The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris

Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.

Gene expression in bumble bee larvae differs qualitatively between high and low concentration imidacloprid exposure levels

Neonicotinoid pesticides negatively impact bumble bee health, even at sublethal concentrations. Responses to the neonicotinoid imidacloprid have been studied largely at individual adult and colony levels, focusing mostly on behavioral and physiological effects. Data from developing larvae, whose health is critical for colony success, are deficient, particularly at the molecular level where transcriptomes can reveal disruption of fundamental biological pathways. We investigated gene expression of Bombus impatiens larvae exposed through food provisions to two field-realistic imidacloprid concentrations (0.7 and 7.0 ppb). We hypothesized both concentrations would alter gene expression, but the higher concentration would have greater qualitative and quantitative effects. We found 678 genes differentially expressed under both imidacloprid exposures relative to controls, including mitochondrial activity, development, and DNA replication genes. However, more genes were differentially expressed with higher imidacloprid exposure; uniquely differentially expressed genes included starvation response and cuticle genes. The former may partially result from reduced pollen use, monitored to verify food provision use and provide additional context to results. A smaller differentially expressed set only in lower concentration larvae, included neural development and cell growth genes. Our findings show varying molecular consequences under different field-realistic neonicotinoid concentrations, and that even low concentrations may affect fundamental biological processes.

Diesel exhaust particles alter gut microbiome and gene expression in the bumblebee Bombus terrestris

Insect decline is a major threat to ecosystems around the world as they provide many important functions, such as pollination or pest control. Pollution is one of the main reasons for the decline, alongside changes in land use, global warming, and invasive species. While negative impacts of pesticides are well-studied, there is still a lack of knowledge about the effects of other anthropogenic pollutants, such as airborne particulate matter, on insects. To address this, we exposed workers of the bumblebee Bombus terrestris to sublethal doses of diesel exhaust particles (DEPs) and brake dust, orally or via air. After 7 days, we looked at the composition of the gut microbiome and tracked changes in gene expression. While there were no changes in the other treatments, oral DEP exposure significantly altered the structure of the gut microbiome. In particular, the core bacterium Snodgrassella had a decreased abundance in the DEP treatment. Similarly, transcriptome analysis revealed changes in gene expression after oral DEP exposure, but not in the other treatments. The changes are related to metabolism and signal transduction, which indicates a general stress response. Taken together, our results suggest potential health effects of DEP exposure on insects, here shown in bumblebees, as gut dysbiosis may increase the susceptibility of bumblebees to pathogens, while a general stress response may lower available energy resources. Those effects may exacerbate under natural conditions where insects face a multiple-stressor environment.

DNA methylation is associated with codon degeneracy in a species of bumblebee

Social insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.

Genomic architecture and sexually dimorphic expression underlying immunity in the red mason bee, Osmia bicornis

Insect pollinators provide crucial ecosystem services yet face increasing environmental pressures. The challenges posed by novel and reemerging pathogens on bee health means we need to improve our understanding of the immune system, an important barrier to infections and disease. Despite the importance of solitary bees, which are ecologically relevant, our understanding of the genomic basis and molecular mechanisms underlying their immune potential, and how intrinsic and extrinsic factors may influence it is limited. To improve our understanding of the genomic architecture underlying immunity of a key solitary bee pollinator, we characterized putative immune genes of the red mason bee, Osmia bicornis. In addition, we used publicly available RNA-seq datasets to determine how sexes differ in immune gene expression and splicing but also how pesticide exposure may affect immune gene expression in females. Through comparative genomics, we reveal an evolutionarily conserved set of more than 500 putative immune-related genes. We found genome-wide patterns of sex-biased gene expression, with greater enrichment of immune-related processes among genes with higher constitutive expression in males than females. Our results also suggest an up-regulation of immune-related genes in response to exposure to two common neonicotinoids, thiacloprid and imidacloprid. Collectively, our study provides important insights into the gene repertoire, regulation and expression differences in the sexes of O. bicornis, as well as providing additional support for how neonicotinoids can affect immune gene expression, which may affect the capacity of solitary bees to respond to pathogenic threats.

Effects of abiotic stresses on the expression of chitinase-like genes in Acyrthosiphon pisum

Insect chitinases play a crucial part to digest chitin in the exoskeleton during the molting process. However, research on insect chitinase related to the environmental stress response is very limited. This study was the first conducted to expression analysis of chitinase- related genes in A. pisum under abiotic stresses. Here, we identified five chitinase-like proteins (ApIDGF, ApCht3, ApCht7, ApCht10 and ApENGase), and clustered them into five groups (group II, III, V, Ⅹ, and ENGase). Developmental expression analysis revealed that the five A. pisum chitinase-related genes were expressed at whole developmental stages with different relative expression patterns. When aphids were exposed to various abiotic stresses including temperature, insecticide and the stress 20-hydroxyecdysone (20E), all five chitinase genes were differentially expressed in A. pisum. The results showed that insecticide such as imidacloprid down-regulated the expression of these five Cht-related genes. Analysis of temperature stress of A. pisum chitinase suggested that ApCht7 expression was high at 10°C, which demonstrates its important role in pea aphids under low temperature. Conversely, ApCht10 was more active under high temperature stress, as it was significantly up-regulated at 30°C. Besides, 20E enhanced ApCht3 and ApCht10 expression in A. pisum, but reduced ApCht7 expression. These findings provide basic information and insights for the study of the role of these genes under abiotic stress, which advances our knowledge in the management of pea aphids under multiple stresses.

Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics

As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides.

Pollen diet mediates how pesticide exposure impacts brain gene expression in nest-founding bumble bee queens

A primary goal in biology is to understand the effects of multiple, interacting environmental stressors on organisms. Wild and domesticated bees are exposed to a wide variety of interacting biotic and abiotic stressors, with widespread declines in floral resources and agrochemical exposure being two of the most important. In this study, we used examinations of brain gene expression to explore the sublethal consequences of neonicotinoid pesticide exposure and pollen diet composition in nest-founding bumble bee queens. We demonstrate for the first time that pollen diet composition can influence the strength of bumble bee queen responses to pesticide exposure at the molecular level. Specifically, one pollen mixture in our study appeared to buffer bumble bee queens entirely against the effects of pesticide exposure, with respect to brain gene expression. Additionally, we detected unique effects of pollen diet and sustained (versus more temporary) pesticide exposure on queen gene expression. Our findings support the hypothesis that nutritional status can help buffer animals against the harmful effects of other stressors, including pesticides, and highlight the importance of using molecular approaches to explore sublethal consequences of stressors.

Phenotypic Plasticity: What Has DNA Methylation Got to Do with It?

How does one genome give rise to multiple, often markedly different, phenotypes in response to an environmental cue? This phenomenon, known as phenotypic plasticity, is common amongst plants and animals, but arguably the most striking examples are seen in insects. Well-known insect examples include seasonal morphs of butterfly wing patterns, sexual and asexual reproduction in aphids, and queen and worker castes of eusocial insects. Ultimately, we need to understand how phenotypic plasticity works at a mechanistic level; how do environmental signals alter gene expression, and how are changes in gene expression translated into novel morphology, physiology and behaviour? Understanding how plasticity works is of major interest in evolutionary-developmental biology and may have implications for understanding how insects respond to global change. It has been proposed that epigenetic mechanisms, specifically DNA methylation, are the key link between environmental cues and changes in gene expression. Here, we review the available evidence on the function of DNA methylation of insects, the possible role(s) for DNA methylation in phenotypic plasticity and also highlight key outstanding questions in this field as well as new experimental approaches to address these questions.

Tools and applications for integrative analysis of DNA methylation in social insects

DNA methylation is a common epigenetic signalling tool and an important biological process which is widely studied in a large array of species. The presence, level and function of DNA methylation vary greatly across species. In some insects, DNA methylation systems are minimal, and overall methylation rates tend to be low in all studied insect species. Low methylation levels probed by whole-genome bisulphite sequencing require great care with respect to data quality control and interpretation. Here, we introduce BWASP/R, a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data. Consistent application of quality control filters and analysis parameters provides fair comparisons among different studies and an integrated view of all experiments on one species. We describe the capabilities of the BWASP/R workflow by re-analysing several publicly available social insect WGBS data sets, comprising 70 samples and cumulatively 147 replicates from four different species. We show that the CpG methylome comprises only about 1.5% of CpG sites in the honeybee genome and that the cumulative data are consistent with genetic signatures of site accessibility and physiological control of methylation levels.

Reproductive Potential Impacts Body Maintenance Parameters and Global DNA Methylation in Honeybee Workers (Apis mellifera L.)

Simple Summary

The queens and sterile workers arise from genetically identical eggs but as imagoes, they differ in their life span, DNA methylation, and their functions. In the absence of the queen, the larvae develop into rebels, i.e., workers with increased reproductive potential. We assumed that since rebels are similar to the queen in many anatomical and behavioral features, they live longer and have lower levels of global DNA methylation, even when infected, e.g., by Nosema spp. Rebels always lived longer in comparison in normal workers and unexpectedly extended longevity of normal workers when they were together, similarly as the presence of a queen did. Rebels became infected more easily but tolerated the infection better. They also had lower level of global DNA methylation than normal workers. These features expand possibilities of the use of honeybees as a model for studies on senescence, nosemosis, eusocial evolution, and epigenetics.

Abstract

The widely accepted hypothesis in life history evolution about the trade-off between fecundity and longevity is not confirmed by long-living and highly fecund queens in eusocial insects. The fact that the queens and facultatively sterile workers usually arise from genetically identical eggs but differ in DNA methylation makes them a good model for studies on senescence, eusocial evolution, and epigenetics. Therefore, honeybees seem to be especially useful here because of long living rebel-workers (RW) with high reproductive potential recently described. Longevity, ovariole number, nosema tolerance, and global DNA methylation have been assayed in normal workers (NW) versus RW in hives and cages. RW always lived longer than NW and unexpectedly extended longevity of NW when they were together, similarly as the presence of a queen did. RW lived longer despite the fact that they had higher Nosema spore load; surprisingly they became infected more easily but tolerated the infection better. Global DNA methylation increased with age, being lower in RW than in NW. Therefore, RW are queen-like considering global DNA methylation and the link between fecundity, longevity, and body maintenance. Presented features of RW expands possibilities of the use of honeybees as a model for studies on senescence, nosemosis, eusocial evolution, and epigenetics.

Chronic Effects of Imidacloprid on Honey Bee Worker Development-Molecular Pathway Perspectives

Sublethal dosages of imidacloprid cause long-term destructive effects on honey bees at the individual and colony levels. In this review, the molecular effects of sublethal imidacloprid were integrated and reported. Several general effects have been observed among different reports using different approaches. Quantitative PCR approaches revealed that imidacloprid treatments during the adult stage are expressed as changes in immuneresponse, detoxification, and oxidation-reduction response in both workers and queens. In addition, transcriptomic approaches suggested that phototransduction, behavior, and somatic muscle development also were affected. Although worker larvae show a higher tolerance to imidacloprid than adults, molecular evidence reveals its potential impacts. Sublethal imidacloprid treatment during the larval stage causes gene expression changes in larvae, pupae, and adults. Transcriptome profiles suggest that the population and functions of affected differentially expressed genes, DEGs, vary among different worker ages. Furthermore, an early transcriptomic switch from nurse bees to foragers was observed, suggesting that precocious foraging activity may occur. This report comprehensively describes the molecular effects of sublethal dosages of imidacloprid on the honey bee Apis mellifera. The corresponding molecular pathways for physiological and neurological responses in imidacloprid-exposed honey bees were validated. Transcriptomic evidence suggests a global and sustained sublethal impact of imidacloprid on honey bee development.

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.

Missing Nurse Bees-Early Transcriptomic Switch From Nurse Bee to Forager Induced by Sublethal Imidacloprid

The environmental residue/sublethal doses of neonicotinoid insecticides are believed to generate a negative impact on pollinators, including honey bees. Here we report our recent investigation on how imidacloprid, one of the major neonicotinoids, affects worker bees by profiling the transcriptomes of various ages of bees exposed to different doses of imidacloprid during the larval stage. The results show that imidacloprid treatments during the larval stage severely altered the gene expression profiles and may induce precocious foraging. Differential expression of foraging regulators was found in 14-day-old treated adults. A high transcriptome similarity between larvae-treated 14-day-old adults and 20-day-old controls was also observed, and the similarity was positively correlated with the dose of imidacloprid. One parts per billion (ppb) of imidacloprid was sufficient to generate a long-term impact on the bee's gene expression as severe as with 50 ppb imidacloprid. The disappearance of nurse bees may be driven not only by the hive member constitution but also by the neonicotinoid-induced precocious foraging behavior.

Agroecological Strategies to Safeguard Insect Pollinators in Biodiversity Hotspots: Chile as a Case Study

Industrial agriculture (IA) has been recognized among the main drivers of biodiversity loss, climate change, and native pollinator decline. Here we summarize the known negative effects of IA on pollinator biodiversity and illustrate these problems by considering the case of Chile, a “world biodiversity hotspot” (WBH) where food exports account for a considerable share of the economy in this country. Most of Chile’s WBH area is currently being replaced by IA at a fast pace, threatening local biodiversity. We present an agroecological strategy for sustainable food production and pollinator conservation in food-producing WBHs. In this we recognize native pollinators as internal inputs that cannot be replaced by IA technological packages and support the development of agroecological and biodiversity restorative practices to protect biodiversity. We suggest four fundamental pillars for food production change based on: (1) sharing the land, restoring and protecting; (2) ecological intensification; (3) localized knowledge, research, and technological development; and (4) territorial planning and implementation of socio-agroecological policies. This approach does not need modification of native pollination services that sustain the world with food and basic subsistence goods, but a paradigm change where the interdependency of nature and human wellbeing must be recognized for ensuring the world’s food security and sovereignty.

Bees and pesticides: the research impact and scientometrics relations

Bees are fundamental insects in agroecosystems, mainly due to pollination. However, its decline has been observed in recent years, and the contamination by pesticides is suspected to be responsible. This relationship is the objective of our research, which is the first scientometric study on this subject. The data were obtained from the Web of Science database (1231) and were analyzed using Microsoft Office Excel and CiteSpace. The results point to a significant increase in pesticide and bee reseach in the last 15 years in the most influential scientific journals. The USA and France have the largest number of publications and a moderade relationship between this trait and GDP (gross domestic product) was observed (r = 0.80; r2 = 0.60). There is no correlation between the use of pesticides and studies of the effects on pollinators and the use of pesticides and the countries' GDP. In general, studies have shown the negative effects of the contamination by pesticides on bees; however, most publications are with bees of the Apis genus, and therefore it is necessary to explore the action of pesticides on bumble bees and wild bees, as well furthur as studies are needed regarding the sublethal effects of these products on bees as the number of molecules used in the management of agricultural crops is vast.

Insecticide exposure affects intergenerational patterns of DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata

Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able to rapidly evolve resistance to them, but how they are able to do so is poorly understood. One possible but largely unexplored explanation is that exposure to sublethal doses of insecticides may alter epigenetic patterns that are heritable. For instance, epigenetic mechanisms, such as DNA methylation that modifies gene expression without changing the underlying genetic code, may facilitate the emergence of resistant phenotypes in complex ways. We assessed the effects of sublethal insecticide exposure, with the neonicotinoid imidacloprid, on DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata, examining both global changes in DNA methylation and specific changes found within genes and transposable elements. We found that exposure to insecticide led to decreases in global DNA methylation for parent and F2 generations and that many of the sites of changes in methylation are found within genes associated with insecticide resistance, such as cytochrome P450s, or within transposable elements. Exposure to sublethal doses of insecticide caused heritable changes in DNA methylation in an agricultural insect herbivore. Therefore, epigenetics may play a role in insecticide resistance, highlighting a fundamental mechanism of evolution while informing how we might better coexist with insect species in agroecosystems.

Impacts of Neonicotinoids on the Bumble Bees Bombus terrestris and Bombus impatiens Examined through the Lens of an Adverse Outcome Pathway Framework

Bumble bees (Bombus sp.) are important pollinators for agricultural systems and natural landscapes and have faced population declines globally in recent decades. Neonicotinoid pesticides have been implicated as one of the reasons for the population reductions in bumble bees and other pollinators due to their widespread use, specificity to the invertebrate nervous system, and toxicity to bees. Adverse outcome pathways (AOPs) are used to describe the mechanism of action of a toxicant through sequential levels of biological organization to understand the key events that occur for a given adverse outcome. We used the AOP framework to organize and present the current literature available on the impacts of neonicotinoids on bumble bees. The present review focuses on Bombus terrestris and B. impatiens, the 2 most commonly studied bumble bees due to their commercial availability. Our review does not seek to describe an AOP for the molecular initiating event shared by neonicotinoids, but rather aims to summarize the current literature and determine data gaps for the Bombus research community to address. Overall, we highlight a great need for additional studies, especially those examining cellular and organ responses in bumble bees exposed to neonicotinoids. Environ Toxicol Chem 2021;40:309-322. © 2020 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.

The effect of DNA methylation on bumblebee colony development

BACKGROUND

Although around 1% of cytosines in bees' genomes are known to be methylated, less is known about methylation's effect on bee behavior and fitness. Chemically altered DNA methylation levels have shown clear changes in the dominance and reproductive behavior of workers in queen-less colonies, but the global effect of DNA methylation on caste determination and colony development remains unclear, mainly because of difficulties in controlling for genetic differences among experimental subjects in the parental line. Here, we investigated the effect of the methylation altering agent decitabine on the developmental rate of full bumblebee colonies. Whole genome bisulfite sequencing was used to assess differences in methylation status.

RESULTS

Our results showed fewer methylated loci in the control group. A total of 22 CpG loci were identified as significantly differentially methylated between treated and control workers with a change in methylation levels of 10% or more. Loci that were methylated differentially between groups participated in pathways including neuron function, oocyte regulation and metabolic processes. Treated colonies tended to develop faster, and therefore more workers were found at a given developmental stage. However, male production followed the opposite trend and it tended to be higher in control colonies.

CONCLUSION

Overall, our results indicate that altered methylation patterns resulted in an improved cooperation between workers, while there were no signs of abnormal worker dominance or caste determination.

Gene expression during larval caste determination and differentiation in intermediately eusocial bumblebees, and a comparative analysis with advanced eusocial honeybees

The queen‐worker caste system of eusocial insects represents a prime example of developmental polyphenism (environmentally‐induced phenotypic polymorphism) and is intrinsic to the evolution of advanced eusociality. However, the comparative molecular basis of larval caste determination and subsequent differentiation in the eusocial Hymenoptera remains poorly known. To address this issue within bees, we profiled caste‐associated gene expression in female larvae of the intermediately eusocial bumblebee Bombus terrestris. In B. terrestris, female larvae experience a queen‐dependent period during which their caste fate as adults is determined followed by a nutrition‐sensitive period also potentially affecting caste fate but for which the evidence is weaker. We used mRNA‐seq and qRT‐PCR validation to isolate genes differentially expressed between each caste pathway in larvae at developmental stages before and after each of these periods. We show that differences in gene expression between caste pathways are small in totipotent larvae, then peak after the queen‐dependent period. Relatively few novel (i.e., taxonomically‐restricted) genes were differentially expressed between castes, though novel genes were significantly enriched in late‐instar larvae in the worker pathway. We compared sets of caste‐associated genes in B. terrestris with those reported from the advanced eusocial honeybee, Apis mellifera, and found significant but relatively low levels of overlap of gene lists between the two species. These results suggest both the existence of low numbers of shared toolkit genes and substantial divergence in caste‐associated genes between Bombus and the advanced eusocial Apis since their last common eusocial ancestor.

Parent of origin gene expression in the bumblebee, Bombus terrestris, supports Haig's kinship theory for the evolution of genomic imprinting

Genomic imprinting is the differential expression alleles in diploid individuals, with the expression being dependent on the sex of the parent from which it was inherited. Haig's kinship theory hypothesizes that genomic imprinting is due to an evolutionary conflict of interest between alleles from the mother and father. In social insects, it has been suggested that genomic imprinting should be widespread. One recent study identified parent-of-origin expression in honey bees and found evidence supporting the kinship theory. However, little is known about genomic imprinting in insects and multiple theoretical predictions must be tested to avoid single-study confirmation bias. We, therefore, tested for parent-of-origin expression in a primitively eusocial bee. We found equal numbers of maternally and paternally biased expressed genes. The most highly biased genes were maternally expressed, offering support for the kinship theory. We also found low conservation of potentially imprinted genes with the honey bee, suggesting rapid evolution of genomic imprinting in Hymenoptera.

DNA methylation suppresses chitin degradation and promotes the wing development by inhibiting Bmara-mediated chitinase expression in the silkworm, Bombyx mori

BACKGROUND

DNA methylation, as an essential epigenetic modification found in mammals and plants, has been implicated to play an important role in insect reproduction. However, the functional role and the regulatory mechanism of DNA methylation during insect organ or tissue development are far from being clear.

RESULTS

Here, we found that DNA methylation inhibitor (5-aza-dC) treatment in newly molted pupae decreased the chitin content of pupal wing discs and adult wings and resulted in wing deformity of Bombyx mori. Transcriptome analysis revealed that the up-regulation of chitinase 10 (BmCHT10) gene might be related to the decrease of chitin content induced by 5-aza-dC treatment. Further, the luciferase activity assays demonstrated that DNA methylation suppressed the promoter activity of BmCHT10 by down-regulating the transcription factor, homeobox protein araucan (Bmara). Electrophoretic mobility shift assay, DNA pull-down and chromatin immunoprecipitation demonstrated that Bmara directly bound to the BmCHT10 promoter. Therefore, DNA methylation is involved in keeping the structural integrity of the silkworm wings from unwanted chitin degradation, as a consequence, it promotes the wing development of B. mori.

CONCLUSIONS

This study reveals that DNA methylation plays an important role in the wing development of B. mori. Our results support that the indirect transcriptional repression of a chitin degradation-related gene BmCHT10 by DNA methylation is necessary to keep the proper wing development in B. mori.

Bumblebee Workers Show Differences in Allele-Specific DNA Methylation and Allele-Specific Expression

Allele-specific expression is when one allele of a gene shows higher levels of expression compared with the other allele, in a diploid organism. Recent work has identified allele-specific expression in a number of Hymenopteran species. However, the molecular mechanism which drives this allelic expression bias remains unknown. In mammals, DNA methylation is often associated with genes which show allele-specific expression. DNA methylation systems have been described in species of Hymenoptera, providing a candidate mechanism. Using previously generated RNA-Seq and whole-genome bisulfite sequencing from reproductive and sterile bumblebee (Bombus terrestris) workers, we have identified genome-wide allele-specific expression and allele-specific DNA methylation. The majority of genes displaying allele-specific expression are common between reproductive and sterile workers and the proportion of allele-specific expression bias generally varies between genetically distinct colonies. We have also identified genome-wide allele-specific DNA methylation patterns in both reproductive and sterile workers, with reproductive workers showing significantly more genes with allele-specific methylation. Finally, there is no significant overlap between genes showing allele-specific expression and allele-specific methylation. These results indicate that cis-acting DNA methylation does not directly drive genome-wide allele-specific expression in this species.

Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes

While many studies have examined the effects of neonicotinoid insecticides and the parasitic mite Varroa destructor on honey bees (Apis mellifera), more information on the combined effects of such stressors on gene expression, including neural related genes, and their impact on biological pathways is needed. This study analyzed the effects of field realistic concentrations of the neonicotinoid clothianidin on adult bees infested and not infested with V. destructor over 21 consecutive days and then determined bee survivorship, weight, deformed wing virus (DWV) levels and gene expression. V. destructor parasitism with or without clothianidin exposure was significantly associated with decreased survivorship, weight loss and higher DWV levels, while clothianidin exposure was only associated with higher levels of DWV. Expression analysis of the neural genes AmNlg-1, BlCh and AmAChE-2 showed that V. destructor caused a significant down-regulation of all of them, whereas clothianidin caused a significant down-regulation of only AmNrx-1 and BlCh. An interaction was only detected for AmNrx-1 expression. RNAseq analysis showed that clothianidin exposure resulted in 6.5 times more up-regulated differentially expressed genes (DEGs) than V. destructor alone and 123 times more than clothianidin combined with V. destructor. Similar results were obtained with down-regulated DEGs, except for a higher number of DEGs shared between V. destructor and the combined stressors. KEGG (Kyoto Encyclopedia of Genes and Genomes) biological pathway analysis of the DEGs showed that the stressor linked to the highest number of KEGG pathways was clothianidin, followed by V. destructor, and then considerably fewer number of KEGG pathways with the combined stressors. The reduced numbers of DEGs and KEGG pathways associated with the DEGs for the combined stressors compared to the stressors alone indicates that the interaction of the stressors is not additive or synergistic, but antagonistic. The possible implications of the antagonistic effect on the number of DEGs are discussed.

Methylation and gene expression differences between reproductive and sterile bumblebee workers

Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on its role in other bee species. In this study, we analyzed whole genome bisulfite sequencing and RNA-seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found that genome-wide methylation in B. terrestris is similar to other holometabolous insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However, we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high intercolony variation in methylation. These findings suggest that methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste-specific methylome as well as its interaction with gene expression and caste-specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in insects.