Genome-based identification and analysis of ionotropic receptors in Spodoptera litura

Genome-wide analysis of gustatory receptor genes and identification of the fructose gustatory receptor in Arma chinensis

Gustatory receptors (GRs) allow insects to sense tastes in their external environment. Gustatory perception is crucial for distinguishing between beneficial and harmful or toxic compounds, affecting survival. This study is the first to identify and classify the GR genes and investigate their expression in the predatory Arma chinensis. Thirteen GR genes (ArmaGr1-ArmaGr13) were identified and classified into four families via phylogenetic analysis. In the predacious developmental stages, ArmaGr7 expression gradually increased from the 2nd to 5th instar stages and then to adults. However, ArmaGr7 was also highly expressed in the non-predation 1st instar nymph and egg stages. ArmaGr7 expression was localized in the antennae, scalpella, forelegs, wings, head, and midgut of male and female adults, with wings displaying the highest expression. Furthermore, ArmaGr7 expression was positively correlated with fructose solution intake; molecular docking results showed that fructose could effectively dock withArmaGr7. A protein structure comparison revealed that the ArmaGr7 structure was different from that of other GR43a-like proteins, which may be related to the gene splicing of the A. chinensis GR gene. These results elucidate the crucial role of ArmaGr7 in fructose recognition by A. chinensis and provide a foundation for further studies on gustatory perception.

Genomic identification and evolutionary analysis of chemosensory receptor gene families in two Phthorimaea pest species: insights into chemical ecology and host adaptation

BACKGROUND

Insects rely on sophisticated sensitive chemosensory systems to sense their complex chemical environment. This sensory process involves a combination of odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) in the chemosensory system. This study focused on the identification and characterization of these three types of chemosensory receptor genes in two closely related Phthorimaea pest species, Phthorimaea operculella (potato tuber moth) and Phthorimaea absoluta (tomato leaf miner).

RESULTS

Based on manual annotation of the genome, we identified a total of 349 chemoreceptor genes from the genome of P. operculella, including 93 OR, 206 GR and 50 IR genes, while for P. absoluta, we identified 72 OR, 122 GR and 46 IR genes. Through phylogenetic analysis, we observed minimal differences in the number and types of ORs and IRs between the potato tuber moth and tomato leaf miner. In addition, we found that compared with those of tomato leaf miners, the gustatory receptor branch of P. operculella has undergone a large expansion, which may be related to P. absoluta having a narrower host range than P. operculella. Through analysis of differentially expressed genes (DEGs) of male and female antennae, we uncovered 45 DEGs (including 32ORs, 9 GRs, and 4 IRs).

CONCLUSIONS

Our research provides a foundation for exploring the chemical ecology of these two pests and offers new insights into the dietary differentiation of lepidopteran insects, while simultaneously providing molecular targets for developing environmentally friendly pest control methods based on insect chemoreception.

Comparative transcriptomics reveals the conservation and divergence of reproductive genes across three sympatric Tomicus bark beetles

Three tree-killing bark beetles belonging to the genus Tomicus, Tomicus yunnanensis, Tomicus brevipilosus and Tomicus minor (Coleoptera; Curculionidae, Scolytinae), are serious wood-borers with larvae feeding on the phloem tissues of Pinus yunnanensis. The three Tomicus beetles, in some cases, coexist in a same habitat, providing a best system for exploring the conservation and divergence of reproductive genes. Here, we applied comparative transcriptomics and molecular biology approaches to characterize reproductive-related genes in three sympatric Tomicus species. Illumina sequencing of female and male reproductive systems and residual bodies generated a large number of clean reads, representing 185,920,232 sequences in T. yunnanensis, 169,153,404 in T. brevipilosus and 178,493,176 in T. minor that were assembled into 32,802, 56,912 and 33,670 unigenes, respectively. The majority of the genes had detectable expression in reproductive tissues (FPKM >1), particularly those genes in T. brevipilosus accounting for 76.61 % of the total genes. From the transcriptomes, totally 838 genes encoding 463 detoxification enzymes, 339 chemosensory membrane proteins and 36 ionotropic glutamate receptors (iGluRs) were identified, including 622 reproductive tissue-expressed genes. Of these, members of carboxylesterases (COEs), ionotropic receptors (IRs), sensory neuron membrane proteins (SNMPs) and iGluRs were highly conserved in gene numbers and sequence identities across three Tomicus species. Further, expression profiling analyses revealed a number of genes expressed in reproductive tissues and the diverse expression characteristics in these beetles. The results provide evidence for the conservation and differences of reproductive genes among three sympatric closely related beetles, helping understand their different reproductive strategies and the maximization of the reproductive success.

Sympatric Pieris butterfly species exhibit a high conservation of chemoreceptors

Sensory processes have often been argued to play a central role in the selection of ecological niches and in the formation of new species. Butterflies are among the best studied animal groups with regards to their evolutionary and behavioral ecology and thereby offer an attractive system to investigate the role of chemosensory genes in sympatric speciation. We focus on two Pieris butterflies with overlapping host-plant ranges: P. brassicae and P. rapae. Host-plant choice in lepidopterans is largely based on their olfactory and gustatory senses. Although the chemosensory responses of the two species have been well characterized at the behavioral and physiological levels, little is known about their chemoreceptor genes. Here, we compared the chemosensory genes of P. brassicae and P. rapae to investigate whether differences in these genes might have contributed to their evolutionary separation. We identified a total of 130 and 122 chemoreceptor genes in the P. brassicae genome and antennal transcriptome, respectively. Similarly, 133 and 124 chemoreceptors were identified in the P. rapae genome and antennal transcriptome. We found some chemoreceptors being differentially expressed in the antennal transcriptomes of the two species. The motifs and gene structures of chemoreceptors were compared between the two species. We show that paralogs share conserved motifs and orthologs have similar gene structures. Our study therefore found surprisingly few differences in the numbers, sequence identities and gene structures between the two species, indicating that the ecological differences between these two butterflies might be more related to a quantitative shift in the expression of orthologous genes than to the evolution of novel receptors as has been found in other insects. Our molecular data supplement the wealth of behavioral and ecological studies on these two species and will thereby help to better understand the role of chemoreceptor genes in the evolution of lepidopterans.

A mouthpart transcriptome for Spodoptera frugiperda adults: identification of candidate chemoreceptors and investigation of expression patterns

Moth mouthparts, consisting of labial palps and proboscis, not only are the feeding device but also are chemosensory organs for the detection of chemical signals from surrounding environment. Up to now, the chemosensory systems in the mouthpart of moths are largely unknown. Here, we performed systematic analyses of the mouthpart transcriptome of adult Spodoptera frugiperda (Lepidoptera: Noctuidae), a notorious pest that spreads worldwide. A total of 48 chemoreceptors, including 29 odorant receptors (ORs), 9 gustatory receptors (GRs), and 10 ionotropic receptors (IRs), were annotated. Further phylogenetic analyses with these genes and homologs from other insect species determined that specific genes, including ORco, carbon dioxide receptors, pheromone receptor, IR co-receptors, and sugar receptors, were transcribed in the mouthpart of S. frugiperda adults. Subsequently, expression profiling in different chemosensory tissues demonstrated that the annotated ORs and IRs were mainly expressed in S. frugiperda antennae, but one IR was also highly expressed in the mouthparts. In comparison, SfruGRs were mainly expressed in the mouthparts, but 3 GRs were also highly expressed in the antennae or the legs. Further comparison of the mouthpart-biased chemoreceptors using RT-qPCR revealed that the expression of these genes varied significantly between labial palps and proboscises. This study provides the first large-scale description of chemoreceptors in the mouthpart of adult S. frugiperda and provides a foundation for further functional studies of chemoreceptors in the mouthpart of S. frugiperda as well as of other moth species.

Identification and expression analysis of chemosensory receptors in the tarsi of fall armyworm, Spodoptera frugiperda (J. E. Smith)

Chemosensation of tarsi provides moths with the ability to detect chemical signals which are important for food recognition. However, molecular mechanisms underlying the chemosensory roles of tarsi are still unknown. The fall armyworm Spodoptera frugiperda is a serious moth pest that can damage many plants worldwide. In the current study, we conducted transcriptome sequencing with total RNA extracted from S. frugiperda tarsi. Through sequence assembly and gene annotation, 23 odorant receptors 10 gustatory receptors and 10 inotropic receptors (IRs) were identified. Further phylogenetic analysis with these genes and homologs from other insect species indicated specific genes, including ORco, carbon dioxide receptors, fructose receptor, IR co-receptors, and sugar receptors were expressed in the tarsi of S. frugiperda. Expression profiling with RT-qPCR in different tissues of adult S. frugiperda showed that most annotated SfruORs and SfruIRs were mainly expressed in the antennae, and most SfruGRs were mainly expressed in the proboscises. However, SfruOR30, SfruGR9, SfruIR60a, SfruIR64a, SfruIR75d, and SfruIR76b were also highly enriched in the tarsi of S. frugiperda. Especially SfruGR9, the putative fructose receptor, was predominantly expressed in the tarsi, and with its levels significantly higher in the female tarsi than in the male ones. Moreover, SfruIR60a was also found to be expressed with higher levels in the tarsi than in other tissues. This study not only improves our insight into the tarsal chemoreception systems of S. frugiperda but also provides useful information for further functional studies of chemosensory receptors in S. frugiperda tarsi.

Sex- and tissue-specific expression of chemosensory receptor genes in a hawkmoth

For the nocturnal hawkmoth Manduca sexta, olfactory and gustatory cues are essential for finding partners, food, and oviposition sites. Three chemosensory receptor families, odorant receptors (ORs), ionotropic receptors (IRs), and gustatory receptors (GRs) are involved in the detection of these stimuli. While many chemosensory receptor genes have been identified, knowledge of their expression profile in potentially chemoreceptive organs is incomplete. Here, we studied the expression patterns of chemosensory receptors in different tissues including the antennae, labial palps, proboscis, legs, wings and ovipositor. We compared the receptors’ expression in female and male moths both before and after mating by using the NanoString platform. This tool allowed us to measure expression levels of chemosensory receptor genes in a single reaction using probes designed against 71 OR, 29 IR and 49 GR transcripts. In all tissues investigated, we detected expression of genes from all three receptor families. The highest number of receptors was detected in the antennae (92), followed by the ovipositor (59), while the least number was detected in the hindlegs (21). The highest number of OR genes were expressed in the antennae (63), of which 24 were specific to this main olfactory organ. The highest number of IRs were also expressed in the antennae (16), followed by the ovipositor (15). Likewise, antennae and ovipositor expressed the highest number of GRs (13 and 14). Expression of the OR co-receptor MsexORCo, presumably a prerequisite for OR function, was found in the antennae, labial palps, forelegs and ovipositor. IR co-receptors MsexIR25a and MsexIR76b were expressed across all tested tissues, while expression of the IR co-receptor MsexIR8a was restricted to antennae and ovipositor. Comparing the levels of all 149 transcripts across the nine tested tissues allowed us to identify sex-biased gene expression in the antennae and the legs, two appendages that are also morphologically different between the sexes. However, none of the chemosensory receptors was differentially expressed based on the moths’ mating state. The observed gene expression patterns form a strong base for the functional characterization of chemosensory receptors and the understanding of olfaction and gustation at the molecular level in M. sexta.

Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

Identification of Chemosensory Genes, Including Candidate Pheromone Receptors, in Phauda flammans (Walker) (Lepidoptera: Phaudidae) Through Transcriptomic Analyses

Olfactory and gustatory systems play an irreplaceable role in all cycles of growth of insects, such as host location, mating, and oviposition. Many chemosensory genes in many nocturnal moths have been identified via omics technology, but knowledge of these genes in diurnal moths is lacking. In our recent studies, we reported two sex pheromone compounds and three host plant volatiles that play a vital role in attracting the diurnal moth, Phauda flammans. The antennal full-length transcriptome sequence of P. flammans was obtained using the Pacbio sequencing to further explore the process of sex pheromone and host plant volatile recognition in P. flammans. Transcriptome analysis identified 166 candidate olfactory and gustatory genes, including 58 odorant-binding proteins (OBPs), 19 chemosensory proteins (CSPs), 59 olfactory receptors (ORs), 16 ionotropic receptors (IRs), 14 gustatory receptors (GRs), and 2 sensory neuron membrane proteins (SNMPs). Subsequently, a phylogenetic tree was established using P. flammans and other lepidopteran species to investigate orthologs. Among the 17 candidate pheromone receptor (PR) genes, the expression levels of PflaOR21, PflaOR25, PflaOR35, PflaOR40, PflaOR41, PflaOR42, PflaOR44, PflaOR49, PflaOR51, PflaOR61, and PflaOR63 in the antennae were significantly higher than those in other non-antennae tissues. Among these PR genes, PflaOR21, PflaOR27, PflaOR29, PflaOR35, PflaOR37, PflaOR40, PflaOR42, PflaOR44, PflaOR60, and PflaOR62 showed male-biased expression, whereas PflaOR49, PflaOR61, and PflaOR63 revealed female-biased expression. The functions of related OR genes were also discussed. This research filled the gap of the chemosensory genes of P. flammans and provided basic data for future functional molecular mechanisms studies on P. flammans olfaction.

Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids

Background

In insects, airborne chemical signals are mainly detected by two receptor families, odorant receptors (ORs) and ionotropic receptors (IRs). Functions of ORs have been intensively investigated in Diptera and Lepidoptera, while the functions and evolution of the more ancient IR family remain largely unexplored beyond Diptera.

Results

Here, we identified a repertoire of 26 IRs from transcriptomes of female and male antennae, and ovipositors in the moth Agrotis segetum. We observed that a large clade formed by IR75p and IR75q expansions is closely related to the acid-sensing IRs identified in Diptera. We functionally assayed each of the five AsegIRs from this clade using Xenopus oocytes and found that two receptors responded to the tested ligands. AsegIR75p.1 responded to several compounds but hexanoic acid was revealed to be the primary ligand, and AsegIR75q.1 responded primarily to octanoic acid, and less so to nonanoic acid. It has been reported that the C₆-C₁₀ medium-chain fatty acids repel various insects including many drosophilids and mosquitos. We show that the C₆-C₁₀ medium-chain fatty acids elicited antennal responses of both sexes of A. segetum, while only octanoic acid had repellent effect to the moths in a behavioral assay. In addition, using fluorescence in situ hybridization, we demonstrated that the five IRs and their co-receptor AsegIR8a are not located in coeloconic sensilla as found in Drosophila, but in basiconic or trichoid sensilla.

Conclusions

Our results significantly expand the current knowledge of the insect IR family. Based on the functional data in combination with phylogenetic analysis, we propose that subfunctionalization after gene duplication plays an important role in the evolution of ligand specificities of the acid-sensing IRs in Lepidoptera.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01235-0.

Neuroligin 3 from common cutworm enhances the GABA-induced current of recombinant SlRDL1 channel

BACKGROUND

Neuroligin (NLG) protein is a nerve cell adhesion molecule and plays a key role in the precision apposition of presynaptic domains on inhibitory and excitatory synapses. Existing studies mainly focused on the function of NLG3 against the excitatory channel. However, the interaction between insect NLG3 and ionotropic GABA receptor, which is the main inhibitory channel, remains unclear. In this study, the Nlg3 of common cutworm (CCW), Spodoptera litura Fabricius, one important agricultural Lepidopteron, is selected to explore its function in the inhibitory channel.

RESULTS

The SlNlg3 was obtained and the SlNLG3 contains the characteristic features including transmembrane domain, PDZ-binding motif and type-B carboxylesterases signature 2 motif. The SlNlg3 messenger RNA (mRNA) was most abundant in midgut, and exhibited multiple expression patterns in different developmental stages and tissues or body parts. Compared with the single injection of SlRDL1, the median effective concentration value of GABA in activating currents was smaller in Xenopus laevis oocytes co-injected with SlRDL1 and SlNlg3. In addition, SlNlg3 could enhance the GABA-induced current of homomeric SlRDL1 channel from -391.86 ± 15.41 to -2152.51 ± 30.09 nA. DsSlNlg3 depressed the expression level of SlNlg3 mRNA more than 64.29% at 6 h. After exposure to median lethal dose of fluralaner, the mortality of CCW injected with dsSlNlg3 was significantly decreased by 13.34% and 30.00% at 24 and 48 h, respectively, compared to injection of dsEGFP.

CONCLUSION

NLG3 should have physiological function on ionotropic GABA receptor in vitro, which provided a favorable foundation for further research on the physiological function of Nlg gene in Lepidopteron. © 2021 Society of Chemical Industry.

Transcriptome Analysis and Characterization of Chemosensory Genes in the Forest Pest, Dioryctria abietella (Lepidoptera: Pyralidae)

In Lepidoptera, RNA sequencing has become a useful tool in identifying chemosensory genes from antennal transcriptomes, but little attention is paid to non-antennal tissues. Though the antennae are primarily responsible for olfaction, studies have found that a certain number of chemosensory genes are exclusively or highly expressed in the non-antennal tissues, such as proboscises, legs and abdomens. In this study, we report a global transcriptome of 16 tissues from Dioryctria abietella, including chemosensory and non-chemosensory tissues. Through Illumina sequencing, totally 952,658,466 clean reads were generated, summing to 142.90 gigabases of data. Based on the transcriptome, 235 chemosensory-related genes were identified, comprising 42 odorant binding proteins (OBPs), 23 chemosensory proteins (CSPs), 75 odorant receptors (ORs), 62 gustatory receptors (GRs), 30 ionotropic receptors (IRs), and 3 sensory neuron membrane proteins (SNMPs). Compared to a previous study in this species, 140 novel genes were found. A transcriptome-wide analysis combined with PCR results revealed that except for GRs, the majority of other five chemosensory gene families in Lepidoptera were expressed in the antennae, including 160 chemosensory genes in D. abietella. Using phylogenetic and expression profiling analyses, members of the six chemosensory gene repertoires were characterized, in which 11 DabiORs were candidates for detecting female sex pheromones in D. abietella, and DabiOR23 may be involved in the sensing of plant-derived phenylacetaldehyde. Intriguingly, more than half of the genes were detected in the proboscises, and one fourth of the genes were found to have the expression in the legs. Our study not only greatly extends and improves the description of chemosensory genes in D. abietella, but also identifies potential molecular targets involved in olfaction, gustation and non-chemosensory functions for control of this pest.

Chemosensory genes in the head of Spodoptera litura larvae

The tobacco cutworm Spodoptera litura (Lepidoptera: Noctuidae) is a polyphagous pest with a highly selective and sensitive chemosensory system involved in complex physiological behaviors such as searching for food sources, feeding, courtship, and oviposition. However, effective management strategies for controlling the insect pest populations under threshold levels are lacking. Therefore, there is an urgent need to formulate eco-friendly pest control strategies based on the disruption of the insect chemosensory system. In this study, we identified 158 putative chemosensory genes based on transcriptomic and genomic data for S. litura, including 45 odorant-binding proteins (OBPs, nine were new), 23 chemosensory proteins (CSPs), 60 odorant receptors (ORs, three were new), and 30 gustatory receptors (GRs, three were new), a number higher than those reported by previous transcriptome studies. Subsequently, we constructed phylogenetic trees based on these genes in moths and analyzed the dynamic expression of various genes in head capsules across larval instars using quantitative real-time polymerase chain reaction. Nine genes-SlitOBP8, SlitOBP9, SlitOBP25, SlitCSP1, SlitCSP7, SlitCSP18, SlitOR34, SlitGR240, and SlitGR242-were highly expressed in the heads of 3- to 5-day-old S. litura larvae. The genes differentially expressed in olfactory organs during larval development might play crucial roles in the chemosensory system of S. litura larvae. Our findings substantially expand the gene inventory for S. litura and present potential target genes for further studies on larval feeding in S. litura.

Identification and expression profiling of chemosensory membrane protein genes in Achelura yunnanensis (Lepidoptera: Zygaenidae)

During the past decade, antennal transcriptome sequencing has been applied to at least 50 species from 16 families of the Lepidoptera order of insects, emphasizing the identification and characterization of chemosensory-related genes. However, little is known about the chemosensory genes in the Zygaenidae family of Lepidoptera. Herein, we report the transmembrane protein gene repertoires involved in chemoreception from Achelura yunnanensis (Lepidoptera: Zygaenidae) through transcriptome sequencing, bioinformatics, phylogenetics and polymerase chain reaction (PCR) approaches. Transcriptome analysis led to the generation of 555.47 million clean reads and accumulation of 83.30 gigabases of data. From this transcriptome, 132 transcripts encoding 69 odorant receptors (ORs), 33 gustatory receptors (GRs), 26 ionotropic receptors (IRs), and four sensory neuron membrane proteins (SNMPs) were identified, 69 of which were full-length sequences. Notably, the number of SNMPs in A. yunnanensis was the largest set in Lepidoptera to date. Phylogenetic analysis combined with sequence homology highlighted several conserved groups of chemoreceptors, including pheromone receptors (a so-called pheromone receptor (PR) clade: AyunOR50 and novel PR members: AyunOR39 and OR40), a phenylacetaldehyde-sensing OR (AyunOR28), carbon dioxide receptors (AyunGR1-3), and antennal IRs (13 A-IRs). In addition, a Zygaenidae-specific OR expansion was observed, including 15 A. yunnanensis members. Expression profiles revealed 99 detectable chemosensory genes in the antennae and 20 in the reproductive tissues, some of which displayed a sex-biased expression. This study identifies potential olfactory molecular candidates for sensing sex pheromones, phenylacetaldehyde or other odorants, and provides preliminary evidence for the putative reproductive function of chemosensory membrane protein genes in A. yunnanensis.

Description of Chemosensory Genes in Unexplored Tissues of the Moth Spodoptera littoralis

Illumina-based transcriptome sequencing of chemosensory organs has become a standard in deciphering the molecular bases of chemical senses in insects, especially in non-model species. A plethora of antennal transcriptomes is now available in the literature, describing large sets of chemosensory receptors and binding proteins in a diversity of species. However, little is still known on other organs such as mouthparts, legs and ovipositors, which are also known to carry chemosensory sensilla. This is the case of the noctuid Spodoptera littoralis, which has been established as a model insect species in molecular chemical ecology thanks to the description of many—but not all—chemosensory genes. To fulfill this gap, we present here an unprecedented transcriptomic survey of chemosensory tissues in this species. RNAseq from male and female proboscis, labial palps, legs and female ovipositors allowed us to annotate 115 putative chemosensory gene transcripts, including 30 novel genes in this species. Especially, we doubled the number of candidate gustatory receptor transcripts described in this species. We also evidenced ectopic expression of many chemosensory genes. Remarkably, one third of the odorant receptors were found to be expressed in the proboscis. With a total of 196 non-overlapping chemosensory genes annotated, the S. littoralis repertoire is one of the most complete in Lepidoptera. We further evaluated the expression of transcripts between males and females, pinpointing sex-specific transcripts. We identified five female-specific transcripts, including one odorant receptor, one gustatory receptor, one ionotropic receptor and one odorant-binding protein, and one male-specific gustatory receptor. Such sex-biased expression suggests that these transcripts participate in sex-specific behaviors, such as host choice for oviposition in females and/or mating partner recognition in both sexes.

Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize

The Mediterranean corn borer (Sesamia nonagrioides, Noctuidae, Lepidoptera) is a major pest of maize in Europe and Africa. Here, we report an assembly of the nuclear and mitochondrial genome of a pool of inbred males and females third-instar larvae, based on short- and long-read sequencing. The complete mitochondrial genome is 15,330 bp and contains all expected 13 and 24 protein-coding and RNA genes, respectively. The nuclear assembly is 1021 Mb, composed of 2553 scaffolds and it has an N50 of 1105 kb. It is more than twice larger than that of all Noctuidae species sequenced to date, mainly due to a higher repeat content. A total of 17,230 protein-coding genes were predicted, including 15,776 with InterPro domains. We provide detailed annotation of genes involved in sex determination (doublesex, insulin-like growth factor 2 mRNA-binding protein, and P-element somatic inhibitor) and of alpha-amylase genes possibly involved in interaction with parasitoid wasps. We found no evidence of recent horizontal transfer of bracovirus genes from parasitoid wasps. These genome assemblies provide a solid molecular basis to study insect genome evolution and to further develop biocontrol strategies against S. nonagrioides.

Combined transcriptomic, proteomic and genomic analysis identifies reproductive-related proteins and potential modulators of female behaviors in Spodoptera litura

The common cutworm, Spodoptera litura, is a polyandrous moth with high reproductive ability. Sexual reproduction is a unique strategy for survival and reproduction of population in this species. However, to date available information about its reproductive genes is rare. Here, we combined transcriptomics, genomics and proteomics approaches to characterize reproductive-related proteins in S. litura. Illumina sequencing in parallel with the reference genome led to the yields of 12,161 reproductive genes, representing 47.83% of genes annotated in the genome. Further, 524 genes of 19 specific gene families annotated in the genome were detected in reproductive tissues of both sexes, some of which exhibited sex-biased and/or tissue-enriched expression. Of these, manual efforts together with the transcriptome analyses re-annotated 54 odorant binding proteins (OBPs) and 23 chemosensory proteins (CSPs) with an increase of 18 OBPs and one CSP compared to those previously annotated in the genome. Interestingly, at least 35 OBPs and 22 CSPs were transcribed in at least one reproductive tissue, suggestive of their involvement in reproduction. Further proteomic analysis revealed 2381 common proteins between virgin and mated female reproductive systems, 79 of which were differentially expressed. More importantly, 74 proteins exclusive to mated females were identified as transferred relatives, coupled with their specific or high expression in male reproductive systems. Of the transferred proteins, several conserved protein classes across insects were observed including OBPs, serpins, trypsins and juvenile hormone-binding proteins. Our current study has extensively surveyed reproductive genes in S. litura with an emphasis on the roles of OBPs and CSPs in reproduction, and identifies potentially transferred proteins serving as modulators of female post-mating behaviors.

Identification and Functional Analysis of SlitOBP11 From Spodoptera litura

Odorant binding proteins (OBPs) play a key role in the olfactory recognition of insects, whose functions have been extensively studied in adult insects but rarely in larvae. In this study, one OBP (SlitOBP11) with high expression in larval antenna but low expression in adult antenna of Spodoptera litura was screened by RNA-seq and verified by quantitative real-time PCR. Furthermore, the function of SlitOBP11 was explored by analysis of the expression patterns and prokaryotic expression of proteins as well as assays of competitive binding. Competitive binding assay demonstrated that SlitOBP11 had high binding affinity to all four female sex pheromone components, but exhibited almost no binding affinity to plant volatiles except for a low affinity to Phenylacetaldehyde and Phenethyl acetate. Homology modeling and molecular docking implied that the shape of these four sex pheromones were linear, which were appropriate for the binding channel of SlitOBP11 and the amino acid residue Asn99 of SlitOBP11 might play an important role in binding. Taken together, our results indicate that SlitOBP11 may be involved in the perception of female sex pheromones by S. litura larvae, and OBPs in the larvae of S. litura play an important role in the olfactory perception process.

Coupling Transcriptomics and Behaviour to Unveil the Olfactory System of Spodoptera exigua Larvae

Insect chemosensation is crucial for many aspects related to food seeking, enemy avoidance, and reproduction. Different families of receptors and binding proteins interact with chemical stimuli, including odorant receptors (ORs), ionotropic receptors (IRs), gustatory receptors (GRs), odorant binding proteins (OBPs) and chemosensory proteins (CSPs). In this work, we describe the chemosensory-related gene repertoire of the worldwide pest Spodoptera exigua (Lepidoptera: Noctuidae), focusing on the transcripts expressed in larvae, which feed on many horticultural crops producing yield losses. A comprehensive de novo assembly that includes reads from chemosensory organs of larvae and adults, and other larval tissues, enabled us to annotate 200 candidate chemosensory-related genes encoding 63 ORs, 28 IRs, 38 GRs, 48 OBPs and 23 CSPs. Of them, 51 transcripts are new annotations. Fifty ORs are expressed in larval heads based on RNA-seq and reverse transcription PCR analyses. Fourteen OBPs are expressed in larval, but not in adult heads. We also observe that expression profiles of ORs are strongly and non-specifically up-regulated upon pre-exposure of larvae to single volatile organic compounds (VOCs). Finally, we develop a behavioural assay to study the attraction/repellence to VOCs in S. exigua larvae and thus identify candidate ecologically relevant odours. A single-dose assay demonstrated that 1-hexanol triggers attraction and indole repels larvae at any timepoint. This work establishes the foundation for the study of chemosensation in S. exigua larvae, allowing further studies aimed to characterize chemosensory-related genes that underlie the ecologically relevant behaviours of larvae.

The ionotropic receptor gene family in Lepidoptera and Trichoptera: Annotation, evolutionary and functional perspectives

Lepidoptera (moths and butterflies) and Trichoptera (caddisflies), belonging to the superorder Amphiesmenoptera, are the most diverse insect orders as representatives of the terrestrial and aquatic insects, respectively. The insects of the two orders possess different biological and behavioral characteristics, especially their larvae, presumably resulting in the differences of the ionotropic receptor (IR) genes in numbers, sequence characteristics or gene structure. Here, we employed genomics, transcriptomics, bioinformatics, phylogenetics and molecular biology strategies to characterize the IR gene repertoire in Lepidoptera and Trichoptera. Genome and transcriptome analyses with exhaustive homology-based searches and manual efforts, in 32 lepidopterans and five trichopterans, led to the identification of 1449 genes encoding IRs with 1170 full-length sequences, representing the most comprehensive set of chemoreceptor superfamilies across the Amphiesmenoptera. Analysis of gene gains and losses in orthologous groups implied that some IRs were lost in related species, and multiple gene copies occurred mainly in divergent IRs (D-IRs) by gene duplications. Phylogenetic analysis of 2442 IR proteins from 67 species revealed that Lepidoptera and Trichoptera IRs could be classified into three subfamilies, i.e., 14 antennal IRs (A-IRs), five Lepidoptera-specific IRs (LS-IRs) and four D-IRs. Of the three subfamilies, A-IRs and LS-IRs members within orthologous groups exhibited high conservation of gene structure, but D-IRs shared extremely low amino acid identities (below 30%). Expression profiles revealed functional diversities of IRs from Bombyx mori and Papilio xuthus involving smell, taste or reproduction, in which some genes displayed sex-biased expression in antennae associated with specific chemosensory behaviors of female or male adults. Our current study has provided insights into the evolution, conservation and divergence of IRs between/within Lepidoptera and Trichoptera, and allows for further experiments to investigate IR functions.

Genome-based analysis reveals a novel SNMP group of the Coleoptera and chemosensory receptors in Rhaphuma horsfieldi

Through an exhaustive homology-based approach, coupled with manual efforts, we annotated and characterized 128 sensory neuron membrane proteins (SNMPs) from genomes and transcriptomes of 22 coleopteran species, with 107 novel candidates. Remarkably, we discovered, for the first time, a novel SNMP group, defined as Group 4 based on the phylogeny, sequence characteristics, gene structure and organization. The lineage-specific expansions in SNMPs occurred mainly in the family Scarabaeidae, harboring 12 representatives in Onthophagus taurus as a typical gene duplication and the most massive set of SNMPs in insects to date. Transcriptome sequencing of Rhaphuma horsfieldi resulted in the yields of approximately 611.9 million clean reads that were further assembled into 543,841 transcripts and 327,550 unigenes, respectively. From the transcriptome, 177 transcripts encoding 84 odorant (ORs), 62 gustatory (GRs), 20 ionotropic (IRs), and 11 ionotropic glutamate (iGluRs) receptors were identified. Phylogenetic analysis classified RhorORs into six groups, RhorGRs into four subfamilies, and RhorIRs into 10 conserved antennal IRs and one divergent IRs. Expression profiles revealed that over 80% of chemosensory genes were specifically or highly transcribed in antennae or tarsi, suggestive of their olfactory and/or gustatory roles. This study has greatly complemented the resources for chemosensory genes in the cerambycid beetles, and most importantly, identifies a novel group of SNMPs in Coleoptera.

Genome-wide identification of chemosensory receptor genes in the small brown planthopper, Laodelphax striatellus

The small brown planthopper (SBPH), Laodelphax striatellus is one of the major insect pests of rice, but little is known about the molecular-level means by which it locates its hosts. SBPH host-seeking behavior heavily relies on chemosensory receptors (CRs). In this study, we utilized genome analysis of the SBPH to identify 169 CRs, including: 133 odorant receptors (ORs), 13 gustatory receptors (GRs) and 23 ionotropic receptors (IRs). The phylogenetic relationships of OR genes from three rice planthoppers and other insect species revealed that the odorant co-receptor (Orco) clade is the most conserved group. Among the candidate GRs, two sugar receptors and five fructose receptors have been identified but no carbon dioxide receptors investigated. Furthermore, we identified homologs of the three highly conserved IR co-receptors. The obtained results will provide us with precious information needed to better understand the interaction between insect pests and crop plants required for effective crop protection.

Antennal ionotropic receptors IR64a1 and IR64a2 of the parasitoid wasp Microplitis mediator (Hymenoptera: Braconidate) collaboratively perceive habitat and host cues

Ionotropic receptors (IRs), as a member of the conserved chemoreceptor families in the peripheral nervous system, play a critical role in the chemoreception of Drosophila. However, little is known about IRs in Hymenoptera insects. Here, we comprehensively characterized the gene structure, topological map and chemosensory roles of antennal IRs (MmedIRs) in the hymenopteran parasitoid wasp Microplitis mediator. We found that the IRs were conserved across various insect species. In the in situ hybridization assays, most IRs showed female antennae biased features, and there was no co-expression of the IRs and the olfactory receptor co-receptor (ORco). Moreover, three IR co-expressed complexes, IR75u-IR8a, IR64a1-IR8a and IR64a2-IR8a, were detected. Two genes with high similarity, IR64a1 and IR64a2, were located in distinct neurons but projected to the same sensillum. In two-electrode voltage-clamp recordings, IR64a1 was widely tuned to the chemicals from habitat cues released from host plants over long distances, whereas IR64a2 responded to a narrow range host cues and plant odors with low-volatility. Notably, IR64a2 was able to perceive Z9-14: Ald, a vital sex pheromone component that is released from Helicoverpa armigera, which is the preferred host of M. mediator. Furthermore, most ligands of IR64a1 and IR64a2 can trigger electrophysiological responses in female wasps. We propose that IR64a1 and IR64a2 collaboratively perceive habitat and host cues to assist parasitoids in efficiently seeking hosts.

Chemosensory Gene Families in the Oligophagous Pear Pest Cacopsylla chinensis (Hemiptera: Psyllidae)

Chemosensory systems play an important role in insect behavior, and some key associated genes have potential as novel targets for pest control. Cacopsylla chinensis is an oligophagous pest and has become one of the main pests of pear trees, but little is known about the molecular-level means by which it locates its hosts. In this study, we assembled the head transcriptome of C. chinensis using Illumina sequencing, and 63,052 Unigenes were identified. A total of 36 candidate chemosensory genes were identified, including five different families: 12 odorant binding proteins (OBPs), 11 chemosensory proteins (CSPs), 7 odorant receptors (ORs), 4 ionotropic receptors (IRs), and 2 gustatory receptors (GRs). The number of chemosensory gene families is consistent with that found in other Hemipteran species, indicating that our approach successfully obtained the chemosensory genes of C. chinensis. The tissue expression of all genes using quantitative real-time PCR (qRT-PCR) found that some genes displayed male head, female head, or nymph-biased specific/expression. Our results enrich the gene inventory of C. chinensis and provide valuable resources for the analysis of the functions of some key genes. This will help in developing molecular targets for disrupting feeding behavior in C. chinensis.