Epigenetics and developmental plasticity in orthopteroid insects

Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects

Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.

Epigenetic studies in insects and the valproic acid perspective

Abstract Valproic acid in association with sodium valproate (VPA) is an important anticonvulsant drug used for decades to treat neurological disorders. VPA also acts as an epigenetic modulator by inhibiting histone deacetylases, permitting histone acetylation, affecting the DNA and histone methylation status and gene expression, and inducing chromatin remodeling. Insects represent an important animal model for studies in several areas of science. Their high phenotypic plasticity makes them alternative models for epigenetic studies. This brief review emphasizes recent reports on insect epigenetics and the contribution of studies on the VPA action in insects, including effects on epigenetic markers, extending the pharmacological understanding of the potential of this drug, and demonstrating the usefulness of insects as an alternative animal model to drug studies.

Epigenetic Diversity Underlying Seasonal and Annual Variations in Brown Planthopper (BPH) Populations as Revealed by Methylation- sensitive Restriction Assay

Background

The brown planthopper (BPH) is a monophagous sap-sucking insect pest of rice that is responsible for massive yield loss. BPH populations, even when genetically homogenous, can display a vast range of phenotypes, and the development of effective pest-management strategies requires a good understanding of what generates this phenotypic variation. One potential source could be epigenetic differences.

Methods

With this premise, we explored epigenetic diversity, structure and differentiation in field populations of BPH collected across the rice-growing seasons over a period of two consecutive years. Using a modified methylation-sensitive restriction assay (MSRA) and CpG island amplification-representational difference analysis, site-specific cytosine methylation of five stress-responsive genes (CYP6AY1, CYP6ER1, Carboxylesterase, Endoglucanase, Tf2-transposon) was estimated, for identifying methylation-based epiallelic markers and epigenetic variation across BPH populations.

Results

Using a cost-effective and rapid protocol, our study, for the first time, revealed the epigenetic component of phenotypic variations in the wild populations of BPH. Besides, results showed that morphologically indistinguishable populations of BPH can be epigenetically distinct.

Conclusion

Screening field-collected BPH populations revealed the presence of previously unreported epigenetic polymorphisms and provided a platform for future studies aimed at investigating their significance for BPH. Furthermore, these findings can form the basis for understanding the contribution(s) of DNA methylation in providing phenotypic plasticity to BPH.

Epigenetic weapons in plant-herbivore interactions: Sulforaphane disrupts histone deacetylases, gene expression, and larval development in Spodoptera exigua while the specialist feeder Trichoplusia ni is largely resistant to these effects

Cruciferous plants produce sulforaphane (SFN), an inhibitor of nuclear histone deacetylases (HDACs). In humans and other mammals, the consumption of SFN alters enzyme activities, DNA-histone binding, and gene expression within minutes. However, the ability of SFN to act as an HDAC inhibitor in nature, disrupting the epigenetic machinery of insects feeding on these plants, has not been explored. Here, we demonstrate that SFN consumed in the diet inhibits the activity of HDAC enzymes and slows the development of the generalist grazer Spodoptera exigua, in a dose-dependent fashion. After consuming SFN for seven days, the activities of HDAC enzymes in S. exigua were reduced by 50%. Similarly, larval mass was reduced by 50% and pupation was delayed by 2-5 days, with no additional mortality. Similar results were obtained when SFN was applied topically to eggs. RNA-seq analyses confirm that SFN altered the expression of thousands of genes in S. exigua. Genes associated with energy conversion pathways were significantly downregulated while those encoding for ribosomal proteins were dramatically upregulated in response to the consumption of SFN. In contrast, the co-evolved specialist feeder Trichoplusia ni was not negatively impacted by SFN, whether it was consumed in their diet at natural concentrations or applied topically to eggs. The activities of HDAC enzymes were not inhibited and development was not disrupted. In fact, SFN exposure sometimes accelerated T. ni development. RNA-seq analyses revealed that the consumption of SFN alters gene expression in T. ni in similar ways, but to a lesser degree, compared to S. exigua. This apparent resistance of T. ni can be overwhelmed by unnaturally high levels of SFN or by exposure to more powerful pharmaceutical HDAC inhibitors. These results demonstrate that dietary SFN interferes with the epigenetic machinery of insects, supporting the hypothesis that plant-derived HDAC inhibitors serve as "epigenetic weapons" against herbivores.

Epigenetic effects of climate change on insects

Climate change has been causing severe modifications to the environment that are predicted to aggravate in the future, which create critical challenges for insects to cope. Populations can respond to the changes depending on the standing genetic variation. Additionally, they could potentially rely on epigenetic mechanisms as a source of phenotypic variation. These mechanisms can influence gene regulation and can respond to the external environment, being implicated in phenotypic plasticity. Thus, epigenetic variation could be advantageous in changing, unpredictable environments. However, little is known about causal relationships between epigenetic marks and insects' phenotypes, and whether the effects are truly beneficial to the fitness. Empirical studies are now urgent to better understand whether epigenetic variation can help or hinder insect populations facing climate change.

Termite sociogenomics: evolution and regulation of caste-specific expressed genes

Termite genomes have been sequenced in at least five species from four different families. Genome-based transcriptome analyses have identified large numbers of protein-coding genes with caste-specific expression patterns. These genes include those involved in caste-specific morphologies and roles, for example high fecundity and longevity in reproductives. Some caste-specific expressed genes belong to multi-gene families, and their genetic architecture and expression profiles indicate they have evolved via tandem gene duplication. Candidate regulatory mechanisms of caste-specific expression include epigenetic regulation (e.g. histone modification and non-coding RNA) and diversification of transcription factors and cis-regulatory elements. We review current knowledge in the area of termite sociogenomics, focussing on the evolution and regulation of caste-specific expressed genes, and discuss future research directions.

Insect Epigenetic Mechanisms Facing Anthropogenic-Derived Contamination, an Overview

Currently, the human species has been recognized as the primary species responsible for Earth's biodiversity decline. Contamination by different chemical compounds, such as pesticides, is among the main causes of population decreases and species extinction. Insects are key for ecosystem maintenance; unfortunately, their populations are being drastically affected by human-derived disturbances. Pesticides, applied in agricultural and urban environments, are capable of polluting soil and water sources, reaching non-target organisms (native and introduced). Pesticides alter insect's development, physiology, and inheritance. Recently, a link between pesticide effects on insects and their epigenetic molecular mechanisms (EMMs) has been demonstrated. EMMs are capable of regulating gene expression without modifying genetic sequences, resulting in the expression of different stress responses as well as compensatory mechanisms. In this work, we review the main anthropogenic contaminants capable of affecting insect biology and of triggering EMMs. EMMs are involved in the development of several diseases in native insects affected by pesticides (e.g., anomalous teratogenic reactions). Additionally, EMMs also may allow for the survival of some species (mainly pests) under contamination-derived habitats; this may lead to biodiversity decline and further biotic homogenization. We illustrate these patterns by reviewing the effect of neonicotinoid insecticides, insect EMMs, and their ecological consequences.

Insects Provide Unique Systems to Investigate How Early-Life Experience Alters the Brain and Behavior

Early-life experiences have strong and long-lasting consequences for behavior in a surprising diversity of animals. Determining which environmental inputs cause behavioral change, how this information becomes neurobiologically encoded, and the functional consequences of these changes remain fundamental puzzles relevant to diverse fields from evolutionary biology to the health sciences. Here we explore how insects provide unique opportunities for comparative study of developmental behavioral plasticity. Insects have sophisticated behavior and cognitive abilities, and they are frequently studied in their natural environments, which provides an ecological and adaptive perspective that is often more limited in lab-based vertebrate models. A range of cues, from relatively simple cues like temperature to complex social information, influence insect behavior. This variety provides experimentally tractable opportunities to study diverse neural plasticity mechanisms. Insects also have a wide range of neurodevelopmental trajectories while sharing many developmental plasticity mechanisms with vertebrates. In addition, some insects retain only subsets of their juvenile neuronal population in adulthood, narrowing the targets for detailed study of cellular plasticity mechanisms. Insects and vertebrates share many of the same knowledge gaps pertaining to developmental behavioral plasticity. Combined with the extensive study of insect behavior under natural conditions and their experimental tractability, insect systems may be uniquely qualified to address some of the biggest unanswered questions in this field.

The Plasticity and Developmental Potential of Termites

Phenotypic plasticity provides organisms with the potential to adapt to their environment and can drive evolutionary innovations. Developmental plasticity is environmentally induced variation in phenotypes during development that arise from a shared genomic background. Social insects are useful models for studying the mechanisms of developmental plasticity, due to the phenotypic diversity they display in the form of castes. However, the literature has been biased toward the study of developmental plasticity in the holometabolous social insects (i.e., bees, wasps, and ants); the hemimetabolous social insects (i.e., the termites) have received less attention. Here, we review the phenotypic complexity and diversity of termites as models for studying developmental plasticity. We argue that the current terminology used to define plastic phenotypes in social insects does not capture the diversity and complexity of these hemimetabolous social insects. We suggest that terminology used to describe levels of cellular potency could be helpful in describing the many levels of phenotypic plasticity in termites. Accordingly, we propose a conceptual framework for categorizing the changes in potential of individuals to express alternative phenotypes through the developmental life stages of termites. We compile from the literature an exemplar dataset on the phenotypic potencies expressed within and between species across the phylogeny of the termites and use this to illustrate how the potencies of different life stages of different species can be described using this framework. We highlight how this conceptual framework can help exploit the rich phenotypic diversity of termites to address fundamental questions about the evolution and mechanisms of developmental plasticity. This conceptual contribution is likely to have wider relevance to the study of other hemimetabolous insects, such as aphids and gall-forming thrips, and may even prove useful for some holometabolous social insects which have high caste polyphenism.

The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp

Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Analyses of the molecular foundations of phenotypic plasticity are challenging, however, especially in the case of complex social phenotypes. Here we apply a machine learning approach to tackle this challenge by analyzing individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen. We find that caste-associated gene expression profiles respond strongly to queen loss, and that this change is partly explained by attributes such as age but occurs even in individuals that appear phenotypically unaffected. These results demonstrate that large changes in gene expression may occur in the absence of outwardly detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic level but not at the levels of ovarian development or behavior.

Epigenetic regulation of post-embryonic development

Modifications to DNA and core histones influence chromatin organization and expression of the genome. DNA methylation plays a significant role in the regulation of multiple biological processes that regulate behavior and caste differentiation in social insects. Histone modifications play significant roles in the regulation of development and reproduction in other insects. Genes coding for acetyltransferases, deacetylases, methyltransferases, and demethylases that modify core histones have been identified in genomes of multiple insects. Studies on the function and mechanisms of action of some of these enzymes uncovered their contribution to post-embryonic development. The results from studies on epigenetic modifiers could help in the identification of inhibitors of epigenetic modifiers that could be developed to control pests and disease vectors.

Epigenetic Molecular Mechanisms in Insects

Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.

The desert locust, Schistocerca gregaria, plastically manipulates egg size by regulating both egg numbers and production rate according to population density

Egg-size adjustment is one of the important plastic life-history traits for animals living in heterogeneous environments. The adaptive investment hypothesis predicts that mothers should increase progeny size according to certain cues predicting adverse future conditions of their offspring. However, reproductive resources are limited, and females have to simultaneously reduce egg number to allocate more resources to increase size. It remains unclear how single individuals alter egg size and number according to temporally heterogeneous environments. In the present study, we examined how desert locusts, Schistocerca gregaria, plastically alter egg size and number according to population density. We also investigated the trans-generational maternal effects on progeny characteristics as well as their own maternal physiological response (oviposition interval). Females kept in crowded conditions laid significantly larger and heavier eggs by reducing clutch size (number of eggs per egg pod) compared to isolated females, suggesting the existence of a reproductive trade-off between the two traits. The crowding-forced isolated females induced concerted changes not only in egg size but also in egg number tending towards those characteristics of gregarious control, implying that single individuals showed trade-off when egg size was increased. Double-blind testing confirmed the rapid crowding effects on egg size. Females also responded to crowding by extending the oviposition interval. As the oviposition interval extended, egg size increased, but clutch size decreased. Eggs from crowding-forced isolated females began to produce gregarious-phase type hatchlings (large and black) instead of solitarious-phase type ones (small and green). These results suggested that S. gregaria plastically manipulate egg size by regulating egg numbers and egg production rate, and indicated the presence of trans-generational maternal effects on progeny phase.

Dynamics of bacterial composition in the locust reproductive tract are affected by the density-dependent phase

The important role that locust gut bacteria play in their host biology is well accepted. Among other roles, gut bacteria are suggested to be involved in the locust swarming phenomenon. In addition, in many insect orders, the reproductive system is reported to serve as a vector for trans-generation bacterial inoculation. Knowledge of the bacterial composition of the locust reproductive tract is, however, practically absent. Here we characterized the reproductive system bacterial composition of gregarious and solitary females. We investigated its temporal dynamics and how it interacts with the locust phase, by comparative sampling and 16S rRNA amplicon sequencing. We revealed that the bacterial composition of the locust female reproductive tract is mostly constructed of three core genera: Micrococcus, Acinetobacter and Staphylococcus. While solitary females maintained a consistent bacterial composition, in the gregarious phase this consortium demonstrated large temporal shifts, mostly manifested by Brevibacterium blooms. These data are in accord with our previous report on the dynamics of locust hindgut bacterial microbiota, further indicating that locust endosymbionts are affected by their host population density. These newly understood dynamics may have implications beyond their contribution to our knowledge of locust ecology, as aggregation and mass migration are prevalent phenomena across many migrating animals.

The puzzle of locust density-dependent phase polyphenism

Locust density-dependent phase polyphenism presents a quintessential example of environmentally induced plasticity. Almost a century of research has yielded ample knowledge regarding the multitude of ecological, physiological, and molecular phase-dependent characteristics. This short review highlights the considerable advances that have been made in our understanding of the locust's extreme plasticity and the highly complex nature of the phase phenomenon. Several challenges in locust research resulting from this unique complexity are also presented. It is concluded that the joint, interdisciplinary collaborative efforts, already underway, hold the promise of translating our ample knowledge into a complete solution to untangling the locust phase puzzle.

By land, air, and sea: hemipteran diversity through the genomic lens

Thanks to a recent spate of sequencing projects, the Hemiptera are the first hemimetabolous insect order to achieve a critical mass of species with sequenced genomes, establishing the basis for comparative genomics of the bugs. However, as the most speciose hemimetabolous order, there is still a vast swathe of the hemipteran phylogeny that awaits genomic representation across subterranean, terrestrial, and aquatic habitats, and with lineage-specific and developmentally plastic cases of both wing polyphenisms and flightlessness. In this review, we highlight opportunities for taxonomic sampling beyond obvious pest species candidates, motivated by intriguing biological features of certain groups as well as the rich research tradition of ecological, physiological, developmental, and particularly cytogenetic investigation that spans the diversity of the Hemiptera.