Transcriptional variation associated with cactus host plant adaptation in Drosophila mettleri populations

Genomic Islands of Divergence Between Drosophila yakuba Subspecies are Predominantly Driven by Chromosomal Inversions and the Recombination Landscape

During the early stages of local adaptation and speciation, genetic differences tend to accumulate at certain regions of the genome leading to the formation of genomic islands of divergence (GIDs). This pattern may be due to selection and/or difference in the rate of recombination. Here, we investigate the possible causes of GIDs in Drosophila yakuba mayottensis, and reconfirm using field collection its association with toxic noni (Morinda citrifolia) fruits on the Mayotte island. Population genomics revealed lack of genetic structure on the island and identified 23 GIDs distinguishing D. y. mayottensis from generalist mainland populations of D. y. yakuba. The GIDs were enriched with gene families involved in the metabolism of lipids, sugars, peptides and xenobiotics, suggesting a role in host shift. We assembled a new genome for D. y. mayottensis and identified five novel chromosomal inversions. Twenty one GIDs (~99% of outlier windows) fell in low recombining regions or subspecies-specific inversions. However, only two GIDs were in collinear, normally recombining regions suggesting a signal of hard selective sweeps. Unlike D. y. mayottensis, D. sechellia, the only other noni-specialist, is known to be homosequential with its generalist relatives. Thus, whereas structural variation may disproportionally shape GIDs in some species, striking parallel adaptations can occur between species despite distinct genomic architectures.

Decoding plant-induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges

The diet breadth of generalist herbivores when compared to specialists tends to be associated with greater transcriptional plasticity. Here, we consider whether it may also contribute to variation in host range among two generalists with different levels of polyphagy. We examined two related polyphagous spider mites with different host ranges, Tetranychus urticae (1200 plants) and Tetranychus truncatus (90 plants). Data from multiple populations of both species domesticated on common beans and transferred to new plant hosts (cotton, cucumber, eggplant) were used to investigate transcriptional plasticity relative to population-based variation in gene expression. Compared to T. truncatus, T. urticae exhibited much higher transcriptional plasticity. Populations of this species also showed much more variable expression regulation in response to a plant host, particularly for genes related to detoxification, transport, and transcriptional factors. In response to the different plant hosts, both polyphagous species showed enriched processes of drug/xenobiotics metabolism, with T. urticae orchestrating a relatively broader array of biological pathways. Through co-expression network analysis, we identified gene modules associated with host plant response, revealing shared hub genes primarily involved in detoxification metabolism when both mites fed on the same plants. After silencing a shared hub CYP gene related to eggplant exposure, the performance of both species on the original bean host improved, but the fecundity of T. truncatus decreased when feeding on eggplant. The extensive transcriptomic variation shown by T. urticae might serve as a potential compensatory mechanism for a deficiency of hub genes in this species. This research points to nuanced differences in transcriptomic variability between generalist herbivores.

Dietary Variation Effect on Life History Traits and Energy Storage in Neotropical Species of Drosophila (Diptera; Drosophilidae)

The ability of an organism to respond to nutritional stress can be a plastic character under the action of natural selection, affecting several characteristics, including life history and energy storage. The genus Drosophila (Diptera; Drosophilidae) presents high variability regarding natural resource exploration. However, most works on this theme have studied the model species D. melanogaster Meigen, 1830 and little is known about Neotropical drosophilids. Here we evaluate the effects of three diets, with different carbohydrate-to-protein ratios, on life history (viability and development time) and metabolic pools (triglycerides, glycogen, and total soluble protein contents) of three Neotropical species of Drosophila: D. maculifrons Duda, 1927; D. ornatifrons Duda, 1927, both of the subgenus Drosophila Sturtevant, 1939, and D. willistoni Sturtevant, 1916 of the subgenus Sophophora Sturtevant, 1939. Our results showed that only D. willistoni was viable on all diets, D. maculifrons was not viable on the sugary diet, while D. ornatifrons was barely viable on this diet. The sugary diet increased the development time of D. willistoni and D. ornatifrons, and D. willistoni glycogen content. Thus, the viability of D. maculifrons and D. ornatifrons seems to depend on a certain amount of protein and/or a low concentration of carbohydrate in the diet. A more evident effect of the diets on triglyceride and protein pools was detected in D. ornatifrons, which could be related to the adult attraction to dung and carrion baited pitfall as food resource tested in nature. Our results demonstrated that the evolutionary history and differential adaptations to natural macronutrient resources are important to define the amplitude of response that a species can present when faced with dietary variation.

Transcriptional signature of host shift in the seed beetle Zabrotes subfasciatus

In phytophagous insects, adaptation to a new host is a dynamic process, in which early and later steps may be underpinned by different features of the insect genome. Here, we tested the hypothesis that early steps of this process are underpinned by a shift in gene expression patterns. We set up a short-term artificial selection experiment (10 generations) for the use of an alternative host (Cicer arietinum) on populations of the bean beetle Zabrotes subfasciatus. Using Illumina sequencing on young adult females, we show the selected populations differ in the expression of genes associated to stimuli, signalling, and developmental processes. Particularly, the "C. arietinum" population shows upregulation of histone methylation genes, which may constitute a strategy for fine-tuning the insect global gene expression network. Using qPCR on body regions, we demonstrated that the "Phaseolus vulgaris" population upregulates the genes polygalacturonase and egalitarian and that the expression of an odorant receptor transcript variant changes over generations. Moreover, in this population we detected the existence of vitellogenin (Vg) variants in both males and females, possibly harbouring canonical reproductive function in females and extracellular unknown functions in males. This study provides the basis for future genomic investigations seeking to shed light on the nature of the proximate mechanisms involved in promoting differential gene expression associated to insect development and adaptation to new hosts.

Gene expression plasticity facilitates different host feeding in Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae)

Host shift is ecologically advantageous and a crucial driver for herbivore insect speciation. Insects on the non-native host obtain enemy-free space and confront reduced competition, but they must adapt to survive. Such signatures of adaptations can often be detected at the gene expression level. It is astonishing how bark beetles cope with distinct chemical environments while feeding on various conifers. Hence, we aim to disentangle the six-toothed bark beetle (Ips sexdentatus) response against two different conifer defences upon host shift (Scots pine to Norway spruce). We conducted bioassay and metabolomic analysis followed by RNA-seq experiments to comprehend the beetle's ability to surpass two different terpene-based conifer defence systems. Beetle growth rate and fecundity were increased when reared exclusively on spruce logs (alternative host) compared to pine logs (native host). Comparative gene expression analysis identified differentially expressed genes (DEGs) related to digestion, detoxification, transporter activity, growth, signalling, and stress response in the spruce-feeding beetle gut. Transporter genes were highly abundant during spruce feeding, suggesting they could play a role in pumping a wide variety of endogenous and xenobiotic compounds or allelochemicals out. Trehalose transporter (TRET) is also up-regulated in the spruce-fed beetle gut to maintain homeostasis and stress tolerance. RT-qPCR and enzymatic assays further corroborated some of our findings. Taken together, the transcriptional plasticity of key physiological genes plays a crucial role after the host shift and provides vital clues for the adaptive potential of bark beetles on different conifer hosts.

Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila

Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species form a tractable system to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic changes brought about key mechanisms underlying the adaptation of the buzzatii cluster species to arid regions in South America.

Sublethal toxicity, transgenerational effects, and transcriptome expression of the neonicotinoid pesticide cycloxaprid on demographic fitness of Coccinella septempunctata

Evaluating side effects of new neonicotinoids in terms of sublethal doses and transcriptome expression is a crucial but challenging part of integrated pest management (IPM) approaches. To this end, a study of lethal and sublethal effects on Coccinella septempunctata larvae was conducted, and an age-stage, two-sex life table procedure was performed to investigate life-table parameters. Cycloxaprid (CYC) was shown to have adverse effects on survival, development, total longevity, reproductive capacity, and predation ability in C. septempunctata. In addition, demographic growth parameters of the F1 generation such as net reproductive rate, and the intrinsic and finite rates of increase were significantly decreased under sublethal dosage LR₃₀ (1.91 g ai/hm²). These results demonstrated that the population growth of C. septempunctata was impacted by a sublethal dosage of CYC. For transcriptome expression, 544 up- and 338 down-regulated significantly differentially expressed genes (DEGs), were observed between LR₃₀ treatment and control groups. Moreover, pathways related to metabolism of retinol, carcinogenesis, biosynthesis of steroid hormone, P450 metabolism, and metabolism of xenobiotics were identified in KEGG pathway analysis. Ten DEGs were chosen and confirmed with quantitative real-time PCR analysis. Based on these findings, CYC should be considered as a component of IPM strategies in the field.

Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet

Drosophila sechellia is an island endemic host specialist that has evolved to consume the toxic fruit of Morinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruit's unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult female D. sechellia and performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization in D. sechellia.

De Novo Transcription Responses Describe Host-Related Differentiation of Paracoccus marginatus (Hemiptera: Pseudococcidae)

Paracoccus marginatus (Hemiptera: Pseudococcidae) is an invasive pest with a diverse host range, strong diffusion, and high fecundity. It has been observed that P. marginatus feeding on Carica papaya have a higher survival rate, fecundity, and longer lifespan than P. marginatus feeding on Solanum tuberosum, indicating their successful adaptation to C. papaya; however, the mechanisms underlying host plant adaptation remain unclear. Therefore, RNA-seq was performed to study the transcriptional responses of P. marginatus feeding on C. papaya and S. tuberosum plants. A total of 408 genes with significant differential expression were defined; most of them were downregulated in S. tuberosum, including those of digestive enzymes, detoxifying enzymes, ribosomes, and reproductive-related genes, which may result from the adaptation of the host to nutritional needs and changes in toxic chemical levels. Enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes showed that lysosome and longevity regulating pathways related to digestion, detoxification, and longevity were enriched. We suggest that C. papaya is a more suitable host than S. tuberosum, and downregulated target genes may have important effects on the adaptation of P. marginatus to host transfer.

Family dinner: Transcriptional plasticity of five Noctuidae (Lepidoptera) feeding on three host plant species

Polyphagous insects often show specialization in feeding on different host plants in terms of survival and growth and, therefore, can be considered minor or major pests of particular hosts. Whether polyphagous insects employ a common transcriptional response to cope with defenses from diverse host plants is under-studied. We focused on patterns of transcriptional plasticity in polyphagous moths (Noctuidae), of which many species are notorious pests, in relation to herbivore performance on different host plants. We compared the transcriptional plasticity of five polyphagous moth species feeding and developing on three different host plant species. Using a comparative phylogenetic framework, we evaluated if successful herbivory, as measured by larval performance, is determined by a shared or lineage-specific transcriptional response. The upregulated transcriptional activity, or gene expression pattern, of larvae feeding on the different host plants and artificial control diet was highly plastic and moth species-specific. Specialization, defined as high herbivore success for specific host plants, was not generally linked to a lower number of induced genes. Moths that were more distantly related and showing high herbivore success for certain host plants showed shared expression of multiple homologous genes, indicating convergence. We further observed specific transcriptional responses within phylogenetic lineages. These expression patterns for specific host plant species are likely caused by shared evolutionary histories, for example, symplesiomorphic patterns, and could therefore not be associated with herbivore success alone. Multiple gene families, with roles in plant digestion and detoxification, were widely expressed in response to host plant feeding but again showed highly moth species-specific. Consequently, high herbivore success for specific host plants is also driven by species-specific transcriptional plasticity. Thus, potential pest moths display a complex and species-specific transcriptional plasticity.

Evolution of the odorant-binding protein gene family in Drosophila

Odorant-binding proteins (OBPs) are encoded by a gene family involved in the perception of olfactory signals in insects. This chemosensory gene family has been advocated as a candidate to mediate host preference and host shifts in insects, although it also participates in other physiological processes. Remarkable differences in the OBP gene repertoire have been described across insect groups, suggesting an accelerated gene turnover rate. The genus Drosophila, is a valuable resource for ecological genomics studies since it comprises groups of ecologically diverse species and there are genome data for many of them. Here, we investigate the molecular evolution of this chemosensory gene family across 19 Drosophila genomes, including the melanogaster and repleta species groups, which are mostly associated with rotting fruit and cacti, respectively. We also compared the OBP repertoire among the closely related species of the repleta group, associated with different subfamilies of Cactaceae that represent disparate chemical challenges for the flies. We found that the gene family size varies widely between species, ranging from 39 to 54 candidate OBPs. Indeed, more than 54% of these genes are organized in clusters and located on chromosomes X, 2, and 5, with a distribution conserved throughout the genus. The family sizes in the repleta group and D. virilis (virilis-repleta radiation) were smaller than in the melanogaster group. We tested alternative evolutionary models for OBP family size and turnover rates based on different ecological scenarios. We found heterogeneous gene turnover rates (GR) in comparisons involving columnar cactus specialists, prickly pear specialists, and fruit dwellers lineages, and signals of rapid molecular evolution compatible with positive selection in specific OBP genes. Taking ours and previous results together, we propose that this chemosensory gene family is involved in host adaptation and hypothesize that the adoption of the cactophilic lifestyle in the repleta group accelerated the evolution of members of the family.

Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species

BACKGROUND

The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this regard, a powerful technique such as RNA-Seq applied to ecologically amenable taxa allows to address issues that are not possible in classic model species. Here, we study gene expression profiles and larval performance of the cactophilic siblings Drosophila buzzatii and D. koepferae reared in media that approximate natural conditions and evaluate both chemical and nutritional components of the diet. These closely related species are complementary in terms of host-plant use since the primary host of one is the secondary of the other. D. koepferae is mainly a columnar cactus dweller while D. buzzatii prefers Opuntia hosts.

RESULTS

Our comparative study shows that D. buzzatii and D. koepferae have different transcriptional strategies to face the challenges posed by their natural resources. The former has greater transcriptional plasticity, and its response is mainly modulated by alkaloids of its secondary host, while the latter has a more canalized genetic response, and its transcriptional plasticity is associated with the cactus species.

CONCLUSIONS

Our study unveils a complex pleiotropic genetic landscape in both species, with functional links that relate detox responses and redox mechanisms with developmental and neurobiological processes. These results contribute to deepen our understanding of the role of host plant shifts and natural stress driving ecological specialization.

Role of Genes in Regulating Host Plants Expansion in Tephritid Fruit Flies (Diptera) and Potential for RNAi-Based Control

Host plant expansion is an important survival strategy for tephritids as they expand their range. Successful host expansion requires tephritids to adapt to the chemical and nonchemical properties of a novel host fruit, such as fruit color, phenology, and phytochemicals. These plant properties trigger a series of processes in tephritids, with each process having its own genetic basis, which means that various genes are involved in regulating host plant expansion by tephritids. This review summarizes current knowledge on the categories and roles of genes involved in host plant expansion in several important tephritid species, including genes related to chemoreception (olfactory and gustation), vision, digestion, detoxification, development, ribosomal and energy metabolism. Chemoreception- and detoxification- and digestion-related genes are stimulated by volatile chemicals and secondary chemicals of different hosts, respectively, which are involved in the regulation of nervous signal transduction that triggers behavioral, physical, and chemical responses to the novel host fruit. Vision-, nerve-, and development-related genes and metabolism-associated genes are activated in response to nonchemical stimuli from different hosts, such as color and phenology, to regulate a comprehensive adaptation of the extending host for tephritids. The chemical and nonchemical signals of hosts activate ribosomal and energy-related genes that result in the basic regulation of many processes of host expansion, including detoxification and development. These genes do not regulate novel host use individually, but multiple genes regulate multilevel adaptation to novel host fruits via multiple mechanisms. These genes may also be potential target genes for RNAi-based control of tephritid pests.

Fruit Fly Larval Survival in Picked and Unpicked Tomato Fruit of Differing Ripeness and Associated Gene Expression Patterns

The larvae of frugivorous tephritid fruit flies feed within fruit and are global pests of horticulture. With the reduced use of pesticides, alternative control methods are needed, of which fruit resistance is one. In the current study, we explicitly tested for phenotypic evidence of induced fruit defences by running concurrent larval survival experiments with fruit on or off the plant, assuming that defence induction would be stopped or reduced by fruit picking. This was accompanied by RT-qPCR analysis of fruit defence and insect detoxification gene expression. Our fruit treatments were picking status (unpicked vs. picked) and ripening stage (colour break vs. fully ripe), our fruit fly was the polyphagous Bactrocera tryoni, and larval survival was assessed through destructive fruit sampling at 48 and 120 h, respectively. The gene expression study targeted larval and fruit tissue samples collected at 48 h and 120 h from picked and unpicked colour-break fruit. At 120 h in colour-break fruit, larval survival was significantly higher in the picked versus unpicked fruit. The gene expression patterns in larval and plant tissue were not affected by picking status, but many putative plant defence and insect detoxification genes were upregulated across the treatments. The larval survival results strongly infer an induced defence mechanism in colour-break tomato fruit that is stronger/faster in unpicked fruits; however, the gene expression patterns failed to provide the same clear-cut treatment effect. The lack of conformity between these results could be related to expression changes in unsampled candidate genes, or due to critical changes in gene expression that occurred during the unsampled periods.

Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892)

BACKGROUND

Members of the genus Novius Mulsant, 1846 (= Rodolia Mulsant, 1850) (Coleoptera, Coccinellidae), play important roles in the biological control of cotton cushion scale pests, especially those belonging to Icerya. Since the best-known species, the vedalia beetle Novius cardinalis (Mulsant, 1850) was introduced into California from Australia, more than a century of successful use in classical biological control, some species of Novius have begun to exhibit some field adaptations to novel but related prey species. Despite their economic importance, relatively little is known about the underlying genetic adaptations associated with their feeding habits. Knowledge of the genome sequence of Novius is a major step towards further understanding its biology and potential applications in pest control.

RESULTS

We report the first high-quality genome sequence for Novius pumilus (Weise, 1892), a representative specialist of Novius. Computational Analysis of gene Family Evolution (CAFE) analysis showed that several orthogroups encoding chemosensors, digestive, and immunity-related enzymes were significantly expanded (P < 0.05) in N. pumilus compared to the published genomes of other four ladybirds. Furthermore, some of these orthogroups were under significant positive selection pressure (P < 0.05). Notably, transcriptome profiling demonstrated that many genes among the significantly expanded and positively selected orthogroups, as well as genes related to detoxification were differentially expressed, when N. pumilus feeding on the nature prey Icerya compared with the no feeding set. We speculate that these genes are vital in the Icerya adaptation of Novius species.

CONCLUSIONS

We report the first Novius genome thus far. In addition, we provide comprehensive transcriptomic resources for N. pumilus. The results from this study may be helpful for understanding the association of the evolution of genes related to chemosensing, digestion, detoxification and immunity with the prey adaptation of insect predators. This will provide a reference for future research and utilization of Novius in biological control programs. Moreover, understanding the possible molecular mechanisms of prey adaptation also inform mass rearing of N. pumilus and other Novius, which may benefit pest control.

Insight into different host range of three planthoppers by transcriptomic and microbiomic analysis

Brown planthopper (BPH), white-backed planthopper (WBPH) and small brown planthopper (SBPH), are the closely related rice pests that perform differentially on wheat plants. Using fecundity as a fitness measure, we found that SBPH well-adapted on wheat plants, followed by WBPH, while BPH had the worst performance. The transcriptomic responses of SBPH and BPH to wheat plants have been compared previously. To understand the different fitness mechanisms of three planthoppers, this study first investigated the transcriptomic responses of WBPH to rice and wheat plants. Genes involved in detoxification, transportation and proteasome were significantly enriched in WBPH in response to different diets. Moreover, comparative analysis demonstrated that most co-regulated genes in BPH and SBPH showed different expression changes; whereas most co-regulated genes in BPH and WBPH exhibited similar expression changes. Subsequently, this study also investigated the influences of host plants on the bacterial community of three planthoppers. The three planthoppers harboured distant diversity of bacterial communities. However, there was no dramatic change in bacterial diversity or relative abundance in planthoppers colonized on different hosts. This study illustrates generic and species-specific changes of three rice planthoppers in response to different plants, which deepen our understanding towards the host fitness for planthopper species.

Comparative transcriptome analysis of the newly discovered insect vector of the pine wood nematode in China, revealing putative genes related to host plant adaptation

BACKGROUND

In many insect species, the larvae/nymphs are unable to disperse far from the oviposition site selected by adults. The Sakhalin pine sawyer Monochamus saltuarius (Gebler) is the newly discovered insect vector of the pine wood nematode (Bursaphelenchus xylophilus) in China. Adult M. saltuarius prefers to oviposit on the host plant Pinus koraiensis, rather than P. tabuliformis. However, the genetic basis of adaptation of the larvae of M. saltuarius with weaken dispersal ability to host environments selected by the adult is not well understood.

RESULTS

In this study, the free amino and fatty acid composition and content of the host plants of M. saltuarius larvae, i.e., P. koraiensis and P. tabuliformis were investigated. Compared with P. koraiensis, P. tabuliformis had a substantially higher content of various free amino acids, while the opposite trend was detected for fatty acid content. The transcriptional profiles of larval populations feeding on P. koraiensis and P. tabuliformis were compared using PacBio Sequel II sequencing combined with Illumina sequencing. The results showed that genes relating to digestion, fatty acid synthesis, detoxification, oxidation-reduction, and stress response, as well as nutrients and energy sensing ability, were differentially expressed, possibly reflecting adaptive changes of M. saltuarius in response to different host diets. Additionally, genes coding for cuticle structure were differentially expressed, indicating that cuticle may be a potential target for plant defense. Differential regulation of genes related to the antibacterial and immune response were also observed, suggesting that larvae of M. saltuarius may have evolved adaptations to cope with bacterial challenges in their host environments.

CONCLUSIONS

The present study provides comprehensive transcriptome resource of M. saltuarius relating to host plant adaptation. Results from this study help to illustrate the fundamental relationship between transcriptional plasticity and adaptation mechanisms of insect herbivores to host plants.

What We Don't Know About Diet-Breadth Evolution in Herbivorous Insects

Half a million species of herbivorous insects have been described. Most of them are diet specialists, using only a few plant species as hosts. Biologists suspect that their specificity is key to their diversity. But why do herbivorous insects tend to be diet specialists? In this review, we catalog a broad range of explanations. We review the evidence for each and suggest lines of research to obtain the evidence we lack. We then draw attention to a second major question, namely how changes in diet breadth affect the rest of a species’ biology. In particular, we know little about how changes in diet breadth feed back on genetic architecture, the population genetic environment, and other aspects of a species’ ecology. Knowing more about how generalists and specialists differ should go a long way toward sorting out potential explanations of specificity, and yield a deeper understanding of herbivorous insect diversity.

Physiological adaptations to sugar-mimic alkaloids: Insights from Bombyx mori for long-term adaption and short-term response

Insects evolved adaptive plasticity to minimize the effects of the chemical defenses of their host plants. Nevertheless, the expressional response and adaptation of phytophagous specialists for long-term adaption and short-term response to host phytochemicals remains largely unexplored. The mulberry (Morus alba)-silkworm (Bombyx mori) interaction is an old and well-known model of plant-insect interaction. In this study, we examined the long-term adaption and short-term response of the mulberry-specialist silkworm to two sugar-mimic alkaloids in mulberry: the commonly encountered 1-deoxynojirimycin (1-DNJ) and occasionally encountered 1,4-dideoxy-1,4-imino-D-arabinitol (D-AB1), respectively. Global transcriptional patterns revealed that the physiological responses induced by the selective expression of genes involved in manifold cellular processes, including detoxification networks, canonical digestion processes, target enzymes, and other fundamental physiological processes, were crucial for regulating metabolic homeostasis. Comparative network analysis of the effects of exposure to D-AB1 and 1-DNJ supported the contention that B. mori produced similar and specific trajectories of changed gene expression in response to different sugar-mimic alkaloids. D-AB1 elicited a substantial proportion of downregulated genes relating to carbohydrate metabolism, catabolic process, lipid metabolism, and glycan biosynthesis and metabolism. This study dramatically expands our knowledge of the physiological adaptations to dietary sugar-mimic alkaloid intake and uncovered both metabolic evolutionarily responses and unique adaptive mechanisms previously unknown in insects.

Transcriptome profiling revealed potentially important roles of defensive gene expression in the divergence of insect biotypes: a case study with the cereal aphid Sitobion avenae

Background

Many insects can develop differential biotypes on variable host plants, but the underlying molecular factors and mechanisms are not well understood. To address this issue, transcriptome profiling analyses were conducted for two biotypes of the cereal aphid, Sitobion avenae (Fabricius), on both original and alternative plants.

Results

Comparisons between both biotypes generated 4174 differentially expressed unigenes (DEGs). In their response to host plant shift, 39 DEGs were shared by both biotypes, whereas 126 and 861 DEGs occurred only in biotypes 1 and 3, respectively. MMC (modulated modularity clustering) analyses showed that specific DEGs of biotypes 1 and 3 clustered into five and nine transcriptional modules, respectively. Among these DEGs, defense-related genes underwent intensive expression restructuring in both biotypes. However, biotype 3 was found to have relatively lower gene transcriptional plasticity than biotype 1. Gene enrichment analyses of the abovementioned modules showed functional divergence in defensive DEGs for the two biotypes in response to host transfer. The expression plasticity for some defense related genes was showed to be directly related to fecundity of S. avenae biotypes on both original and alternative plants, suggesting that expression plasticity of key defensive genes could have significant impacts on the adaptive potential and differentiation of S. avenae biotypes on different plants.

Conclusions

The divergence patterns of transcriptional plasticity in defense related genes may play important roles in the phenotypic evolution and differentiation of S. avenae biotypes. Our results can provide insights into the role of gene expression plasticity in the divergence of insect biotypes and adaptive evolution of insect populations.

Detoxification Genes Differ Between Cactus-, Fruit-, and Flower-Feeding Drosophila

We use annotated genomes of 14 Drosophila species covering diverse host use phenotypes to test whether 4 gene families that often have detoxification functions are associated with host shifts among species. Bark, slime flux, flower, and generalist necrotic fruit-feeding species all have similar numbers of carboxyl/cholinesterase, glutathione S-transferase, cytochrome P450, and UDP-glucuronosyltransferase genes. However, species feeding on toxic Morinda citrifolia fruit and the fresh fruit-feeding Drosophila suzukii have about 30 and 60 more, respectively. ABC transporters show a different pattern, with the flower-feeding D. elegans and the generalist necrotic fruit and cactus feeder D. hydei having about 20 and >100 more than the other species, respectively. Surprisingly, despite the complex secondary chemistry we find that 3 cactophilic specialists in the mojavensis species cluster have variably fewer genes than any of the other species across all 4 families. We also find 82 positive selection events across the 4 families, with the terminal D. suzukii and M. citrifolia-feeding D. sechellia branches again having the highest number of such events in proportion to their respective branch lengths. Many of the genes involved in these host-use-specific gene number differences or positive selection events lie in specific clades of the gene families that have been recurrently associated with detoxification. Several genes are also found to be involved in multiple duplication and/or positive selection events across the species studied regardless of their host use phenotypes; the most frequently involved are the ABC transporter CG1718, which is not in a specific clade associated with detoxification, and the α-esterase gene cluster, which is.

Evolutionary genomics of host plant adaptation: insights from Drosophila

Variation in gene expression in response to the use of alternate host plants can reveal genetic and physiological mechanisms explaining why insect-host relationships vary from host specialism to generalism. Interpreting transcriptome variation relies on well-annotated genomes, making drosophilids valuable model systems, particularly those species with tractable ecological associations. Patterns of whole genome expression and alternate gene splicing in response to growth on different hosts have revealed expression of gene networks of known detoxification genes as well as novel functionally enriched genes of diverse metabolic and structural functions. Integrating trancriptomic responses with fitness differences and levels of phenotypic plasticity in response to alternate hosts will help to reveal the general nature of genotype-phenotype relationships.

Derived esterase activity in Drosophila sechellia contributes to evolved octanoic acid resistance

The dietary specialist fruit fly Drosophila sechellia has evolved resistance to the secondary defence compounds produced by the fruit of its host plant, Morinda citrifolia. The primary chemicals that contribute to lethality of M. citrifolia are the medium-chain fatty acids octanoic acid (OA) and hexanoic acid. At least five genomic regions contribute to this adaptation in D. sechellia and whereas the fine-mapped major effect locus for OA resistance on chromosome 3R has been thoroughly analysed, the remaining four genomic regions that contribute to toxin resistance remain uncharacterized. To begin to identify the genetic basis of toxin resistance in this species, we removed the function of well-known detoxification gene families to determine whether they contribute to toxin resistance. Previous work found that evolution of cytochrome P450 enzymatic activity or expression is not responsible for the OA resistance in D. sechellia. Here, we tested the role of the two other major detoxification gene families in resistance to Morinda fruit toxins - glutathione-S-transferases and esterases - through the use of the pesticide synergists diethyl maleate and tribufos that inhibit the function of these gene families. This work suggests that one or more esterase(s) contribute to evolved OA resistance in D. sechellia.

Gene Expression and Diet Breadth in Plant-Feeding Insects: Summarizing Trends

Transcriptomic studies lend insights into the role of transcriptional plasticity in adaptation and specialization. Recently, there has been growing interest in understanding the relationship between variation in herbivorous insect gene expression and the evolution of diet breadth. We review the studies that have emerged on insect gene expression and host plant use, and outline the questions and approaches in the field. Many candidate genes underlying herbivory and specialization have been identified, and a few key studies demonstrate increased transcriptional plasticity associated with generalist compared with specialist species. Addressing the roles that transcriptional variation plays in insect diet breadth will have important implications for our understanding of the evolution of specialization and the genetic and environmental factors that govern insect-plant interactions.

De novo comparative transcriptome analysis of a rare cicada, with identification of candidate genes related to adaptation to a novel host plant and drier habitats

Background

Although the importance of host plant chemistry in plant–insect interactions is widely recognized, our understanding about the genetic basis underlying the relationship between changes in midgut proteins and adaptation of plant-feeding insects to novel host plants and habitats is very limited. To address this knowledge gap, the transcriptional profiles of midguts among three populations of the cicada Subpsaltria yangi Chen were compared. Among which, the Hancheng (HC) and Fengxiang (FX) populations occurring in the Loess Plateau feed on Ziziphus jujuba Mill. var. spinosa (Bunge) Hu ex H. F. Chow, while the population occurring in a much drier habitat in the Helan (HL) Mountains is locally specialized on a chemically divergent plant, Ephedra lepidosperma C. Y. Cheng.

Results

Based on comparative analysis, 1826 (HL vs HC) differentially expressed genes (DEGs) and 723 DEGs (HL vs FX) were identified between the populations utilizing different host plants, including 20, 36, 2, 5 and 2 genes related to digestion, detoxification, oxidation-reduction, stress response and water-deprivation response, respectively, and 35 genes presumably associated with osmoregulation. However, only 183 DEGs were identified between the HC and FX populations, including two genes related to detoxification, two genes related to stress response, and one gene presumably associated with osmoregulation. These results suggest that the weakest expression differences were between the populations utilizing the same host plant and occurring in the closest habitats, which may help explain the metabolic mechanism of adaptation in S. yangi populations to novel host plants and new niches.

Conclusions

The observed differences in gene expression among S. yangi populations are consistent with the hypothesis that the host plant shift and habitat adaptation in the HL population was facilitated by differential regulation of genes related to digestion, detoxification, oxidation-reduction, stress response, water-deprivation response and osmoregulation. The results may inform future studies on the molecular mechanisms underlying the relationship between changes in midgut proteins and adaptation of herbivorous insects to novel host plants and new niches.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5547-y) contains supplementary material, which is available to authorized users.

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species

BACKGROUND

Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adaptations in the past. Here we investigate the genetic changes associated with adaptation to arid environments, specifically climatic extremes and new cactus hosts, through such an analysis of five repleta group Drosophila species.

RESULTS

We find disproportionately high rates of gene gains in internal branches in the species' phylogeny where cactus use and subsequently cactus specialisation and high heat and desiccation tolerance evolved. The terminal branch leading to the most heat and desiccation resistant species, Drosophila aldrichi, also shows disproportionately high rates of both gene gains and positive selection. Several Gene Ontology terms related to metabolism were enriched in gene gain events in lineages where cactus use was evolving, while some regulatory and developmental genes were strongly selected in the Drosophila aldrichi branch. Transcriptomic analysis of flies subjected to sublethal heat shocks showed many more downregulation responses to the stress in a heat sensitive versus heat resistant species, confirming the existence of widespread regulatory as well as structural changes in the species' differing adaptations. Gene Ontology terms related to metabolism were enriched in the differentially expressed genes in the resistant species while terms related to stress response were over-represented in the sensitive one.

CONCLUSION

Adaptations to new cactus hosts and hot desiccating environments were associated with periods of accelerated evolutionary change in diverse biochemistries. The hundreds of genes involved suggest adaptations of this sort would be difficult to achieve in the timeframes projected for anthropogenic climate change.

Small and genetically highly structured populations in a long-legged bee, Rediviva longimanus, as inferred by pooled RAD-seq

Adaptation to local host plants may impact a pollinator's population genetic structure by reducing gene flow and driving population genetic differentiation, representing an early stage of ecological speciation. South African Rediviva longimanus bees exhibit elongated forelegs, a bizarre adaptation for collecting oil from floral spurs of their Diascia hosts. Furthermore, R. longimanus foreleg length (FLL) differs significantly among populations, which has been hypothesised to result from selection imposed by inter-population variation in Diascia floral spur length. Here, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to investigate the population genetic structure of R. longimanus and to test if phenotypic differences in FLL translate into increased genetic differentiation (i) between R. longimanus populations and (ii) between phenotypes across populations. We also inferred the effects of demographic processes on population genetic structure and tested for genetic markers underpinning local adaptation. RESULTS: Populations showed marked genetic differentiation (average FST = 0.165), though differentiation was not statistically associated with differences between populations in FLL. All populations exhibited very low genetic diversity and were inferred to have gone through recent bottleneck events, suggesting extremely low effective population sizes. Genetic differentiation between samples pooled by leg length (short versus long) rather than by population of origin was even higher (FST = 0.260) than between populations, suggesting reduced interbreeding between long and short-legged individuals. Signatures of selection were detected in 1119 (3.8%) of a total of 29,721 SNP markers, CONCLUSIONS: Populations of R. longimanus appear to be small, bottlenecked and isolated. Though we could not detect the effect of local adaptation (FLL in response to floral spurs of host plants) on population genetic differentiation, short and long legged bees appeared to be partially differentiated, suggesting incipient ecological speciation. To test this hypothesis, greater resolution through the use of individual-based whole-genome analyses is now needed to quantify the degree of reproductive isolation between long and short legged bees between and even within populations.

Transcriptomic response of female adult moths to host and non-host plants in two closely related species

BACKGROUND

Divergent selection has been shown to promote speciation in many taxa and especially in phytophagous insects. In the Ostrinia species complex, the European corn borer (ECB) and adzuki bean borer (ABB) are two sibling species specialized to different host plants. The first is a well-known maize pest, whereas the second is a polyphagous species associated with various dicotyledons. Their specialization to host plants is driven by morphological, behavioral and physiological adaptations. In particular, previous studies have shown that ECB and ABB display marked behavior with regard to plant choice during oviposition, involving specific preference and avoidance mechanisms. In this study, our goal was to identify the mechanisms underlying this host-plant specialization in adult females through an analysis of their gene expression. We assembled and annotated a de novo reference transcriptome and measured differences in gene expression between ECB and ABB females, and between environments. We related differentially expressed genes to host preference behavior, and highlighted the functional categories involved. We also conducted a specific analysis of chemosensory genes, which are considered to be good candidates for host recognition before oviposition.

RESULTS

We recorded more differentially expressed genes in ECB than in ABB samples, and noticed that the majority of genes potentially involved in the host preference were different between the two species. At the functional level, the response to plant environment in adult females involved many processes, including the metabolism of carbohydrates, lipids, proteins, and amino acids; detoxification mechanisms and immunity; and the chemosensory repertoire (as expected). Until now, most of the olfactory receptors described in Ostrinia spp. had been tested for their putative role in pheromone recognition by males. Here we observed that one specific olfactory receptor was clearly associated with ECB's discrimination between maize and mugwort conditions, highlighting a potential new candidate involved in plant odor discrimination in adult females.

CONCLUSIONS

Our results are a first step toward the identification of candidate genes and functions involved in chemosensory processes, carbohydrate metabolism, and virus and retrovirus dynamics. These candidates provide new avenues for research into understanding the role of divergent selection between different environments in species diversification.

The Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 is a molecular host-associated cue for the salmon louse (Lepeophtheirus salmonis)

Chemical signals are a key element of host-parasite interactions. In marine ecosystems, obligate ectoparasites, such as sea lice, use chemical cues and other sensory signals to increase the probability of encountering a host and to identify appropriate hosts on which they depend to complete their life cycle. The chemical compounds that underlie host identification by the sea lice are not fully described or characterized. Here, we report a novel compound - the Atlantic salmon (Salmo salar) antimicrobial peptide cathelicidin-2 (Cath-2) – that acts as an activation cue for the marine parasitic copepod Lepeophtheirus salmonis. L. salmonis were exposed to 0, 7, 70 and 700 ppb of Cath-2 and neural activity, swimming behaviour and gene expression profiles of animals in response to the peptide were evaluated. The neurophysiological, behavioural and transcriptomic results were consistent: L. salmonis detects Cath-2 as a water-soluble peptide released from the skin of salmon, triggering chemosensory neural activity associated with altered swimming behaviour of copepodids exposed to the peptide, and chemosensory-related genes were up-regulated in copepodids exposed to the peptide. L. salmonis are activated by Cath-2, indicating a tight link between this peptide and the salmon louse chemosensory system.

Physiological and Evolutionary Changes in a Biological Control Agent During Prey Shifts Over Several Generations

Biological control agents usually suffer from a shortage of target prey or hosts in their post-release stage. Some predatory agents turn to attacking other prey organisms, which may induce physiological and evolutionary changes. In this study, we investigated life history traits, gene expression and genotype frequency in the predatory ladybird beetle Cryptolaemus montrouzieri during experimental prey shifts. C. montrouzieri were either continuously fed on aphids Megoura japonica as an alternative prey for four generations or were shifted back to the initial prey mealybugs Planococcus citri in each generation. In general, the utilization of aphids resulted in reduced performance and severe physiological adjustments, indicated by significant changes in development and fecundity traits and a large number of differentially expressed genes between the two offering setup prey treatments. Within the aphid-fed lines, performance regarding the developmental time, the adult weight and the survival rate recovered to some level in subsequent generations, possibly as a result of adaptive evolution. In particular, we found that a shift back to mealybugs caused a gradual increase in fecundity. Accordingly, a genotype of the fecundity-related gene vitellogenin, of which there were several minor alleles in the initial population, became the main genotype within four generations. The present study explored the short-term experimental evolution of a so-call specialist predator under prey shift conditions. This potential rapid adaptation of biological control agents to novel prey will increase environmental risks associated with non-target effects.

Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

Background

Most phytophagous insects have morphological, behavioral and physiological adaptations allowing them to specialize on one or a few plant species. Identifying the mechanisms involved in host plant specialization is crucial to understand the role of divergent selection between different environments in species diversification, and to identify sustainable targets for the management of insect pest species. In the present study, we measured larval phenotypic and transcriptomic responses to host plants in two related phytophagous lepidopteran species: the European corn borer (ECB), a worldwide pest of maize, and the adzuki bean borer (ABB), which feeds of various dicotyledons. Our aim was to identify the genes and functions underlying host specialization and/or divergence between ECB and ABB.

Results

At the phenotypic level, we observed contrasted patterns of survival, weight gain and developmental time between ECB and ABB, and within ECB and ABB reared on two different host plants. At the transcriptomic level, around 8% of the genes were differentially expressed (DE) between species and/or host plant. 70% of these DE genes displayed a divergent pattern of expression between ECB and ABB, regardless of the host, while the remaining 30% were involved in the plastic response between hosts. We further categorized plastic DE genes according to their parallel or opposite pattern between ECB and ABB to specifically identify candidate genes involved in the species divergence by host specialization. These candidates highlighted a comprehensive response, involving functions related to plant recognition, digestion, detoxification, immunity and development. Last, we detected viral, bacterial, and yeast genes whose incidence contrasted ECB and ABB samples, and maize and mugwort conditions. We suggest that these microorganism communities might influence the survival, metabolism and defense patterns observed in ECB and ABB larvae.

Conclusions

The comprehensive approach developed in the present study allowed to identify phenotypic specialization patterns and underlying candidate molecular mechanisms, and highlighted the putative role of microorganisms in the insect-host plant interaction. These findings offer the opportunity to pinpoint specific and sustainable molecular or physiological targets for the regulation of ECB pest populations.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4589-x) contains supplementary material, which is available to authorized users.

The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens

Intraspecific variation in ecologically important traits is a cornerstone of Darwin's theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant use in the Lepidopteran subfamily Heliothinae suggest that architecture may not constrain ecological adaptation in this group. Here we investigate the response of Chloridea virescens, a generalist that feeds on diverse plant species, to selection for performance on a novel host, Physalis angulata (Solanaceae). P. angulata is the preferred host of Chloridea subflexa, a narrow specialist on the genus Physalis. In previous experiments, we found that the performance of C. subflexa on P. angulata depends on many loci of small effect distributed throughout the genome, but whether the same architecture would be involved in the generalist's adoption of P. angulata was unknown. Here we report a rapid response to selection in C. virescens for performance on P. angulata, and establish that the genetic architecture of intraspecific variation is quite similar to that of the interspecific differences in terms of the number, distribution, and effect sizes of the QTL involved. We discuss the impact of genetic architecture on the ability of Heliothine moths to respond to varying ecological selection pressures.

Differential gene expression in the evolution of sex pheromone communication in New Zealand's endemic leafroller moths of the genera Ctenopseustis and Planotortrix

Background

Sex pheromone communication in moths has attracted the attention of evolutionary biologists due to the vast array of pheromone compounds used, addressing questions of how this diversity arose and how male reception has evolved in step with the female signal. Here we examine the role of changing gene expression in the evolution of mate recognition systems in leafroller moths, particularly focusing on genes involved in the biosynthetic pathways of sex pheromones in female pheromone glands and the peripheral reception repertoire in the antennae of males. From tissue-specific transcriptomes we mined and compared a database of genes expressed in the pheromone glands and antennae of males and females of four closely related species of leafroller moths endemic to New Zealand, Ctenopseutis herana and C. obliquana, and Planotortrix excessana and P. octo. The peculiarity of this group, compared to other Lepidoptera, is the use of (Z)-5-tetradecenyl acetate, (Z)-7-tetradecenyl acetate, and (Z)-8-tetradecenyl acetate as sex pheromone components.

Results

We identify orthologues of candidate genes from the pheromone biosynthesis pathway, degradation and transport, as well as genes of the periphery olfactory repertoire, including large families of binding proteins, receptors and odorant degrading enzymes. The production of distinct pheromone blends in the sibling species is associated with the differential expression of two desaturase genes, deast5 and desat7, in the pheromone glands. In male antennae, three odorant receptors, OR74, OR76a and OR30 are over-expressed, but their expression could not be clearly associated with the detection of species-specific pheromones components. In addition these species contain duplications of all three pheromone binding proteins (PBPs) that are also differentially expressed among species.

Conclusions

While in females differences in the expression of desaturases may be sufficient to explain pheromone blend differences among these New Zealand leafroller species, in males differential expression of several genes, including pheromone binding proteins, may underpin differences in the response by males to changing pheromone components among the species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4451-1) contains supplementary material, which is available to authorized users.

Transcriptional profile and differential fitness in a specialist milkweed insect across host plants varying in toxicity

Interactions between plants and herbivorous insects have been models for theories of specialization and co-evolution for over a century. Phytochemicals govern many aspects of these interactions and have fostered the evolution of adaptations by insects to tolerate or even specialize on plant defensive chemistry. While genomic approaches are providing new insights into the genes and mechanisms insect specialists employ to tolerate plant secondary metabolites, open questions remain about the evolution and conservation of insect counterdefences, how insects respond to the diversity defences mounted by their host plants, and the costs and benefits of resistance and tolerance to plant defences in natural ecological communities. Using a milkweed-specialist aphid (Aphis nerii) model, we test the effects of host plant species with increased toxicity, likely driven primarily by increased secondary metabolites, on aphid life history traits and whole-body gene expression. We show that more toxic plant species have a negative effect on aphid development and lifetime fecundity. When feeding on more toxic host plants with higher levels of secondary metabolites, aphids regulate a narrow, targeted set of genes, including those involved in canonical detoxification processes (e.g., cytochrome P450s, hydrolases, UDP-glucuronosyltransferases and ABC transporters). These results indicate that A. nerii marshal a variety of metabolic detoxification mechanisms to circumvent milkweed toxicity and facilitate host plant specialization, yet, despite these detoxification mechanisms, aphids experience reduced fitness when feeding on more toxic host plants. Disentangling how specialist insects respond to challenging host plants is a pivotal step in understanding the evolution of specialized diet breadths.

Rapid response to changing environments during biological invasions: DNA methylation perspectives

Dissecting complex interactions between species and their environments has long been a research hot spot in the fields of ecology and evolutionary biology. The well-recognized Darwinian evolution has well-explained long-term adaptation scenarios; however, "rapid" processes of biological responses to environmental changes remain largely unexplored, particularly molecular mechanisms such as DNA methylation that have recently been proposed to play crucial roles in rapid environmental adaptation. Invasive species, which have capacities to successfully survive rapidly changing environments during biological invasions, provide great opportunities to study molecular mechanisms of rapid environmental adaptation. Here, we used the methylation-sensitive amplified polymorphism (MSAP) technique in an invasive model ascidian, Ciona savignyi, to investigate how species interact with rapidly changing environments at the whole-genome level. We detected quite rapid DNA methylation response: significant changes of DNA methylation frequency and epigenetic differentiation between treatment and control groups occurred only after 1 hr of high-temperature exposure or after 3 hr of low-salinity challenge. In addition, we detected time-dependent hemimethylation changes and increased intragroup epigenetic divergence induced by environmental stresses. Interestingly, we found evidence of DNA methylation resilience, as most stress-induced DNA methylation variation maintained shortly (~48 hr) and quickly returned back to the control levels. Our findings clearly showed that invasive species could rapidly respond to acute environmental changes through DNA methylation modifications, and rapid environmental changes left significant epigenetic signatures at the whole-genome level. All these results provide fundamental background to deeply investigate the contribution of DNA methylation mechanisms to rapid contemporary environmental adaptation.

Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus

Sexually dimorphic phenotypes arise largely from sex-specific gene expression, which has mainly been characterized in sexually naïve adults. However, we expect sexual dimorphism in transcription to be dynamic and dependent on factors such as reproductive status. Mating induces many behavioral and physiological changes distinct to each sex and is therefore expected to activate regulatory changes in many sex-biased genes. Here, we first characterized sexual dimorphism in gene expression in Callosobruchus maculatus seed beetles. We then examined how females and males respond to mating and how it affects sex-biased expression, both in sex-limited (abdomen) and sex-shared (head and thorax) tissues. Mating responses were largely sex-specific and, as expected, females showed more genes responding compared with males (∼2,000 vs. ∼300 genes in the abdomen, ∼500 vs. ∼400 in the head and thorax, respectively). Of the sex-biased genes present in virgins, 16% (1,041 genes) in the abdomen and 17% (243 genes) in the head and thorax altered their relative expression between the sexes as a result of mating. Sex-bias status changed in 2% of the genes in the abdomen and 4% in the head and thorax following mating. Mating responses involved de-feminization of females and, to a lesser extent, de-masculinization of males relative to their virgin state: mating decreased rather than increased dimorphic expression of sex-biased genes. The fact that regulatory changes of both types of sex-biased genes occurred in both sexes suggests that male- and female-specific selection is not restricted to male- and female-biased genes, respectively, as is sometimes assumed.

Comparative transcriptome analysis reveals host-associated differentiation in Chilo suppressalis (Lepidoptera: Crambidae)

The striped stem borer, Chilo suppressalis Walker (Lepidoptera: Crambidae), is one of the most serious rice pests. Besides attacking rice, it also feeds on an economically important vegetable crop, water-oat Zizania latifolia. The species feeding on water-oat has higher growth and survival rate than those on rice, suggesting their success in adaptation to the new host plant. However, little is known about the molecular mechanisms of host plant adaptation. Here we investigated the midgut transcriptome responses of C. suppressalis larvae reared on rice and water-oat. A total of 1,633 differentially expressed genes were identified, with a greater number up-regulated on the more delicious new host. The up-regulation of most digestive and detoxification-related genes may be the result of adaptation to the changes in nutritional requirements and toxic chemicals during host shift. In contrast, down-regulation of ribosomal genes may be related to their better development performance when feeding on the new host. In conclusion, our results suggest that transcriptional regulation of genes related to digestion, detoxification and ribosome may play an important role in adaptation of C. suppressalis to a new host plant.

Polyphagy and diversification in tussock moths: Support for the oscillation hypothesis from extreme generalists

Theory on plasticity driving speciation, as applied to insect-plant interactions (the oscillation hypothesis), predicts more species in clades with higher diversity of host use, all else being equal. Previous support comes mainly from specialized herbivores such as butterflies, and plasticity theory suggests that there may be an upper host range limit where host diversity no longer promotes diversification. The tussock moths (Erebidae: Lymantriinae) are known for extreme levels of polyphagy. We demonstrate that this system is also very different from butterflies in terms of phylogenetic signal for polyphagy and for use of specific host orders. Yet we found support for the generality of the oscillation hypothesis, in that clades with higher diversity of host use were found to contain more species. These clades also consistently contained the most polyphagous single species. Comparing host use in Lymantriinae with related taxa shows that the taxon indeed stands out in terms of the frequency of polyphagous species. Comparative evidence suggests that this is most probably due to its nonfeeding adults, with polyphagy being part of a resulting life history syndrome. Our results indicate that even high levels of plasticity can drive diversification, at least when the levels oscillate over time.

Gut Transcriptome Analysis Shows Different Food Utilization Efficiency by the Grasshopper Oedaleous asiaticus (Orthoptera: Acrididae)

Oedaleus asiaticus B. Bienko is a persistent pest occurring in north Asian grasslands. We found that O. asiaticus feeding on Stipa krylovii Roshev. had higher approximate digestibility (AD), efficiency of conversion of ingested food (ECI), and efficiency of conversion of digested food (ECD), compared with cohorts feeding on Leymus chinensis (Trin.) Tzvel, Artemisia frigida Willd., or Cleistogenes squarrosa (Trin.) Keng. Although this indicated high food utilization efficiency for S. krylovii, the physiological processes and molecular mechanisms underlying these biological observations are not well understood. Transcriptome analysis was used to examine how gene expression levels in O. asiaticus gut are altered by feeding on the four plant species. Nymphs (fifth-instar female) that fed on S. krylovii had the largest variation in gene expression profiles, with a total of 88 genes significantly upregulated compared with those feeding on the other three plants, mainly including nutrition digestive genes of protein, carbohydrate, and lipid digestion. GO and KEGG enrichment also showed that feeding S. krylovii could upregulate the nutrition digestion-related molecular function, biological process, and pathways. These changes in transcripts levels indicate that the physiological processes of activating nutrition digestive enzymes and metabolism pathways can well explain the high food utilization of S. krylovii by O. asiaticus.

Do changes in gene expression contribute to sexual isolation and reinforcement in the house mouse?

Expression divergence, rather than sequence divergence, has been shown to be important in speciation, particularly in the early stages of divergence of traits involved in reproductive isolation. In the two European subspecies of house mice, Mus musculus musculus and Mus musculus domesticus, earlier studies have demonstrated olfactory-based assortative mate preference in populations close to their hybrid zone. It has been suggested that this behaviour evolved following the recent secondary contact between the two taxa (~3,000 years ago) in response to selection against hybridization. To test for a role of changes in gene expression in the observed behavioural shift, we conducted a RNA sequencing experiment on mouse vomeronasal organs. Key candidate genes for pheromone-based subspecies recognition, the vomeronasal receptors, are expressed in these organs. Overall patterns of gene expression varied significantly between samples from the two subspecies, with a large number of differentially expressed genes between the two taxa. In contrast, only ~200 genes were found repeatedly differentially expressed between populations within M. m. musculus that did or did not display assortative mate preferences (close to or more distant from the hybrid zone, respectively), with an overrepresentation of genes belonging to vomeronasal receptor family 2. These receptors are known to play a key role in recognition of chemical cues that handle information about genetic identity. Interestingly, four of five of these differentially expressed receptors belong to the same phylogenetic cluster, suggesting specialization of a group of closely related receptors in the recognition of odorant signals that may allow subspecies recognition and assortative mating.

Gene expression plasticity across hosts of an invasive scale insect species

For plant-eating insects, we still have only a nascent understanding of the genetic basis of host-use promiscuity. Here, to improve that situation, we investigated host-induced gene expression plasticity in the invasive lobate lac scale insect, Paratachardina pseudolobata (Hemiptera: Keriidae). We were particularly interested in the differential expression of detoxification and effector genes, which are thought to be critical for overcoming a plant's chemical defenses. We collected RNA samples from P. pseudolobata on three different host plant species, assembled transcriptomes de novo, and identified transcripts with significant host-induced gene expression changes. Gene expression plasticity was pervasive, but the expression of most detoxification and effector genes was insensitive to the host environment. Nevertheless, some types of detoxification genes were more differentially expressed than expected by chance. Moreover, we found evidence of a trade-off between expression of genes involved in primary and secondary metabolism; hosts that induced lower expression of genes for detoxification induced higher expression of genes for growth. Our findings are largely consonant with those of several recently published studies of other plant-eating insect species. Thus, across plant-eating insect species, there may be a common set of gene expression changes that enable host-use promiscuity.

Comparative Transcriptional Analysis of the Host-Specialized Aphids Aphis gossypii (Hemiptera: Aphididae)

Host specialization is an ubiquitous character in aphid populations. Many polyphagous aphid populations usually consist of several subpopulations that have strong fidelity to a specific host or a subset of host range. Host specialization is an evolutional result of food habit of insects. However, genetic basis and molecular mechanism of host specialization are still unclear. In this study, we presented a comparative analysis on global gene expression profiles of three lineages of Aphis gossypii Glover: cotton-specialized (CO), cucurbit-specialized (CU), and CU reared on cowpea (CU-cowpea), using RNA-Seq method. More than 157 million clean reads and 38,398 different unigenes were generated from transcriptomes of these three aphid lineages. The 1,106 down- and 2,835 up-regulated genes were found between CO and CU, and 812 down- and 14,492 up-regulated genes between CU-cowpea and CU. Differentially expressed genes between CO and CU were enriched in sugar metabolism, immune system process, pathogen infection or symbiosis, and salivary secretion. Genes associated with cytochrome P450, major facilitator superfamily, and salivary effector were differentially expressed between CO and CU, which might be involved in determining host specialization. UDP-glycosyltransferases genes were sensitive to host shift. Carboxylesterases and digestion-related protease genes were related to both the host specialization and host shift of aphids. Expression levels of 22 out of 24 genes of CO and CU measured by RT-qPCR method were as similar as the results from RNA-seq method. This study provides a road map for future study on molecular mechanism of host specialization in aphids.

Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila

High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome-wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a harmful host, rich in mescaline and other related phenylethylamine alkaloids. We assessed the transcriptomic responses of larvae reared in Opuntia sulphurea and T. terscheckii, with and without the addition of alkaloids extracted from the latter. Whole-genome expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially expressed genes were mainly related to detoxification, oxidation-reduction and stress response; however, we also found genes involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional plasticity in response to alternative rearing environments.

Differential gene expression according to race and host plant in the pea aphid

Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host plant, indicating the importance of gene expression in aphid-plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host races may result from genetic drift and reproductive isolation and possibly divergent selection. Expression differences related to plant adaptation include a subset of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies' findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change.

A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects

Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales-from variation within populations to divergence among populations-to form a comprehensive view of adaptation in herbivorous insects.