, wherein the number of genes gained through duplication roughly equals the number of genes lost through pseudogenization, thus maintaining Or and Gr repertoires comprising approximately 60 genes each [5, 21, 37, 80]. Our chemoreceptor annotations in the suzukii-takahashii clade revealed similar patterns (Fig. 4; Additional file 2: Tables S3 and S4). The size of the Or repertoires in D. suzukii and D. biarmipes are roughly the same as other melanogaster group flies, while D. takahashii has several additional Ors that make its repertoire the largest among all the annotated species in this group with 77 intact Ors. The size of the Gr repertoires in D. suzukii, D. biarmipes and D. takahashii are all relatively large compared to other melanogaster group members, with 81, 83 and 91 total proteins, respectively. Analysis of the evolutionary history of duplications and losses revealed that the expansions of the Gr lineages in the suzukii-takahashii clade occurred prior to D. suzukii’s divergence from D. biarmipes, ~7.3 mya . Thus, the expanded Gr lineage is not a direct consequence of D. suzukii’s adaptation to its expanded ecological niche, but could have simply helped facilitate the shift by providing ample variation for evolution to act upon.
Expansions and losses
Despite the maintenance of a standard repertoire size, gene births and deaths during trophic shifts can produce unique and rapidly evolving chemosensory repertoires. A study by McBride  showed that D. sechellia, a species endemic to the Seychelles and a specialist on the fruit of Morinda citrifolia, experienced an accelerated rate of chemoreceptor gene loss during its evolution to a specialist life style. A similar trend in the Grs was found in D. erecta, a specialist on Pandanus candelabrum . A recent study further demonstrated a relationship between host-choice and chemoreceptor repertoire wherein four widely conserved Ors (Or9a, Or22a, Or42b and Or85d) that detect yeast-derived and fruit related compounds were uniquely lost in an herbivorous Drosophila, Scaptomyza flava, while Or67b, a receptor shown to enhance the sensitivity and detection of plant derived green leaf volatiles, was uniquely expanded . These unique changes in the Or repertoire were considered as adaptive losses and gains towards the evolution of herbivory in Scaptomyza from its ancestral drosophilids that feed on yeast [18, 81].
The D. suzukii and D. takahashii Or repertoires are distinct in having two large expansions, Or23a and Or67a, while only the Or67a expansion was retained in D. biarmipes. In D. melanogaster, Or23a is expressed on the surface of the B cell in antennal intermediate 2 (ai2) sensilla , formerly classified as antennal trichoid 2 (at2) sensilla . And despite screening with a large panel of compounds using SSRs and the Δ-halo system in D. melanogaster, no strong ligands for Or23a have been identified [83, 84]. In D. melanogaster, Or67a is expressed on the surface of the B cell in ab10 sensilla (Couto et al. 2005), where methyl benzoate and ethyl benzoate elicited strong excitatory responses (≥100 spikes/s) at a low dose of 10−4 dilutions . Five functional copies of Or67a in the D. suzukii strain from Italy have been found , while we identified only four intact copies and one pseudogene in the North American isolate, suggesting that the number of functional genes in the Or67a lineage can be variable across geographical regions. This group also suggested that D. suzukii’s increased sensitivity to isoamyl acetate [33, 39], a yeast-derived and fresh fruit volatile, could be due to the expanded Or67a copy-numbers .
Interestingly, of the three species annotated here, D. suzukii’s repertoire of Ors underwent the most gene deaths, with losses of Or74a, Or85a and Or98b. This results in the smallest number of Or lineages (51) among the nine drosophilids studied here (Additional file 2: Table S3). It is worth mentioning that this number of lineages is even smaller than D. sechellia’s and D. erecta’s, both of which have a very restricted diet. Of the three lost lineages, Or74a in D. melanogaster is a larval specific receptor expressed in a sub-set of ORNs in the larval dorsal organ (LDO) [85, 86] (Table 4). A heterologous expression using Δ-halo system revealed excitatory responses to linear aliphatic compounds such as 1-hexanol, (E)-2-hexenal, 1-heptanol and 1-nonanol (≥100 spikes/s), compounds commonly associated with fruits  (Table 4). The second, Or85a, is a narrowly tuned receptor expressed on the B cell of ab2 sensilla in D. melanogaster where ethyl 3-hydroxybutyrate elicits a strong excitatory response . Single sensillum recordings (SSRs) by Keesey et al.  showed similar response profiles for the B cell in ab2 sensilla in D. biarmipes and D. melanogaster, but not for D. suzukii. Ethyl 3-hydroxybutyrate still elicited a strong response, but 2-heptanone elicited the strongest response in D. suzukii (Table 4). However, 2-heptanone did not elicit a response in D. biarmipes or D. melanogaster, suggesting that a different, more broadly tuned Or is being expressed in D. suzukii’s ab2 sensillum, which lends physiological evidence for the loss of Or85a from D. suzukii’s repertoire of functional Ors. Very little is known about the function of Or98b, except for its co-expression with Or85b in the A cell of the ab6 sensillum in D. melanogaster .
Finally, we made numerous attempts to sequence all three lost lineages in the D. suzukii genome. Our sequencing of Or74a and Or85a confirmed the highly degraded state of the loci in the North American isolate . However, these two genes were considerably less degraded in the genome assembly from the Italian isolate, but pseudogenizations were still apparent . Conversely, we were unsuccessful in sequencing the Or98b locus in D. suzukii. Amplicon size was consistent with that of a full length gene, but sequencing indicated that the locus is polymorphic in the North American assembly. However, we were able to build an intact gene model for Or98b in the genome assembly from the Italian assembly , and that sequence is provided in Additional file 1, Table S1. Polymorphism in Or98b among D. melanogaster strains was also reported, wherein several functional and pseudogene alleles were found in the Ives strain, a single pseudogene was found in the New Jersey strain, and no allele could not be amplified in the Oregon R strain .
Measures of divergence provide insights into the molecular evolution which can often be correlated with conserved and divergent physiological processes. Our measure of divergence (dN/dS) implies that both chemoreceptor families have evolved under strong purifying selection. However, these values are larger than the genome wide estimates of 0.095 for X chromosome genes and 0.090 for autosomal genes , demonstrating that these gene families are more divergent than average. Comparisons between dN, dS, and dN/dS of Ors and Grs using unpaired tests showed that Grs are more divergent than Ors in all three species (Table 3).
Among the most conserved Ors, Orco tops the list, followed by Or47a, Or92a, Or42b and Or24a. These genes are also highly conserved in D. takahashii and D. biarmipes. Expression studies in D. melanogaster have revealed Orco to be a non-canonical receptor with a wide distribution [9, 10, 77], whereas expression of the remaining Ors is confined to basiconic sensilla  except for Or24a which is larval specific in D. melanogaster . Interestingly Or92a and Or42b are expressed in ab1 sensilla on the A and B ORNs, respectively. This high level of conservation corresponds with the electrophysiological data of ab1 that showed similar responses to a panel of ab1-sensitive odorants in D. melanogaster, D. biarmipes and D. suzukii . An earlier study showed similar findings comparing nine species in the melanogaster subgroup . Combined, these findings suggest that the role of ab1 sensilla has largely been conserved during at least the last ~13 million years of melanogaster group evolution. In fact, McBride and Arguello  proposed this phenomenon to be applicable for all the large basiconic sensilla (ab1-3) in five members of the melanogaster subgroup.
On the other hand, the expression of the most divergent receptors in D. suzukii is predicted to be among three different sensilla types. Of these, both Or19a and Or23a are expressed in intermediate sensilla [71, 82], Or33a and Or69aA are restricted to a basiconic [71, 82], and Or65a is expressed in a trichoid . Potential response characteristic and the significance of these Ors in D. suzukii remains an exciting avenue to explore. Three of these five homologues in D. melanogaster (Or23a, Or65a, and Or69aA) did not respond with high sensitivity to any of the odorants tested heterologously . Physiological data is lacking for DmelOr33a. Two different studies reported DmelOr19a responding to limonene, a major citrus fruit volatile [83, 88].
Among the gustatory receptors in the suzukii-takahashii clade, Gr21a was the most conserved, surpassing even Orco. The other highly conserved Grs include Gr28bB, Gr28a, Gr63a and Gr64c. It is worth mentioning that Gr21a and Gr63a are highly conserved among insects [5, 80], and together confer the sensitivity to carbon dioxide [89, 90], whereas Gr28bB and Gr28a are part of the bitter receptor family and are shown to be ubiquitously expressed in a wide array of sensory and non-sensory tissue [91, 92]. The five most divergent Grs include Gr10b, Gr93d, Gr92a, Gr85a and Gr22c; little is known about their expression or response characteristics.
Our set of 11 chemoreceptor lineages with signatures of positive selection in the nine species is smaller than the reported 20 in an earlier study that compared chemosensory repertoires in 12 Drosophila, even though two genes (Or9a and Gr5a) were common in both studies . These differences could be due to multiple reasons. Our study focused on the drosophilids from the melanogaster group that have a relatively comparable host range , while the other study included six species outside the melanogaster group. In addition, we adjusted the p-values based on more stringent Holm-Bonferroni corrections which reduced the number of significant candidates. However, we note that our corrections were performed within, but not across gene sets; therefore, these results should be interpreted with caution.
Of the 11 genes, we found four genes (Or2a, Gr5a, Gr58a and Gr97a) that were significant in the branches leading to D. suzukii. In D. melanogaster, Or2a is expressed in ai3 sensilla [76, 82] and has been shown to respond to ethyl 3-hydroxybutyrate and isoamyl acetate eliciting only moderate responses (~50 spikes/s) . It is interesting to note that isoamyl acetate has been identified as a strong ligand from suzukii-associated yeasts  and host fruits . Among the Grs, DmelGr5 has been studied in detail. Molecular, physiological and behavioral studies identified it as a sugar receptor with a strong selectivity and sensitivity to trehalose [93, 94]. Importance of sugars in D. suzukii is more pronounced since this fly also uses a variety of non-conventional sugar sources such as nectar and cherry blossom in the field . Functional data on DmelGr58a and DmelGr97a is lacking . Our restricted aBSREL analysis of the four largest expanded lineages (Or23a, Or67a, Gr59a and Gr59d) in the suzukii-takahashii clade revealed evidence for positive selection only in Or67a, where three copies showed signatures of positive selection (Fig. 6a). Overall, adaptation of D. suzukii to novel niches appears to be facilitated by unique expansions and losses of chemosensory lineages. Together with our earlier that described the volatile chemical landscapes of D. suzukii , present study further provides novel insights into the synchronous evolution of signaling and reception in flies.
We manually annotated the olfactory and gustatory receptor families of the pest fly, D. suzukii to complement our earlier analysis of the evolution of olfactory signals in this fly that showed salience of a set of yeast derived odorants enriched in the D. suzukii landscape . We further annotated two close relatives, D. biarmipes and D. takahashii to compare and contrast their chemosensory repertoire with that of D. suzukii. This revealed three unique losses of Ors (Or74a, Or85, Or98b) in D. suzukii among the three species in the suzukii-takahashii clade, and two large expansions in the olfactory receptors, Or23a and Or67a. There was an overall pattern of purifying selection in both chemoreceptor families, with Ors exhibiting greater conservation. The gustatory genome repertoire size in this clade was by far the largest among all the annotated species of the melanogaster group. Finally, our analysis for the signature of positive episodic selection in D. suzukii led to the identification of Or2a and one copy of Or67a as strong candidates. Taken together, this study provides detailed insights into the molecular evolution of the two major chemoreceptor families in an invasive and pestiferous fly. The evolution of a serrated ovipositor for piercing the skin of fresh fruits is a unique innovation that conferred a distinct advantage in fruit flies to exploit fruits of varying ripeness. In tephritids, this innovation facilitated the radiation of thousands of species . Surprisingly, this innovation exists in only two known drosophilids, D. suzukii and D. subpulchrella, both of which are members of the suzukii subgroup . The recent sequencing of D. suzukii (pest) and D. biarmipes (non-pest) within the suzukii subgroup provided us with an excellent opportunity to explore the contribution of chemosensation in the evolution of pestilence in D. suzukii.
aBSREL, adaptive branch-site random effects likelihood; Gr, gustatory receptor; LRT, likelihood ratio tests; Or, odorant receptor; Orco, olfactory receptor co-receptor; ORN, olfactory receptor neuron; SEM, scanning electron microscopy; VOC, volatile organic compounds
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The authors thank Frank Zalom and Johanna Chiu (both at the University of California, Davis), Michael Prender, Yiyuan Li and RJ Nowling (all at the University of Notre Dame) for advice and helpful discussions. We gratefully acknowledge Hugh Robertson (The University of Illinois at Urbana–Champaign) for much discussions, advice, and exchange of ideas. We also thank Julien Pelletier (Keele University, UK), Johanna Chiu (UC-Davis), and Carolyn (Lindy) McBride (Princeton University) for constructive comments on an earlier version of this manuscript.
This work was supported by grants to ZS from the California Cherry Marketing and Research Board grant (G00001951), UC Davis-Notre Dame Research Agreement award (201224810), and USDA National Institute for Food and Agriculture (NIFA) Specialty Crops Research Initiative (SCRI) Award (2015-51181-24252) as a subcontract between the University of Notre Dame and North Carolina State University.
Availability of data and material
All relevant data are available within the manuscript and its additional files (Additional file 1 has Table S1 through S6 that contain all the annotated Or and Gr coding and peptide sequences for D. suzukii, D. biarmipes and D. takahashii. Additional file 3, 4, 5 and 6 are aligned peptide sequence and phylogeny tree files for Or and Grs, respectively. The phylogenetic data and the support files have been deposited at the: http://datadryad.org/review?doi=doi:10.5061/dryad.5q1h4view?doi=doi:10.5061/dryad.5q1h4.
PVH carried out the gene annotation and molecular evolution analysis and drafted the manuscript. CLR participated in the phylogenetic and molecular evolution analysis. CMJ and GJR assisted in PCR amplifications and sequencing. MS participated in early annotations of D. suzukii receptors. ZS had the research idea, and participated in developing the study design and drafting the manuscript along with PVH. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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D. suzukii Or coding and peptide sequences. Table S2. D. suzukii Gr coding and peptide sequences. Table S3. D. biarmipes Or coding and peptide sequences. Table S4. D. biarmipes Gr coding and peptide sequences. Table S5. D. takahashii Or coding and peptide sequences. Table S6. D. takahashii Gr coding and peptide sequences. (XLSX 379 kb)
Non-synonymous (dN) and synonymous (dS) substation rates and ratios (dN/dS) of Ors in members of the suzukii-takahashii clade using D. melanogaster as an outgroup. Table S2. Non-synonymous (dN) and synonymous (dS) substation rates and ratios (dN/dS) of Grs in members of the suzukii-takahashii clade using D. melanogaster as an outgroup. Table S3. The number of functional Or genes in each orthologous group for nine species in the melanogaster group based on Almeida et al. . Table S4. The number of functional Gr genes in each orthologous group for nine species in the melanogaster group based on Almeida et al. . Table S5. Summary of the chemoreceptors in the suzukii-takahashii clade under episodic positive selection as revealed by aBSREL analyses. (XLSX 35 kb)
Or alignment file (Phylip). Olfactory receptor peptide sequences of Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) ≥ 360 aa in length were multiply aligned using MUSCLE v3.8.31. (PHY 229 kb)
Or phylogenetic tree file (Nexus). Phylogenetic analysis of Ors in Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) using a Maximum Likelihood method. Evolutionary history was inferred using a Maximum Likelihood method based on the JTT matrix-based model. The tree was constructed using RAxML under the JTT model of substitution with NNI topology search, based on an amino acid alignment by MUSCLE. Branch support was estimated using 500 bootstrap replications. The tree is rooted with Orco. (NEX 26 kb)
Gr alignment file (Phylip). Gustatory receptor peptide sequences of Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) ≥ 340 aa in length were multiply aligned using MUSCLE v3.8.31. (PHY 274 kb)
Gr phylogenetic tree file (Nexus). Phylogenetic analysis of Grs in Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) using a Maximum Likelihood method. Evolutionary history was inferred using a Maximum Likelihood method based on the JTT matrix-based model. The tree was constructed using RAxML under the JTT model of substitution with NNI topology search, based on an amino acid alignment by MUSCLE. Branch support was estimated using 500 bootstrap replications. The tree is rooted with Gr21a. (NEX 31 kb)
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Hickner, P.V., Rivaldi, C.L., Johnson, C.M. et al. The making of a pest: Insights from the evolution of chemosensory receptor families in a pestiferous and invasive fly, Drosophila suzukii . BMC Genomics 17, 648 (2016). https://doi.org/10.1186/s12864-016-2983-9
- Odorant receptors
- Gustatory receptors
- Niche utilization
- Molecular evolution
- Episodic selection