Alternative splicing of a single transcription factor drives selfish reproductive behavior in honeybee workers (Apis mellifera)

The eusocial non-code: Unveiling the impact of noncoding RNAs on Hymenoptera eusocial evolution

Eusociality, characterized by reproductive division of labor, cooperative brood care, and multi-generational cohabitation, represents a pinnacle of complex social evolution, most notably manifested within the Hymenoptera order including bees, ants, and wasps. The molecular underpinnings underlying these sophisticated social structures remain an enigma, with noncoding RNAs (ncRNAs) emerging as crucial regulatory players. This article delves into the roles of ncRNAs in exerting epigenetic control during the development and maintenance of Hymenopteran eusociality. We consolidate current findings on various classes of ncRNAs, underscoring their influence on gene expression regulation pertinent to caste differentiation, developmental plasticity, and behavioral modulation. Evidence is explored supporting the hypothesis that ncRNAs contribute to epigenetic landscapes fostering eusocial traits through genomic regulation. They are likely to play an important role in eusociality "point of no return". Critical analysis is provided on the functional insights garnered from ncRNA profiles correlated with caste-specific phenotypes, specifical for phylogenetic branches and transitional sociality models, drawing from comparative genomics and transcriptomics studies. Overall, ncRNA provides a missed understanding of both "genetic toolkit" and "unique genes" hypotheses of eusociality development. Moreover, it points to gaps in current knowledge, advocating for integrative approaches combining genomics, proteomics, and epigenetics to decipher the complexity of eusociality. Understanding the ncRNA contributions offers not only a window into the molecular intricacies of Hymenoptera sociality but also extends our comprehension of how complex biological systems evolve and function.

Postsynaptic lncRNA Sera/Pkm2 pathway orchestrates the transition from social competition to rank by remodeling the neural ensemble in mPFC

Individuals' continuous success in competitive interactions with conspecifics strongly affects their social hierarchy. Medial prefrontal cortex (mPFC) is the key brain region mediating both social competition and hierarchy. However, the molecular regulatory mechanisms underlying the neural ensemble in the mPFC remains unclear. Here, we demonstrate that in excitatory neurons of prelimbic cortex (PL), lncRNA Sera remodels the utilization of Pkm Exon9 and Exon10, resulting in a decrease in the Pkm1/2 ratio in highly competitive mice. By employing a tet-on/off system, we disrupt or rebuild the normal Pkm1/2 ratio by controlling the expression of Pkm2 in PL excitatory neurons. We find that long-term Pkm2 modulation induces timely competition alteration and hysteretic rank change, through phosphorylating the Ser845 site of GluA1. Together, this study uncovers a crucial role of lncRNA Sera/Pkm2 pathway in the transition of social competition to rank by remodeling neural ensemble in mPFC.

Alternative splicing and environmental adaptation in wild house mice

A major goal of evolutionary genetics is to understand the genetic and molecular mechanisms underlying adaptation. Previous work has established that changes in gene regulation may contribute to adaptive evolution, but most studies have focused on mRNA abundance and only a few studies have investigated the role of post-transcriptional processing. Here, we use a combination of exome sequences and short-read RNA-Seq data from wild house mice (Mus musculus domesticus) collected along a latitudinal transect in eastern North America to identify candidate genes for local adaptation through alternative splicing. First, we identified alternatively spliced transcripts that differ in frequency between mice from the northern-most and southern-most populations in this transect. We then identified the subset of these transcripts that exhibit clinal patterns of variation among all populations in the transect. Finally, we conducted association studies to identify cis-acting splicing quantitative trait loci (cis-sQTL), and we identified cis-sQTL that overlapped with previously ascertained targets of selection from genome scans. Together, these analyses identified a small set of alternatively spliced transcripts that may underlie environmental adaptation in house mice. Many of these genes have known phenotypes associated with body size, a trait that varies clinally in these populations. We observed no overlap between these genes and genes previously identified by changes in mRNA abundance, indicating that alternative splicing and changes in mRNA abundance may provide separate molecular mechanisms of adaptation.

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.

Putting hornets on the genomic map

Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets, Vespa crabro and Vespa velutina. We compare their genomes with those of other social Hymenoptera, including the northern giant hornet Vespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges. Vespa crabro has experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.

Honey bee functional genomics using symbiont-mediated RNAi

Honey bees are indispensable pollinators and model organisms for studying social behavior, development and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. Most functional genomics studies in bees currently utilize double-stranded RNA (dsRNA) injection or feeding to induce RNAi-mediated knockdown of a gene of interest. However, dsRNA injection is laborious and harmful, and dsRNA feeding is difficult to scale cheaply. Further, both methods require repeated dsRNA administration to ensure a continued RNAi response. To fill this gap, we engineered the bee gut bacterium Snodgrassella alvi to induce a sustained host RNA interference response that reduces expression of a targeted gene. To employ this functional genomics using engineered symbionts (FUGUES) procedure, a dsRNA expression plasmid is cloned in Escherichia coli using Golden Gate assembly and then transferred to S. alvi. Adult worker bees are then colonized with engineered S. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by 5 d after colonization. This protocol can be accomplished in 4 weeks by bee researchers with microbiology and molecular cloning skills. FUGUES currently offers a streamlined and scalable approach for studying the biology of honey bees. Engineering other microbial symbionts to influence their hosts in ways that are similar to those described in this protocol may prove useful for studying additional insect and animal species in the future.

Alternative splicing as a source of phenotypic diversity

A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.

Detection of alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) in association with eCry3.1Ab resistance using RNA-seq and PacBio Iso-Seq

Alternative splicing is a common feature in eukaryotes that not only increases the transcript diversity, but also has functional consequences. In insects, alternative splicing has been found associated with resistance to pesticides and Bt toxins. Up to date, the alternative splicing in western corn rootworm (Diabrotica virgifera virgifera LeConte) has not been studied. To investigate its alternative splicing pattern and relation to Bt resistance, we carried out single-molecule real-time (SMRT) transcript sequencing and Iso-seq analysis on resistant, eCry3.1Ab-selected and susceptible, unselected, western corn rootworm neonate midguts which fed on seedling maize with and without eCry3.1Ab for 12 and 24 h. We present transcriptome-wide alternative splicing patterns of western corn rootworm midgut in response to feeding on eCry3.1Ab-expressing corn using a comprehensive approach that combines both RNA-seq and SMRT transcript sequencing techniques. The results showed genes in western corn rootworm are highly alternatively spliced, which happens on 67.73% of multi-exon genes. One of the alternative splicing events we identified was a novel peritrophic matrix protein with two alternative splicing isoforms. Analysis of differential exon usage between resistant and susceptible colonies showed that in eCry3.1Ab-resistant western corn rootworm, expression of one isoform was significantly higher than in the susceptible colony, while no significant differences between colonies were observed with the other isoform. Our results provide the first survey of alternative splicing in western corn rootworm and suggest that the observed alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.

Pheromonal Regulation of the Reproductive Division of Labor in Social Insects

The reproductive altruism in social insects is an evolutionary enigma that has been puzzling scientists starting from Darwin. Unraveling how reproductive skew emerges and maintains is crucial to understand the reproductive altruism involved in the consequent division of labor. The regulation of adult worker reproduction involves conspecific inhibitory signals, which are thought to be chemical signals by numerous studies. Despite the primary identification of few chemical ligands, the action modes of primer pheromones that regulate reproduction and their molecular causes and effects remain challenging. Here, these questions were elucidated by comprehensively reviewing recent advances. The coordination with other modalities of queen pheromones (QPs) and its context-dependent manner to suppress worker reproduction were discussed under the vast variation and plasticity of reproduction during colony development and across taxa. In addition to the effect of QPs, special attention was paid to recent studies revealing the regulatory effect of brood pheromones. Considering the correlation between pheromone and hormone, this study focused on the production and perception of pheromones under the endocrine control and highlighted the pivotal roles of nutrition-related pathways. The novel chemicals and gene pathways discovered by recent works provide new insights into the understanding of social regulation of reproductive division of labor in insects.

Evidence of capacitation in the parasitoid wasp, Nasonia vitripennis, and its potential role in sex allocation

The allocation of resources to the production of one sex or another has been observed in a large variety of animals. Its theoretical basis allows accurate predictions of offspring sex ratios in many species, but the mechanisms by which sex allocation is controlled are poorly understood. Using previously published data, we investigated whether alternative splicing, combined with differential gene expression, was involved with sex allocation in the parasitoid wasp, Nasonia vitripennis. We found that sex allocation is not controlled by alternative splicing but changes in gene and transcript-specific expression, which were identified to be involved with oviposition, were shown to be similar to those involved in sperm motility and capacitation. Genes involved in cholesterol efflux, a key component of capacitation, along with calcium transport, neurotransmission, trypsin, and MAPKinase activity were regulated in ovipositing wasps. The results show evidence for regulation of sperm motility and of capacitation in an insect which, in the context of the physiology of the N. vitripennis spermatheca, could be important for sex allocation.

Leveraging technological innovations to investigate evolutionary transitions to eusociality

The study of the major transition to eusociality presents several challenges to researchers, largely resulting from the importance of complex behavioral phenotypes and the shift from individual to group level selection. These challenges are being met with corresponding technological improvements. Advances in resource development for non-model taxa, behavioral tracking, nucleic acid sequencing, and reverse genetics are facilitating studies of hypotheses that were previously intractable. These innovations are resulting in the development of new model systems tailored to the exploration of specific behavioral phenotypes and the querying of underlying molecular mechanisms that drive eusocial behaviors. Here, we present a brief overview of how methodological innovations are advancing our understanding of the evolution of eusociality.

Social Parasitism in the Honeybee (Apis mellifera) Is Not Controlled by a Single SNP

The Cape bee (Apis mellifera capensis) is a subspecies of the honeybee, in which workers commonly lay diploid unfertilized eggs via a process known as thelytoky. A recent study aimed to map the genetic basis of this trait in the progeny of a single capensis queen where workers laid either diploid (thelytokous) or haploid (arrhenotokous) eggs. A nonsynonymous single nucleotide polymorphism (SNP) in a gene of unknown function was reported to be strongly associated with thelytoky in this colony. Here, we analyze genome sequences from a global sample of A. mellifera and identify populations where the proposed thelytoky allele at this SNP is common but thelytoky is absent. We also analyze genome sequences of three capensis queens produced by thelytoky and find that, contrary to predictions, they do not carry the proposed thelytoky allele. The proposed SNP is therefore neither sufficient nor required to produce thelytoky in A. mellifera.

Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera

RNA-seq has proven to be a powerful tool to unravel various aspects of the transcriptome, especially the quantification of alternative splicing (AS) that leads to isoform diversity. The honey bee (Apis mellifera) is an important model organism for studying the molecular underpinnings of behavioral plasticity and social behavior, and recent RNA-seq studies of honey bees have revealed AS patterns and their regulation by DNA methylation. However, tissue-specific AS patterns have not been fully explored. In this paper, we characterized AS patterns in two different honey bee tissue types, and also explored their conservation and regulation. We used the RNA-seq data from brain and fat body to improve the existing models of honey bee genes and identified tissue-specific AS patterns. We found that AS genes show high conservation between honey bee and Drosophila melanogaster. We also confirmed and extended previous findings of a correlation between gene body DNA methylation and AS patterns, providing further support for the role of DNA methylation in regulating AS. In addition, our analysis suggests distinct functional roles for tissue-specific alternatively spliced genes. Taken together, our work provides new insights into the conservation and dynamics of AS patterns across different tissue types.

A Single SNP Turns a Social Honey Bee (Apis mellifera) Worker into a Selfish Parasite

The evolution of altruism in complex insect societies is arguably one of the major transitions in evolution and inclusive fitness theory plausibly explains why this is an evolutionary stable strategy. Yet, workers of the South African Cape honey bee (Apis mellifera capensis) can reverse to selfish behavior by becoming social parasites and parthenogenetically producing female offspring (thelytoky). Using a joint mapping and population genomics approach, in combination with a time-course transcript abundance dynamics analysis, we show that a single nucleotide polymorphism at the mapped thelytoky locus (Th) is associated with the iconic thelytokous phenotype. Th forms a linkage group with the ecdysis-triggering hormone receptor (Ethr) within a nonrecombining region under strong selection in the genome. A balanced detrimental allele system plausibly explains why the trait is specific to A. m. capensis and cannot easily establish itself into genomes of other honey bee subspecies.

Sex loss in insects: causes of asexuality and consequences for genomes

Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.

Diverse Factors Affecting Efficiency of RNAi in Honey Bee Viruses

Infection and transmission of honey bee viruses pose a serious threat to the pollination services of crops and wild plants, which plays a vital role in agricultural economy and ecology. RNA interference (RNAi) is an effective defense mechanism against commonly occurring viral infections of animals and plants. However, recent studies indicate that the effects of RNAi on the honey bee can induce additional impacts and might not always be effective in suppressing the virus. Moreover, the RNAi responses differed in relation to the developmental stage of the insect and the target tissue used, even though the same method of delivery was used. These results indicate that further analysis and field experiments should be performed to characterize the varying effectiveness of RNAi-based methods for treating honey bee viral infections. In this review, we provide an overview of the current knowledge and the recent progress in RNAi-based anti-viral treatments for honey bees, focusing in particular highlight the role of the dsRNA-delivery method used and its effect on RNAi efficiency and demonstrate the potential practical value of this tool for controlling the virus. We conclude studying the gene function and disease control of honey bee by RNAi technology requires a complex consideration from physiology, genetics to environment.

Reproductive parasitism by worker honey bees suppressed by queens through regulation of worker mandibular secretions

Social cohesion in social insect colonies can be achieved through the use of chemical signals whose production is caste-specific and regulated by social contexts. In honey bees, queen mandibular gland pheromones (QMP) maintain reproductive dominance by inhibiting ovary activation and production of queen-like mandibular gland signals in workers. We investigated whether honey bee queens can control reproductively active workers of the intraspecific social parasite Apis mellifera capensis, parasitising A. m. scutellata host colonies. Our results show that the queen’s QMP suppresses ovarian activation and inhibits the production of QMP pheromone signals by the parasitic workers, achieved through differential expression of enzymes involved in the biosynthesis of these pheromones at two points in the biosynthetic pathway. This is the first report showing that honey bee queens can regulate reproduction in intraspecific social parasites and deepens our understanding of the molecular mechanisms involved in the regulation of worker reproduction in social insects.

Building a new research framework for social evolution: intralocus caste antagonism

The breeding and non‐breeding ‘castes’ of eusocial insects provide a striking example of role‐specific selection, where each caste maximises fitness through different morphological, behavioural and physiological trait values. Typically, queens are long‐lived egg‐layers, while workers are short‐lived, largely sterile foragers. Remarkably, the two castes are nevertheless produced by the same genome. The existence of inter‐caste genetic correlations is a neglected consequence of this shared genome, potentially hindering the evolution of caste dimorphism: alleles that increase the productivity of queens may decrease the productivity of workers and vice versa, such that each caste is prevented from reaching optimal trait values. A likely consequence of this ‘intralocus caste antagonism’ should be the maintenance of genetic variation for fitness and maladaptation within castes (termed ‘caste load’), analogous to the result of intralocus sexual antagonism. The aim of this review is to create a research framework for understanding caste antagonism, drawing in part upon conceptual similarities with sexual antagonism. By reviewing both the social insect and sexual antagonism literature, we highlight the current empirical evidence for caste antagonism, discuss social systems of interest, how antagonism might be resolved, and challenges for future research. We also introduce the idea that sexual and caste antagonism could interact, creating a three‐way antagonism over gene expression. This includes unpacking the implications of haplodiploidy for the outcome of this complex interaction.

Glandular sources of pheromones used to control host workers (Apis mellifera scutellata) by socially parasitic workers of Apis mellifera capensis

Pheromonal control by the honey bee queen is achieved through the use of secretions from diverse glandular sources, but the use of pheromones from a variety of glandular sources by reproductively dominant workers, has not previously been explored. Using the social parasite, Apis mellifera capensis clonal worker we studied the diversity of glandular sources used for pheromonal control of reproductively subordinate A. m. scutellata workers. To determine whether pheromones from different glandular sources are used by reproductively active workers to achieve dominance and evaluate the degree of pheromonal competition between workers of the two sub-species, we housed groups of workers of the two sub-species together in cages and analysed mandibular and tergal gland secretions as well as, ovarian activation status of each worker after 21days. The results showed that A. m. capensis invasive clones used both mandibular and tergal gland secretions to achieve reproductive dominance and suppress ovarian activation in their A. m. scutellata host workers. The reproductively dominant workers (false queens) produced more queen-like pheromones and inhibited ovarian activation in subordinate A. m. scutellata workers. These results show that tergal gland pheromones working in synergy with pheromones from other glands allow individual workers (false queens) to establish reproductive dominance within these social groups and to act in a manner similar to that of queens. Thus suggesting that, the evolution of reproductively dominant individuals (queens or false queens) and subordinate individuals (workers) in social insects like the honey bee is the result of a complex interplay of pheromonal signals from different exocrine glands.

The honeybee as a model insect for developmental genetics

Honeybees are an important component of modern agricultural systems, and a fascinating and scientifically engrossing insect. Honeybees are not commonly used as model systems for understanding development in insects despite their importance in agriculture. Honeybee embryogenesis, while being superficially similar to Drosophila, is molecularly very different, especially in axis formation and sex determination. In later development, much of honeybee biology is modified by caste development, an as yet poorly understood, but excellent, system to study developmental plasticity. In adult stages, developmental plasticity of the ovaries, related to reproductive constraint exhibits another aspect of plasticity. Here they review the tools, current knowledge and opportunities in honeybee developmental biology, and provide an updated embryonic staging scheme to support future studies.

Negligible uptake and transfer of diet-derived pollen microRNAs in adult honey bees

The putative transfer and gene regulatory activities of diet-derived miRNAs in ingesting animals are still debated. Importantly, no study to date has fully examined the role of dietary uptake of miRNA in the honey bee, a critical pollinator in both agricultural and natural ecosystems. After controlled pollen feeding experiments in adult honey bees, we observed that midguts demonstrated robust increases in plant miRNAs after pollen ingestion. However, we found no evidence of biologically relevant delivery of these molecules to proximal or distal tissues of recipient honey bees. Our results, therefore, support the premise that pollen miRNAs ingested as part of a typical diet are not robustly transferred across barrier epithelia of adult honey bees under normal conditions. Key future questions include whether other small RNA species in honey bee diets behave similarly and whether more specialized and specific delivery mechanisms exist for more efficient transport, particularly in the context of stressed barrier epithelia.

Notch signalling mediates reproductive constraint in the adult worker honeybee

The hallmark of eusociality is the reproductive division of labour, in which one female caste reproduces, while reproduction is constrained in the subordinate caste. In adult worker honeybees (Apis mellifera) reproductive constraint is conditional: in the absence of the queen and brood, adult worker honeybees activate their ovaries and lay haploid male eggs. Here, we demonstrate that chemical inhibition of Notch signalling can overcome the repressive effect of queen pheromone and promote ovary activity in adult worker honeybees. We show that Notch signalling acts on the earliest stages of oogenesis and that the removal of the queen corresponds with a loss of Notch protein in the germarium. We conclude that the ancient and pleiotropic Notch signalling pathway has been co-opted into constraining reproduction in worker honeybees and we provide the first molecular mechanism directly linking ovary activity in adult worker bees with the presence of the queen.

In honeybees, pheromones produced by the queen inhibit reproduction by workers and enforce a eusocial division of labour. Here, Duncan, Hyink and Dearden show that this inhibition is mediated by the Notch signalling pathway in the workers' ovaries.

Ties between ageing plasticity and reproductive physiology in honey bees (Apis mellifera) reveal a positive relation between fecundity and longevity as consequence of advanced social evolution

Honey bees (Apis mellifera) are the best studied model of ageing among the social insects. As in other social insects, the reproductive queen far outlives her non-reproductive workers despite developing from the same genome in the same colony environment. Thus, the different social roles of the two female castes are critical for the profound phenotypic plasticity. In several special cases, such as the reproductive workers of Apis mellifera capensis, within-caste plasticity enables further studies of the fecundity-longevity syndrome in honey bees. At present, molecular evidence suggests that a reorganization of physiological control pathways may facilitate longevity of reproductive individuals. However, the social role and social environment of the different colony members are also very important and one of the key future questions is how much social facilitation versus internal regulation is responsible for the positive association between fecundity and longevity in honey bees.

Identification of Multiple Loci Associated with Social Parasitism in Honeybees

In colonies of the honeybee Apis mellifera, the queen is usually the only reproductive female, which produces new females (queens and workers) by laying fertilized eggs. However, in one subspecies of A. mellifera, known as the Cape bee (A. m. capensis), worker bees reproduce asexually by thelytoky, an abnormal form of meiosis where two daughter nucleii fuse to form single diploid eggs, which develop into females without being fertilized. The Cape bee also exhibits a suite of phenotypes that facilitate social parasitism whereby workers lay such eggs in foreign colonies so their offspring can exploit their resources. The genetic basis of this switch to social parasitism in the Cape bee is unknown. To address this, we compared genome variation in a sample of Cape bees with other African populations. We find genetic divergence between these populations to be very low on average but identify several regions of the genome with extreme differentiation. The regions are strongly enriched for signals of selection in Cape bees, indicating that increased levels of positive selection have produced the unique set of derived phenotypic traits in this subspecies. Genetic variation within these regions allows unambiguous genetic identification of Cape bees and likely underlies the genetic basis of social parasitism. The candidate loci include genes involved in ecdysteroid signaling and juvenile hormone and dopamine biosynthesis, which may regulate worker ovary activation and others whose products localize at the centrosome and are implicated in chromosomal segregation during meiosis. Functional analysis of these loci will yield insights into the processes of reproduction and chemical signaling in both parasitic and non-parasitic populations and advance understanding of the process of normal and atypical meiosis.

Knockdown of juvenile hormone acid methyl transferase severely affects the performance of Leptinotarsa decemlineata (Say) larvae and adults

BACKGROUND

Juvenile hormone (JH) plays a critical role in the regulation of metamorphosis in Leptinotarsa decemlineata, a notorious defoliator of potato. JH acid methyltransferase (JHAMT) is involved in one of the final steps of JH biosynthesis.

RESULTS

A putative JHAMT cDNA (LdJHAMT) was cloned. Two double-stranded RNAs (dsRNAs) (dsJHAMT1 and dsJHAMT2) against LdJHAMT were constructed and bacterially expressed. Experiments were conducted to investigate the effectiveness of RNAi in both second- and fourth-instar larvae. Dietary introduction of dsJHAMT1 and dsJHAMT2 successfully knocked down the target gene, lowered JH titre in the haemolymph and reduced the transcript of Krüppel homologue 1 gene. Ingestion of dsJHAMT caused larval death and weight loss, shortened larval developmental period and impaired pupation. Moreover, the dsJHAMT-fed pupae exhibited lower adult emergence rates. The resulting adults weighed an average of 50 mg less than the control group, and the females did not deposit eggs. Application of pyriproxyfen to the dsJHAMT-fed insects rescued all the negative effects.

CONCLUSIONS

LdJHAMT expresses functional JHAMT enzyme. The RNAi targeting LdJHAMT could be used for control of L. decemlineata. © 2015 Society of Chemical Industry.

RNAi and Antiviral Defense in the Honey Bee

Honey bees play an important agricultural and ecological role as pollinators of numerous agricultural crops and other plant species. Therefore, investigating the factors associated with high annual losses of honey bee colonies in the US is an important and active area of research. Pathogen incidence and abundance correlate with Colony Collapse Disorder- (CCD-) affected colonies in the US and colony losses in the US and in some European countries. Honey bees are readily infected by single-stranded positive sense RNA viruses. Largely dependent on the host immune response, virus infections can either remain asymptomatic or result in deformities, paralysis, or death of adults or larvae. RNA interference (RNAi) is an important antiviral defense mechanism in insects, including honey bees. Herein, we review the role of RNAi in honey bee antiviral defense and highlight some parallels between insect and mammalian immune systems. A more thorough understanding of the role of pathogens on honey bee health and the immune mechanisms bees utilize to combat infectious agents may lead to the development of strategies that enhance honey bee health and result in the discovery of additional mechanisms of immunity in metazoans.

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

Alternative Splice in Alternative Lice

Genomic and transcriptomics analyses have revealed human head and body lice to be almost genetically identical; although con-specific, they nevertheless occupy distinct ecological niches and have differing feeding patterns. Most importantly, while head lice are not known to be vector competent, body lice can transmit three serious bacterial diseases; epidemictyphus, trench fever, and relapsing fever. In order to gain insights into the molecular bases for these differences, we analyzed alternative splicing (AS) using next-generation sequencing data for one strain of head lice and one strain of body lice. We identified a total of 3,598 AS events which were head or body lice specific. Exon skipping AS events were overrepresented among both head and body lice, whereas intron retention events were underrepresented in both. However, both the enrichment of exon skipping and the underrepresentation of intron retention are significantly stronger in body lice compared with head lice. Genes containing body louse-specific AS events were found to be significantly enriched for functions associated with development of the nervous system, salivary gland, trachea, and ovarian follicle cells, as well as regulation of transcription. In contrast, no functional categories were overrepresented among genes with head louse-specific AS events. Together, our results constitute the first evidence for transcript pool differences in head and body lice, providing insights into molecular adaptations that enabled human lice to adapt to clothing, and representing a powerful illustration of the pivotal role AS can play in functional adaptation.

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq

Alternative splicing is an important biological process in the generation of multiple functional transcripts from the same genomic sequences. Differential analysis of splice junctions (SJs) and intron retentions (IRs) is helpful in the detection of alternative splicing events. In this study, we conducted differential analysis of SJs and IRs by use of DEXSeq, a Bioconductor package originally designed for differential exon usage analysis in RNA-seq data analysis. We set up an analysis pipeline including mapping of RNA-seq reads, the preparation of count tables of SJs and IRs as the input files, and the differential analysis in DEXSeq. We analyzed the public RNA-seq datasets generated from RNAi experiments on Drosophila melanogaster S2-DRSC cells to deplete RNA-binding proteins (GSE18508). The analysis confirmed previous findings on the alternative splicing of the trol and Ant2 (sesB) genes in the CG8144 (ps)-depletion experiment and identified some new alternative splicing events in other RNAi experiments. We also identified IRs that were confirmed in our SJ analysis. The proposed method used in our study can output the genomic coordinates of differentially used SJs and thus enable sequence motif search. Sequence motif search and gene function annotation analysis helped us infer the underlying mechanism in alternative splicing events. To further evaluate this method, we also applied the method to public RNA-seq data from human breast cancer (GSE45419) and the plant Arabidopsis (SRP008262). In conclusion, our study showed that DEXSeq can be adapted to differential analysis of SJs and IRs, which will facilitate the identification of alternative splicing events and provide insights into the molecular mechanisms of transcription processes and disease development.

Allele specific expression in worker reproduction genes in the bumblebee Bombus terrestris

Methylation has previously been associated with allele specific expression in ants. Recently, we found methylation is important in worker reproduction in the bumblebee Bombus terrestris. Here we searched for allele specific expression in twelve genes associated with worker reproduction in bees. We found allele specific expression in Ecdysone 20 monooxygenase and IMP-L2-like. Although we were unable to confirm a genetic or epigenetic cause for this allele specific expression, the expression patterns of the two genes match those predicted for imprinted genes.

Inheritance of thelytoky in the honey bee Apis mellifera capensis

Asexual reproduction via thelytokous parthenogenesis is widespread in the Hymenoptera, but its genetic underpinnings have been described only twice. In the wasp Lysiphlebus fabarum and the Cape honey bee Apis mellifera capensis the origin of thelytoky have each been traced to a single recessive locus. In the Cape honey bee it has been argued that thelytoky (th) controls the thelytoky phenotype and that a deletion of 9 bp in the flanking intron downstream of exon 5 (tae) of the gemini gene switches parthenogenesis from arrhenotoky to thelytoky. To further explore the mode of inheritance of thelytoky, we generated reciprocal backcrosses between thelytokous A. m. capensis and the arrhenotokous A. m. scutellata. Ten genetic markers were used to identify 108 thelytokously produced offspring and 225 arrhenotokously produced offspring from 14 colonies. Patterns of appearance of thelytokous parthenogenesis were inconsistent with a single locus, either th or tae, controlling thelytoky. We further show that the 9 bp deletion is present in the arrhenotokous A. m. scutellata population in South Africa, in A. m. intermissa in Morocco and in Africanized bees from Brazil and Texas, USA, where thelytoky has not been reported. Thus the 9  p deletion cannot be the cause of thelytoky. Further, we found two novel tae alleles. One contains the previously described 9 bp deletion and an additional deletion of 7 bp nearby. The second carries a single base insertion with respect to the wild type. Our data are consistent with the putative th locus increasing reproductive capacity.

Differential involvement of glutamate-gated chloride channel splice variants in the olfactory memory processes of the honeybee Apis mellifera

Glutamate-gated chloride channels (GluCl) belong to the cys-loop ligand-gated ion channel superfamily and their expression had been described in several invertebrate nervous systems. In the honeybee, a unique gene amel_glucl encodes two alternatively spliced subunits, Amel_GluCl A and Amel_GluCl B. The expression and differential localization of those variants in the honeybee brain had been previously reported. Here we characterized the involvement of each variant in olfactory learning and memory processes, using specific small-interfering RNA (siRNA) targeting each variant. Firstly, the efficacy of the two siRNAs to decrease their targets' expression was tested, both at mRNA and protein levels. The two proteins showed a decrease of their respective expression 24h after injection. Secondly, each siRNA was injected into the brain to test whether or not it affected olfactory memory by using a classical paradigm of conditioning the proboscis extension reflex (PER). Amel_GluCl A was found to be involved only in retrieval of 1-nonanol, whereas Amel_GluCl B was involved in the PER response to 2-hexanol used as a conditioned stimulus or as new odorant. Here for the first time, a differential behavioral involvement of two highly similar GluCl subunits has been characterized in an invertebrate species.

The dietary proportion of essential amino acids and Sir2 influence lifespan in the honeybee

Dietary essential amino acids have an important influence on the lifespan and fitness of animals. The expression of the NAD(+)-dependent histone deacetylase, Sir2, can be influenced by diet, but its role in the extension of lifespan has recently been challenged. Here, we used the honeybee to test how the dietary balance of carbohydrates and essential amino acids and/or Sir2 affected lifespan. Using liquid diets varying in their ratio of essential amino acids to carbohydrate (EAA:C), we found that adult worker bees fed diets high in essential amino acids (≥1:10) had shorter lifespans than bees fed diets containing low levels of dietary amino acids. Bees fed a 1:500 EAA:C diet lived longer and, in contrast to bees fed any of the other diets, expressed Sir2 at levels tenfold higher or more than bees fed a 1:5 EAA:C diet. When bees were fed the 1:500 diet, small interfering RNA (siRNA)-mediated knock-down of Sir2 expression shortened lifespan but did not reduce survival to the same extent as the 1:5 diet, indicating that Sir2 contributes to mechanisms that determine lifespan in response to differences in macronutrient intake but is not the sole determinant. These data show that the ratio of dietary amino acids to carbohydrate influences Sir2 expression and clearly demonstrate that Sir2 is one of the factors that can determine honeybee lifespan. We propose that effects of dietary amino acids and Sir2 on lifespan may depend on the simultaneous activation of multiple nutrient sensors that respond to relative levels of essential amino acids and carbohydrates.

dsRNA uptake and persistence account for tissue-dependent susceptibility to RNA interference in the migratory locust, Locusta migratoria

RNA interference (RNAi) by introducing double-stranded RNA (dsRNA) is a powerful approach to the analysis of gene function in insects; however, RNAi responses vary dramatically in different insect species and tissues, and the underlying mechanisms remain poorly understood. The migratory locust, a destructive insect pest and a hemimetabolic insect with panoistic ovaries, is considered to be a highly susceptible species to RNAi via dsRNA injection, but its ovary appears to be completely insensitive. In the present study, we showed that dsRNA persisted only briefly in locust haemolymph. The ovariole sheath was permeable to dsRNA, but injected dsRNA was not present in the follicle cells and oocytes. The lack of dsRNA uptake into the follicle cells and oocytes is likely to be the primary factor that contributes to the ineffective RNAi response in locust ovaries. These observations provide insights into tissue-dependent variability of RNAi and help in achieving successful gene silencing in insensitive tissues.

Genomic analysis of the interactions between social environment and social communication systems in honey bees (Apis mellifera)

Social context is often a primary regulator of social behavior, but genes that affect or are affected by social context have rarely been investigated. In social insects, caste specific pheromones are key modulators of social behavior, e.g., in honey bees the queen mandibular gland (MG) pheromone mediates reproductive dominance, its absence prompting ovary activation and queen pheromone production in workers. Here, we investigate the effect of social environment on genome-wide expression patterns in the MG, to determine how social context modulates expression of genes that, in turn alter social environment. We used microarrays to examine the MGs of virgin and mated queens, and queenright (QR) and queenless (QL) workers with or without activated ovaries. Approximately 2554 transcripts were significantly differentially expressed among these groups, with caste and social context being the main regulators of gene expression patterns, while physiological state (ovary activation) only minimally affecting gene expression. Thus, social context strongly regulates expression of genes, which, in turn, shape social environment. Among these, 25 genes that are putatively involved in caste selective production of the fatty-acid derived MG pheromone were differentially expressed in queens and workers. These genes whose functions correspond with enzymatic or transport processes emphasize the occurrence of disparate pheromone biosynthetic pathways for queens and workers, adding another dimension regarding the regulation of these important pheromones. Gene ontology analysis also revealed genes of different functional categories whose expression was impacted by caste or by the social environment, suggesting that the MG has broader functions than pheromone biosynthesis.

Reproduction of honeybee workers is regulated by epidermal growth factor receptor signaling

Eusocial insect societies display a remarkable reproductive division of labor between a single fertile queen and thousands of largely sterile workers. In most species, however, the workers retain the capacity to reproduce, particularly in queenless colonies where typically many workers lay eggs. As yet, the molecular determinants that initiate this shift in worker fertility are still poorly documented. By using RNA interference we here demonstrate that the knockdown of epidermal growth factor receptor, a gene which was previously shown to be involved in queen-worker caste differentiation, also induces reproduction in worker honeybees (Apis mellifera). These data show that worker fertility and queen-worker caste determination partly rely on the same gene regulatory networks, thereby providing a major breakthrough in our understanding of the molecular determinants of the social insects' spectacular reproductive division of labor.

Did the fire ant supergene evolve selfishly or socially?

The genetic basis for animal social organization is poorly understood. Fire ants provide one of the rare cases where variation in social organization has been demonstrated to be under genetic control, which amazingly, segregates as a single Mendelian locus. A recent genetic, genomic, and cytological analysis revealed that this locus actually consists of over 600 genes locked together in a supergene that possesses many characteristics of sex chromosomes. The fire ant social supergene also behaves selfishly, and an interesting evolutionary question is whether the genes incorporated first into the social supergene were those for social adaptation, selfish genetic drive, or something else. In depth, functional molecular genetic analysis in fire ants and comparative genomics in other closely related socially polymorphic species will be required to resolve this question.

Caste load and the evolution of reproductive skew

Reproductive skew theory seeks to explain how reproduction is divided among group members in animal societies. Existing theory is framed almost entirely in terms of selection, though nonadaptive processes must also play some role in the evolution of reproductive skew. Here I propose that a genetic correlation between helper fecundity and breeder fecundity may frequently constrain the evolution of reproductive skew. This constraint is part of a wider phenomenon that I term "caste load," which is defined as the decline in mean fitness caused by caste-specific selection pressures, that is, differential selection on breeding and nonbreeding individuals. I elaborate the caste load hypothesis using quantitative and population genetic arguments and individual-based simulations. Although selection can sometimes erode genetic correlations and resolve caste load, this may be constrained when mutations have similar pleiotropic effects on breeder and helper traits. I document evidence for caste load, identify putative genomic adaptations to it, and suggest future research directions. The models highlight the value of considering adaptation within the boundaries imposed by genetic architecture and incidentally reaffirm that monogamy promotes the evolutionary transition to eusociality.

Characterisation of the RNA interference response against the long-wavelength receptor of the honeybee

Targeted knock-down is the method of choice to advance the study of sensory and brain functions in the honeybee by using molecular techniques. Here we report the results of a first attempt to interfere with the function of a visual receptor, the long-wavelength-sensitive (L-) photoreceptor. RNA interference to inhibit this receptor led to a reduction of the respective mRNA and protein. The interference effect was limited in time and space, and its induction depended on the time of the day most probably because of natural daily variations in opsin levels. The inhibition did not effectively change the physiological properties of the retina. Possible constraints and implications of this method for the study of the bee's visual system are discussed. Overall this study underpins the usefulness and feasibility of RNA interference as manipulation tool in insect brain research.

Control of neuronal voltage-gated calcium ion channels from RNA to protein

Voltage-gated calcium ion (CaV) channels convert neuronal activity into rapid intracellular calcium signals to trigger a myriad of cellular responses. Their involvement in major neurological and psychiatric diseases, and importance as therapeutic targets, has propelled interest in subcellular-specific mechanisms that align CaV channel activity to specific tasks. Here, we highlight recent studies that delineate mechanisms controlling the expression of CaV channels at the level of RNA and protein. We discuss the roles of RNA editing and alternative pre-mRNA splicing in generating CaV channel isoforms with activities specific to the demands of individual cells; the roles of ubiquitination and accessory proteins in regulating CaV channel expression; and the specific binding partners that contribute to both pre- and postsynaptic CaV channel function.

Origin and function of the major royal jelly proteins of the honeybee (Apis mellifera) as members of the yellow gene family

In the honeybee, Apis mellifera, the queen larvae are fed with a diet exclusively composed of royal jelly (RJ), a secretion of the hypopharyngeal gland of young worker bees that nurse the brood. Up to 15% of RJ is composed of proteins, the nine most abundant of which have been termed major royal jelly proteins (MRJPs). Although it is widely accepted that RJ somehow determines the fate of a female larva and in spite of considerable research efforts, there are surprisingly few studies that address the biochemical characterisation and functions of these MRJPs. Here we review the research on MRJPs not only in honeybees but in hymenopteran insects in general and provide metadata analyses on genome organisation of mrjp genes, corroborating previous reports that MRJPs have important functions for insect development and not just a nutritional value for developing honeybee larvae.

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.

TrueSight: a new algorithm for splice junction detection using RNA-seq

RNA-seq has proven to be a powerful technique for transcriptome profiling based on next-generation sequencing (NGS) technologies. However, due to the short length of NGS reads, it is challenging to accurately map RNA-seq reads to splice junctions (SJs), which is a critically important step in the analysis of alternative splicing (AS) and isoform construction. In this article, we describe a new method, called TrueSight, which for the first time combines RNA-seq read mapping quality and coding potential of genomic sequences into a unified model. The model is further utilized in a machine-learning approach to precisely identify SJs. Both simulations and real data evaluations showed that TrueSight achieved higher sensitivity and specificity than other methods. We applied TrueSight to new high coverage honey bee RNA-seq data to discover novel splice forms. We found that 60.3% of honey bee multi-exon genes are alternatively spliced. By utilizing gene models improved by TrueSight, we characterized AS types in honey bee transcriptome. We believe that TrueSight will be highly useful to comprehensively study the biology of alternative splicing.

Thelytokous parthenogenesis in eusocial Hymenoptera

Female parthenogenesis, or thelytoky, is particularly common in solitary Hymenoptera. Only more recently has it become clear that many eusocial species also regularly reproduce thelytokously, and here we provide a comprehensive overview. Especially in ants, thelytoky underlies a variety of idiosyncratic life histories with unique evolutionary and ecological consequences. In all eusocial species studied, thelytoky probably has a nuclear genetic basis and the underlying cytological mechanism retains high levels of heterozygosity. This is in striking contrast to many solitary wasps, in which thelytoky is often induced by cytoplasmic bacteria and results in an immediate loss of heterozygosity. These differences are likely related to differences in haplodiploid sex determination mechanisms, which in eusocial species usually require heterozygosity for female development. At the same time, haplodiploidy might account for important preadaptations that can help explain the apparent ease with which Hymenoptera transition between sexual and asexual reproduction.

Understanding the relationship between brain gene expression and social behavior: lessons from the honey bee

Behavior is a complex phenotype that is plastic and evolutionarily labile. The advent of genomics has revolutionized the field of behavioral genetics by providing tools to quantify the dynamic nature of brain gene expression in relation to behavioral output. The honey bee Apis mellifera provides an excellent platform for investigating the relationship between brain gene expression and behavior given both the remarkable behavioral repertoire expressed by members of its intricate society and the degree to which behavior is influenced by heredity and the social environment. Here, we review a linked series of studies that assayed changes in honey bee brain transcriptomes associated with natural and experimentally induced changes in behavioral state. These experiments demonstrate that brain gene expression is closely linked with behavior, that changes in brain gene expression mediate changes in behavior, and that the association between specific genes and behavior exists over multiple timescales, from physiological to evolutionary.

Genetics of reproduction and regulation of honeybee (Apis mellifera L.) social behavior

Honeybees form complex societies with a division of labor for reproduction, nutrition, nest construction and maintenance, and defense. How does it evolve? Tasks performed by worker honeybees are distributed in time and space. There is no central control over behavior and there is no central genome on which selection can act and effect adaptive change. For 22 years, we have been addressing these questions by selecting on a single social trait associated with nutrition: the amount of surplus pollen (a source of protein) that is stored in the combs of the nest. Forty-two generations of selection have revealed changes at biological levels extending from the society down to the level of the gene. We show how we constructed this vertical understanding of social evolution using behavioral and anatomical analyses, physiology, genetic mapping, and gene knockdowns. We map out the phenotypic and genetic architectures of food storage and foraging behavior and show how they are linked through broad epistasis and pleiotropy affecting a reproductive regulatory network that influences foraging behavior. This is remarkable because worker honeybees have reduced reproductive organs and are normally sterile; however, the reproductive regulatory network has been co-opted for behavioral division of labor.