Effects of tefluthrin and guadipyr on the midgut bacteria of adult Apis mellifera.

The objective of this study is to assess the potential impact of tefluthrin and guadipyr on the gut microbial composition and metabolism in adult Apis mellifera ligustica, thereby elucidating the underlying mechanisms of insecticide action and its practical implications for bee protection. In this investigation, A. mellifera were subjected to one of three dietary conditions: (1) control sugar water, (2) tefluthrin-infused sugar water, or (3) guadipyr-infused sugar water. After a 10-day exposure period, genomic DNA from the gut bacteria was extracted. High-throughput sequencing was employed to evaluate the potential influence of tefluthrin and guadipyr treatments on the diversity and abundance of gut bacteria. Among the A. mellifera specimens, a total of twenty species of gut bacteria were identified, spanning across five phyla, six classes, eleven orders, eleven families, and fifteen genera. The dominant phyla within the gut bacterial community were Proteobacteria and Bacteroidetes. In comparison to the control group, both the tefluthrin-treated and deltamethrin-treated groups exhibited alterations in the composition of their gut bacterial flora. At the phylum level, there was a significant decrease in the relative abundance of Cyanobacteria (P < 0.05). On the genus level, the tefluthrin group displayed a significant increase in the relative abundance of Bartonella and Serratia (P < 0.05). In the guadipyr-treated group, the relative abundance of Gilliamella and Frischella increased significantly (P < 0.05), while the relative abundance of norank_o_Chloroplast and Enterobacter decreased significantly (P < 0.05). Further analysis of cluster of orthologous genes predicted functional changes in gut microbial metabolism following tefluthrin exposure but no significant changes after guadipyr exposure. Consequently, exposure to tefluthrin and guadipyr can induce shifts in both the composition and metabolic activity of the gut bacteria in A. mellifera. Notably, the impact of tefluthrin on the gut bacteria of A. mellifera appears to be more pronounced compared to that of guadipyr.

Combined pesticides in field doses weaken honey bee (Apis cerana F.) flight ability and analyses of transcriptomics and metabolomics.

Imidacloprid, chlorpyrifos, and glyphosate rank among the most extensively employed pesticides worldwide. The effects of these pesticides and their combined on the flight capability of Apis cerana, and the potential underlying mechanisms remain uncertain. To investigate these effects, we carried out flight mill, transcriptome, and metabolome experiments. Our findings reveal that individual acute oral treatments with pesticides, specifically 20 µL of 10 ng/g imidacloprid (0.2 ng per bee), 30 ng/g chlorpyrifos (0.6 ng per bee), and 60 ng/g glyphosate (1.2 ng per bee), did not impact the flight capability of the bees. However, when bees were exposed to a combination of two or three pesticides, a notable reduction in flight duration and distance was observed. In the transcriptomic and metabolomic analyses, we identified 307 transcripts and 17 metabolites that exhibited differential expression following exposure to combined pesticides, primarily associated with metabolic pathways involved in energy regulation. Our results illuminate the intricate effects and potential hazards posed by combined pesticide exposures on bee behavior. These findings offer valuable insights into the synergistic potential of pesticide combinations and their capacity to impair bee behavior. Understanding these complex interactions is essential for comprehending the broader consequences of pesticide formulations on honey bee populations.

Impact of chronic exposure to field level glyphosate on the food consumption, survival, gene expression, gut microbiota, and metabolomic profiles of honeybees.

Glyphosate (GLY) is among the most widely used pesticides in the world. However, there are a lot of unknowns about chronic exposure to GLY's effects on Honeybee (HB) behavior and physiology. To address this, we carried out five experiments to study the impact of chronic exposure to 5 mg/kg GLY on sugar consumption, survival, gene expression, gut microbiota, and metabolites of HB workers. Our results find a significant decrease in sugar consumption and survival probability of HB after chronic exposure to GLY. Further, genes associated with immune response, energy metabolism, and longevity were conspicuously altered. In addition, a total of seven metabolites were found to be differentially expressed in the metabolomic profiles, mainly related the sucrose metabolism. There was no significant difference in the gut microbiota. Results suggest that chronic exposure to field-level GLY altered the health of HB and the intricate toxic mechanisms. Our data provided insights into the chronic effects of GLY on HB behavior in food intake and health, which represents the field conditions where HB are exposed to pesticides over extended periods.

Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera).

Conflict between genes inherited from the mother (matrigenes) and the father (patrigenes) is predicted to arise during social interactions among offspring if these genes are not evenly distributed among offspring genotypes. This intragenomic conflict drives parent-specific transcription patterns in offspring resulting from parent-specific epigenetic modifications. Previous tests of the kinship theory of intragenomic conflict in honey bees (Apis mellifera) provided evidence in support of theoretical predictions for variation in worker reproduction, which is associated with extreme variation in morphology and behavior. However, more subtle behaviors - such as aggression - have not been extensively studied. Additionally, the canonical epigenetic mark (DNA methylation) associated with parent-specific transcription in plant and mammalian model species does not appear to play the same role as in honey bees, and thus the molecular mechanisms underlying intragenomic conflict in this species is an open area of investigation. Here, we examined the role of intragenomic conflict in shaping aggression in honey bee workers through a reciprocal cross design and Oxford Nanopore direct RNA sequencing. We attempted to probe the underlying regulatory basis of this conflict through analyses of parent-specific RNA m6A and alternative splicing patterns. We report evidence that intragenomic conflict occurs in the context of honey bee aggression, with increased paternal and maternal allele-biased transcription in aggressive compared to non-aggressive bees, and higher paternal allele-biased transcription overall. However, we found no evidence to suggest that RNA m6A or alternative splicing mediate intragenomic conflict in this species.

Genomic signatures underlying the oogenesis of the ectoparasitic mite Varroa destructor on its new host Apis mellifera.

INTRODUCTION: Host shift of parasites may have devastating effects on the novel hosts. One remarkable example is that of the ectoparasitic mite Varroa destructor, which has shifted its host from Eastern honey bees (Apis cerana) to Western honey bees (Apis mellifera) and posed a global threat to apiculture. OBJECTIVES: To identify the genetic factors underlying the reproduction of host-shifted V. destructor on the new host. METHODS: Genome sequencing was conducted to construct the phylogeny of the host-shifted and non-shifted mites and to screen for genomic signatures that differentiated them. Artificial infestation experiment was conducted to compare the reproductive difference between the mites, and transcriptome sequencing was conducted to find differentially expressed genes (DEGs) during the reproduction process. RESULTS: The host-shifted and non-shifted V. destructor mites constituted two genetically distinct lineages, with 15,362 high-FST SNPs identified between them. Oogenesis was upregulated in host-shifted mites on the new host A. mellifera relative to non-shifted mites. The transcriptomes of the host-shifted and non-shifted mites differed significantly as early as 1h post-infestation. The DEGs were associated with nine genes carrying nonsynonymous high-FST SNPs, including mGluR2-like, Lamb2-like and Vitellogenin 6-like, which were also differentially expressed, and eIF4G, CG5800, Dap160 and Sas10, which were located in the center of the networks regulating the DEGs based on protein-protein interaction analysis. CONCLUSIONS: The annotated functions of these genes were all associated with oogenesis. These genes appear to be the key genetic determinants of the oogenesis of host-shifted mites on the new host. Further study of these candidate genes will help elucidate the key mechanism underlying the success of host shifts of V. destructor.

Pesticide residues in beebread and honey in Apis cerana cerana and their hazards to honey bees and human.

The residue of pesticides in bee products such as beebread and honey threaten the survival of pollinators and human health. Apis cerana cerana is one of the leading managed honey bees in China. However, little is known about the residues of pesticides in hive products of A. c. cerana in China. Here, we investigated the pesticide residues in beebread and honey. The risk of detected residues of pesticides to honey bees was evaluated with hazard quotient (HQ) and BeeREX. Furthermore, we assessed the chronic and acute risks to humans according to the dietary exposure. Our results suggest that the pesticide residues detection ratio (25.4% for beebread and 2.8% for honey) and the concentrations of these residues is lower than previously reported. Additional risk assessments indicate that the residue levels of pesticides in tested honey of A. c. cerana do not pose a risk for human consumers. Among all identified pesticides, only thiamethoxam raises the concern for further risk assessment in the risk evaluation of honey bee colonies and thiamethoxam was safe for colonies in higer tier studies.

Assessing the toxicological interaction effects of imidacloprid, thiamethoxam, and chlorpyrifos on Bombus terrestris based on the combination index.

In modern agricultural production, a variety of pesticides are widely used to protect crops against pests. However, extensive residues of these pesticides in the soil, water, and pollen have negatively affected the health of nontarget organisms, especially among pollinators such as bumblebees. As an important pollinator, the bumblebee plays a vital role in agricultural production and the maintenance of ecosystem diversity. Previous research has focused on the effects of a single pesticide on pollinating insects; however, the synergistic effects of multiple agents on bumblebees have been not studied in detail. Imidacloprid, thiamethoxam, and chlorpyrifos are three of common pesticides known for severe effects on bumblebee health. It is still unknown what synergistic effects of these pesticides on pollinators. In our test, the individual and combined toxicities of chlorpyrifos, thiamethoxam, and imidacloprid to bumblebees after 48 h of oral administration were documented by the equivalent linear equation method. Our results showed that the toxicity of each single pesticide exposure, from high to low, was imidacloprid, thiamethoxam, and chlorpyrifos. All binary and ternary combinations showed synergistic or additive effects. Therefore, our research not only shows that the mixed toxicity of insecticides has a significant effect on bumblebees, but also provides scientific guidelines for assessing the safety risks to bumblebees of these three insecticide compounds. In assessing the risk to pollinating insects, the toxicity levels of laboratory experiments are much lower than the actual toxicity in the field.

The Life Span and Levels of Oxidative Stress in Foragers Between Feral and Managed Honey Bee Colonies.

Molecular damage caused by oxidative stress may lead to organismal aging and result in acute mortality to organisms. Thus, oxidative stress resistance and longevity are closely linked. Honey bees (Apis mellifera) are the most important managed pollinator in agriculture, but the long-term survival of honey bees is seriously threatened. Feral honey bee colonies can be used as natural resources to improve honey bee health. One question we ask here is whether feral honey bees are stress resistant or survive longer than managed bee populations. More work is needed to determine the impact of oxidative stress on honey bee health and survival. In this study, we used paired colony designs to compare the life span of worker bees (foragers) between feral and managed colonies and their levels of oxidative stress. Each pair of colonies shared similar foraging resources. The results indicated that foragers in feral colonies had longer survival times and life spans than those in managed colonies. The levels of oxidative stress from lipid damage content in feral colonies were higher than those in managed colonies, indicating that they used a tolerance mechanism rather than a repair mechanism to survive. Our study provides new insights into a colony difference in the physiology and oxidative stress resistance of feral honey bees compared with managed colony stocks.

Pesticide residues in the pollen and nectar of oilseed rape (Brassica napus L.) and their potential risks to honey bees.

Research evidence suggests that pesticide residues are one of the leading potential causes of the decline in pollinators, especially during vulnerable periods such as foraging in the early springtime. In China, no research quantifies pesticide residues in the nectar and pollen of honey bee colonies during this period or examines the potential risks and toxicity of pesticides to honey bees. Oilseed rape is one of the first and primary bee-attractive plants in most parts of China. Here, we investigated the pesticide residues in the oilseed rape of the years 2017 and 2018 in China. The hazard quotient (HQ) from pollen and nectar and the BeeREX risk assessment were used to evaluate the potential risks of the pesticide residues to honey bees. We detected 48 pesticides in pollen samples and 34 chemicals in nectar samples. The maximum pollen HQ (PHQ) values (contact or oral) ranged from 0.16 to 706,421, and the maximum nectar HQ (NHQ) values (contact or oral) ranged from 0.07 to 185,135. In particular, carbofuran, cyfluthrin, deltamethrin, and fenpropathrin have relatively high PHQ and NHQ values. Our results indicated that further investigation of nearly half of the tested compounds is needed because their PHQ or NHQ values are more than 50. Especially cyfluthrin and carbofuran need advanced tier assessment due to their maximum RQ (risk quotient) values exceeding the level of concern. These results provide valuable guidance for protecting bees and other pollinators in China.

Differential state-dependent effects of deltamethrin and tefluthrin on sodium channels in central neurons of Helicoverpa armigera.

The cotton bollworm, Helicoverpa armigera is one of the worldwide pests. Electrophysiological properties of voltage-gated sodium channels in central neurons of sensitive and pyrethroid resistant H. armigera were investigated using whole-cell patch clamp technique. The modification effects of pyrethroid insecticides deltamethrin and tefluthrin on sodium channels were also compared. The V0.5 of voltage dependence of activation of resistant H. armigera sodium channels (resistant channels) exhibited an obvious depolarizing shift by 13.52 mV compared to that of sensitive H. armigera sodium channels (sensitive channels). In contrast, the V0.5 of the voltage dependence of steady-state inactivation of the resistant channels showed a significant hyperpolarizing shift by 7.59 mV in comparison with that of the sensitive channels. The time course of recovery from inactivation for the resistant channels was prolonged significantly, by 0.17 ms, compared with that for the sensitive channels. We also assessed the use-dependent effects of deltamethrin and tefluthrin on sensitive sodium channels. Repetitive depolarization remarkably increased the extent of the sensitive channel modification by 10 µM deltamethrin by ~4.61-fold but had no effect on the extent of sensitive channel modifications by 10 µM tefluthrin. These results provide more direct evidence for the presence of nerve insensitivity in resistant H. armigera strains in North of China. The sodium channels of the resistant H. armigera differ from those of the sensitive H. armigera in the fundamental electrophysiological properties, and correspondingly, have a different response to the modification of pyrethroids. Both deltamethrin and tefluthrin have effects on the closed state of the sensitive sodium channels, but deltamethrin has higher affinity to the open state of these channels.

Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection.

Honey bees (Apis mellifera L.) suffer from many brood pathogens, including viruses. Despite considerable research, the molecular responses and dynamics of honey bee pupae to viral pathogens remain poorly understood. Israeli Acute Paralysis Virus (IAPV) is emerging as a model virus since its association with severe colony losses. Using worker pupae, we studied the transcriptomic and methylomic consequences of IAPV infection over three distinct time points after inoculation. Contrasts of gene expression and 5 mC DNA methylation profiles between IAPV-infected and control individuals at these time points - corresponding to the pre-replicative (5 h), replicative (20 h), and terminal (48 h) phase of infection - indicate that profound immune responses and distinct manipulation of host molecular processes accompany the lethal progression of this virus. We identify the temporal dynamics of the transcriptomic response to with more genes differentially expressed in the replicative and terminal phases than in the pre-replicative phase. However, the number of differentially methylated regions decreased dramatically from the pre-replicative to the replicative and terminal phase. Several cellular pathways experienced hyper- and hypo-methylation in the pre-replicative phase and later dramatically increased in gene expression at the terminal phase, including the MAPK, Jak-STAT, Hippo, mTOR, TGF-beta signaling pathways, ubiquitin mediated proteolysis, and spliceosome. These affected biological functions suggest that adaptive host responses to combat the virus are mixed with viral manipulations of the host to increase its own reproduction, all of which are involved in anti-viral immune response, cell growth, and proliferation. Comparative genomic analyses with other studies of viral infections of honey bees and fruit flies indicated that similar immune pathways are shared. Our results further suggest that dynamic DNA methylation responds to viral infections quickly, regulating subsequent gene activities. Our study provides new insights of molecular mechanisms involved in epigenetic that can serve as foundation for the long-term goal to develop anti-viral strategies for honey bees, the most important commercial pollinator.

Impact of acute oral exposure to thiamethoxam on the homing, flight, learning acquisition and short-term retention of Apis cerana.

BACKGROUND: Thiamethoxam (TMX) represents the second generation of neonicotinoids that has been widely applied in agricultural activities, while how TMX alters the behavior of Apis cerana, an important native honey bee species in China, is not clear. We carried out three independent experiments to study the impact of acute oral treatment of 20 µL TMX at concentrations of 2.4 ppb (0.048 ng/bee) and 10 ppb (0.2 ng/bee) on the homing, flight, learning acquisition and short-term retention ability of A. cerana. The homing ability was assessed by the catch-and-release method, the flight ability was assessed by flight mills, and the learning acquisition and short-term retention were evaluated by the proboscis extension response method. RESULTS: When treated with 10 ppb of TMX, bees had a significantly higher average homing time, mean flight velocity, flying distance, and flying duration than the control, whereas 2.4 ppb concentration did not cause any significant effect on homing or flight ability. Bees treated with either 2.4 ppb or 10 ppb TMX had significantly lower learning acquisition and short-term retention ability. CONCLUSION: Results suggest that acute oral exposure to 10 ppb of TMX altered the short-distance homing time, flight ability, and learning acquisition and short-term retention ability. Our study also highlights the concern that acute oral exposure to a low concentration of 2.4 ppb could have consequences on the behavior of A. creana. Those multiple sublethal alterations on A. cerana's behavior indicate that TMX are likely having complex but negative consequences on bee health in the field. © 2019 Society of Chemical Industry.

Key Transport and Ammonia Recycling Genes Involved in Aphid Symbiosis Respond to Host-Plant Specialization.

Microbes are known to influence insect-plant interactions; however, it is unclear if host-plant diet influences the regulation of nutritional insect symbioses. The pea aphid, Acyrthosiphon pisum, requires its nutritional endosymbiont, Buchnera, for the production of essential amino acids. We hypothesize that key aphid genes that regulate the nutritional symbioses respond to host-plant diet when aphids feed on a specialized (alfalfa) compared to a universal host-plant diet (fava), which vary in amino acid profiles. Using RNA-Seq and whole genome bisulfite sequencing, we measured gene expression and DNA methylation profiles for such genes when aphids fed on either their specialized or universal host-plant diets. Our results reveal that when aphids feed on their specialized host-plant they significantly up-regulate and/or hypo-methylate key aphid genes in bacteriocytes related to the amino acid metabolism, including glutamine synthetase in the GOGAT cycle that recycles ammonia into glutamine and the glutamine transporter ApGLNT1 Moreover, regardless of what host-plant aphids feed on we observed significant up-regulation and differential methylation of key genes involved in the amino acid metabolism and the glycine/serine metabolism, a metabolic program observed in proliferating cancer cells potentially to combat oxidative stress. Based on our results, we suggest that this regulatory response of key symbiosis genes in bacteriocytes allows aphids to feed on a suboptimal host-plant that they specialize on.

Plant Defense Inhibitors Affect the Structures of Midgut Cells in Drosophila melanogaster and Callosobruchus maculatus.

Plants produce proteins such as protease inhibitors and lectins as defenses against herbivorous insects and pathogens. However, no systematic studies have explored the structural responses in the midguts of insects when challenged with plant defensive proteins and lectins across different species. In this study, we fed two kinds of protease inhibitors and lectins to the fruit fly Drosophila melanogaster and alpha-amylase inhibitors and lectins to the cowpea bruchid Callosobruchus maculatus. We assessed the changes in midgut cell structures by comparing them with such structures in insects receiving normal diets or subjected to food deprivation. Using light and transmission electron microscopy in both species, we observed structural changes in the midgut peritrophic matrix as well as shortened microvilli on the surfaces of midgut epithelial cells in D. melanogaster. Dietary inhibitors and lectins caused similar lesions in the epithelial cells but not much change in the peritrophic matrix in both species. We also noted structural damages in the Drosophila midgut after six hours of starvation and changes were still present after 12 hours. Our study provided the first evidence of key structural changes of midguts using a comparative approach between a dipteran and a coleopteran. Our particular observation and discussion on plant-insect interaction and dietary stress are relevant for future mode of action studies of plant defensive protein in insect physiology.

Migratory management and environmental conditions affect lifespan and oxidative stress in honey bees.

Most pollination in large-scale agriculture is dependent on managed colonies of a single species, the honey bee Apis mellifera. More than 1 million hives are transported to California each year just to pollinate the almonds, and bees are trucked across the country for various cropping systems. Concerns have been raised about whether such "migratory management" causes bees undue stress; however to date there have been no longer-term studies rigorously addressing whether migratory management is detrimental to bee health. To address this issue, we conducted field experiments comparing bees from commercial and experimental migratory beekeeping operations to those from stationary colonies to quantify effects on lifespan, colony health and productivity, and levels of oxidative damage for individual bees. We detected a significant decrease in lifespan of migratory adult bees relative to stationary bees. We also found that migration affected oxidative stress levels in honey bees, but that food scarcity had an even larger impact; some detrimental effects of migration may be alleviated by a greater abundance of forage. In addition, rearing conditions affect levels of oxidative damage incurred as adults. This is the first comprehensive study on impacts of migratory management on the health and oxidative stress of honey bees.

Honey bee (Apis mellifera) drones survive oxidative stress due to increased tolerance instead of avoidance or repair of oxidative damage.

Oxidative stress can lead to premature aging symptoms and cause acute mortality at higher doses in a range of organisms. Oxidative stress resistance and longevity are mechanistically and phenotypically linked; considerable variation in oxidative stress resistance exists among and within species and typically covaries with life expectancy. However, it is unclear whether stress-resistant, long-lived individuals avoid, repair, or tolerate molecular damage to survive longer than others. The honey bee (Apis mellifera L.) is an emerging model system that is well-suited to address this question. Furthermore, this species is the most economically important pollinator, whose health may be compromised by pesticide exposure, including oxidative stressors. Here, we develop a protocol for inducing oxidative stress in honey bee males (drones) via Paraquat injection. After injection, individuals from different colony sources were kept in common social conditions to monitor their survival compared to saline-injected controls. Oxidative stress was measured in susceptible and resistant individuals. Paraquat drastically reduced survival but individuals varied in their resistance to treatment within and among colony sources. Longer-lived individuals exhibited higher levels of lipid peroxidation than individuals dying early. In contrast, the level of protein carbonylation was not significantly different between the two groups. This first study of oxidative stress in male honey bees suggests that survival of an acute oxidative stressor is due to tolerance, not prevention or repair, of oxidative damage to lipids. It also demonstrates colony differences in oxidative stress resistance that might be useful for breeding stress-resistant honey bees.

Transcriptomic response of cowpea bruchids to N-acetylglucosamine-specific lectins.

Griffonia simplicifolia lectin II (GSII) and wheat germ agglutinin (WGA) are N-acetylglucosamine-binding lectins. Previous studies demonstrated that they have anti-insect activity, a property potentially useful in pest control. To gain some insight into the insect response to dietary lectins, we performed transcriptomic analysis using the cowpea bruchid (Callosobruchus maculatus) midgut microarray platform we built. Compared to the nonnutritional cellulose treatment, dietary lectins induced more profound changes in gene expression. Ingestion of relatively high doses of lectins for 24 h resulted in alteration of gene expression involved in sugar and lipid metabolism, transport, development, defense, and stress tolerance. Metabolic genes were largely downregulated. Moreover, we observed disorganized microvilli resulting from ingestion of WGA. This morphological change is consistent with the lectin-induced changes in genes related to midgut epithelial cell repair. In addition, suboptimal nutrient conditions may serve as a stress signal to trigger senescence processes, leading to growth arrest and developmental delay.

Socially responsive effects of brain oxidative metabolism on aggression.

Despite ongoing high energetic demands, brains do not always use glucose and oxygen in a ratio that produces maximal ATP through oxidative phosphorylation. In some cases glucose consumption exceeds oxygen use despite adequate oxygen availability, a phenomenon known as aerobic glycolysis. Although metabolic plasticity seems essential for normal cognition, studying its functional significance has been challenging because few experimental systems link brain metabolic patterns to distinct behavioral states. Our recent transcriptomic analysis established a correlation between aggression and decreased whole-brain oxidative phosphorylation activity in the honey bee (Apis mellifera), suggesting that brain metabolic plasticity may modulate this naturally occurring behavior. Here we demonstrate that the relationship between brain metabolism and aggression is causal, conserved over evolutionary time, cell type-specific, and modulated by the social environment. Pharmacologically treating honey bees to inhibit complexes I or V in the oxidative phosphorylation pathway resulted in increased aggression. In addition, transgenic RNAi lines and genetic manipulation to knock down gene expression in complex I in fruit fly (Drosophila melanogaster) neurons resulted in increased aggression, but knockdown in glia had no effect. Finally, honey bee colony-level social manipulations that decrease individual aggression attenuated the effects of oxidative phosphorylation inhibition on aggression, demonstrating a specific effect of the social environment on brain function. Because decreased neuronal oxidative phosphorylation is usually associated with brain disease, these findings provide a powerful context for understanding brain metabolic plasticity and naturally occurring behavioral plasticity.

RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.

Studies of DNA methylation from fungi, plants, and animals indicate that gene body methylation is ancient and highly conserved in eukaryotic genomes, but its role has not been clearly defined. It has been postulated that regulation of alternative splicing of transcripts was an original function of DNA methylation, but a direct experimental test of the effect of methylation on alternative slicing at the whole genome level has never been performed. To do this, we developed a unique method to administer RNA interference (RNAi) in a high-throughput and noninvasive manner and then used it to knock down the expression of DNA methyl-transferase 3 (dnmt3), which is required for de novo DNA methylation. We chose the honey bee (Apis mellifera) for this test because it has recently emerged as an important model organism for studying the effects of DNA methylation on development and social behavior, and DNA methylation in honey bees is predominantly on gene bodies. Here we show that dnmt3 RNAi decreased global genomic methylation level as expected and in addition caused widespread and diverse changes in alternative splicing in fat tissue. Four different types of splicing events were affected by dnmt3 gene knockdown, and change in two types, exon skipping and intron retention, was directly related to decreased methylation. These results demonstrate that one function of gene body DNA methylation is to regulate alternative splicing.

Genome-wide analysis of genes associated with moderate and high DDT resistance in Drosophila melanogaster.

BACKGROUND: Moderate to high DDT resistance in generally associated with overexpression of multiple genes and therefore has been considered to be polygenic. However, very little information is available about the molecular mechanisms that insect populations employ when evolving increased levels of resistance. The presence of common regulatory motifs among resistance-associated genes may help to explain how and why certain suites of genes are preferentially represented in genomic-scale analyses. RESULTS: A set of commonly differentially expressed genes associated with DDT resistance in the fruit fly was identified on the basis of genome-wide microarray analysis followed by qRT-PCR verification. More genes were observed to be overtranscribed in the highly resistant strain (91-R) than in the moderately resistant strain (Wisconsin) and susceptible strain (Canton-S). Furthermore, possible transcription factor binding sites that occurred in coexpressed resistance-associated genes were discovered by computational motif discovery methods. CONCLUSION: A glucocorticoid receptor (GR)-like putative transcription factor binding motif (TFBM) was observed to be associated with genes commonly differentially transcribed in both the 91-R and Wisconsin lines of DDT-resistant Drosophila.