MicroRNA functions in insects

Epigenetics in Insects: Genome Regulation and the Generation of Phenotypic Diversity

Epigenetic inheritance is fundamentally important to cellular differentiation and developmental plasticity. In this review, we provide an introduction to the field of molecular epigenetics in insects. Epigenetic information is passed across cell divisions through the methylation of DNA, the modification of histone proteins, and the activity of noncoding RNAs. Much of our knowledge of insect epigenetics has been gleaned from a few model species. However, more studies of epigenetic information in traditionally nonmodel taxa will help advance our understanding of the developmental and evolutionary significance of epigenetic inheritance in insects. To this end, we also provide a brief overview of techniques for profiling and perturbing individual facets of the epigenome. Doing so in diverse cellular, developmental, and taxonomic contexts will collectively help shed new light on how genome regulation results in the generation of diversity in insect form and function.

MicroRNAs derived from the insect virus HzNV-1 promote lytic infection by suppressing histone methylation

Heliothis zea nudivirus-1 (HzNV-1) is an insect virus that can induce both lytic and latent infections in various insect cell lines. During latent infection, several microRNAs (miRNAs) are produced from persistency-associated gene 1 (pag1) as the only detectable HzNV-1 transcript. Previous studies have shown that the pag1 gene suppresses the immediate-early gene hhi1 and promotes host switching into a latent infection via miRNAs derived from pag1. Although other functions of the miRNAs derived from pag1 have not yet been elucidated, several studies have suggested that miRNAs encoded from latency-associated genes can regulate histone-associated enzymes. Because pag1 is a noncoding transcript, it potentially regulates host chromatin structure through miRNAs upon infection. Nevertheless, the exact mechanism by which pag1 alters viral infections remains unknown. In this study, we found that the pag1-encoded miRNA miR-420 suppresses expression of the histone modification-associated enzyme su(var)3-9. Therefore, this miRNA causes histone modification to promote HzNV-1 infection. These results suggest that HzNV-1 may directly influence epigenetic regulation in host cells through interactions with pag1 miRNAs to promote lytic infection. This study provides us with a better understanding of both the HzNV-1 infection pathway and the relationship between viral miRNAs and epigenetic regulation.

RNA interference-based antiviral immune response against the salivary gland hypertrophy virus in Glossina pallidipes

Background

Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae) is a non-occluded dsDNA virus that specifically infects the adult stages of the hematophagous tsetse flies (Glossina species, Diptera: Glossinidae). GpSGHV infections are usually asymptomatic, but unknown factors can result to a switch to acute symptomatic infection, which is characterized by the salivary gland hypertrophy (SGH) syndrome associated with decreased fecundity that can ultimately lead to a colony collapse. It is uncertain how GpSGHV is maintained amongst Glossina spp. populations but RNA interference (RNAi) machinery, a conserved antiviral defense in insects, is hypothesized to be amongst the host’s mechanisms to maintain the GpSGHV in asymptomatic (persistent or latent) infection state. Here, we investigated the involvement of RNAi during GpSGHV infections by comparing the expression of three key RNAi machinery genes, Dicer (DCR), Argonaute (AGO) and Drosha, in artificially virus injected, asymptomatic and symptomatic infected G. pallidipes flies compared to PBS injected (controls) individuals. We further assessed the impact of AGO2 knockdown on virus infection by RT-qPCR quantification of four selected GpSGHV genes, i.e. odv-e66, dnapol, maltodextrin glycosyltransferase (a tegument gene) and SGHV091 (a capsid gene).

Results

We show that in response to hemocoelic injections of GpSGHV into G. pallidipes flies, increased virus replication was accompanied by significant upregulation of the expression of three RNAi key genes; AGO1, AGO2 and DCR2, and a moderate increase in the expression of Drosha post injection compared to the PBS-injected controls. Furthermore, compared to asymptomatically infected individuals, symptomatic flies showed significant downregulation of AGO1, AGO2 and Drosha, but a moderate increase in the expression of DCR2. Compared to the controls, knockdown of AGO2 did not have a significant impact on virus infection in the flies as evidenced by unaltered transcript levels of the selected GpSGHV genes.

Conclusion

The upregulation of the expression of the RNAi genes implicate involvement of this machinery in controlling GpSGHV infections and the establishment of symptomatic GpSGHV infections in Glossina. These findings provide a strategic foundation to understand GpSGHV infections and to control latent (asymptomatic) infections in Glossina spp. and thereby control SGHVs in insect production facilities.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1298-1) contains supplementary material, which is available to authorized users.

Genome-Wide Profiling of Cardinium-Responsive MicroRNAs in the Exotic Whitefly, Bemisia tabaci (Gennadius) Biotype Q

Although the bacterial symbiont Cardinium has profound effects on the ecological adaptation of its host, the whitefly Bemisia tabaci (Gennadius) biotype Q (hereafter referred to as B. tabaci Q), the molecular mechanism underlying interactions between these two organisms is not yet fully understood. In this study, sRNA libraries were constructed, amplified, and sequenced for Cardinium-infected (C⁺) and uninfected (C^∗−) B. tabaci Q with identical genetic backgrounds. Subsequently, the genes targeted by the differentially expressed miRNAs were predicted by integrating the B. tabaci Q genome data. A total of 125 known and 100 novel miRNAs were identified, among which 23 significant differentially expressed miRNAs were identified in both libraries. It is noteworthy that an analysis of target genes showed that Cardinium-responsive miRNA-regulated genes were functional in apoptosis, reproduction, development, immune response, thermotolerance and insecticide resistance. GO and KEGG pathway analysis revealed that some miRNA-target genes are closely associated with energy metabolism. A major finding of this study was the identification of several miRNAs that may be involved in physiological processes in response to environmental stress, i.e., insecticides and high temperatures. This information will provide a foundation to help further elucidate the functions of Cardinium in B. tabaci Q.

Expressing MicroRNA Bantam Sponge Drastically Improves the Insecticidal Activity of Baculovirus via Increasing the Level of Ecdysteroid Hormone in Spodoptera exigua Larvae

Bantam is a conserved miRNA highly expressed in insects. We previously showed that the antisense inhibitor (antagomiR) of bantam improved the infection by baculovirus Autographa californica nucleopolyhedrovirus (AcMNPV) in Spodoptera exigua and S. litura larvae. Here, we constructed a recombinant AcMNPV (vPH-banS) expressing bantam sponge, an mRNA containing eight antisense binding sites for bantam. Infection with wild type AcMNPV (WT) or the control recombinant virus vPH resulted in a significant increase of bantam level, whereas infection with vPH-banS led to an approximately 40% reduction of bantam in both Sf9 cells and S. exigua larvae. Although, comparable production of budded virus and polyhedra were detected in vPH-banS-, vPH-, and WT-infected Sf9 cells, vPH-banS showed remarkably increased insecticidal activity in S. exigua larvae. The 50% lethal concentration and the median lethal time of vPH-banS was only 1/40 and 1/2, respectively, of both vPH and WT. Further analysis showed that the level of molting hormone 20-hydroxyecdysone (20E) was significantly higher in larvae infected with vPH-banS than those infected with vPH or WT. This was confirmed by the result that the larvae treated with bantam inhibitor also had a markedly increased 20E level. Moreover, feeding larvae with 20E increased the virus-mediated mortality, whereas feeding with juvenile hormone partially reverted the high insecticidal effect of vPH-banS. Together, our results revealed that vPH-banS infection suppresses the level of bantam, and in turn elevates level of 20E in infected insects, resulting in increased susceptibility to baculovirus infection. Our study provided a novel approach to improve a baculovirus bio-insecticide by interfering with a key homeostasis-regulating miRNA of the host.

Does the Pollen Diet Influence the Production and Expression of Antimicrobial Peptides in Individual Honey Bees?

We investigated the importance of protein nutrition for honey bee immunity. Different protein diets (monofloral pollen of Helianthus spp., Sinapis spp., Asparagus spp., Castanea spp., a mixture of the four different pollen and the pollen substitute Feedbee^TM) were fed to honey bees in cages ad libitum. After 18 days of feeding, apidaecin 1 isoforms concentration in the thorax were measured using nanoflow liquid chromatography coupled with mass spectrometry. Expression levels of genes, coding for apidaecins and abaecin in the abdomen were determined using quantitative PCR. The results indicate that protein-containing nutrition in adult worker honey bees can trigger certain metabolic responses. Bees without dietary protein showed lower apidaecin 1 isoforms concentrations. The significantly lowest concentration of apidaecin 1 isoforms was found in the group that was fed no pollen diet when compared to Asparagus, Castanea, Helianthus, and Sinapis pollen or the pollen supplement FeedBee^TM. Expression levels of the respective genes were also affected by the protein diets and different expression levels of these two antimicrobial peptides were found. Positive correlation between concentration and gene expression of apidaecins was found. The significance of feeding bees with different protein diets, as well as the importance of pollen nutrition for honey bee immunity is demonstrated.

miRNAs in Insects Infected by Animal and Plant Viruses

Viruses vectored by insects cause severe medical and agricultural burdens. The process of virus infection of insects regulates and is regulated by a complex interplay of biomolecules including the small, non-coding microRNAs (miRNAs). Considered an anomaly upon its discovery only around 25 years ago, miRNAs as a class have challenged the molecular central dogma which essentially typifies RNAs as just intermediaries in the flow of information from DNA to protein. miRNAs are now known to be common modulators or fine-tuners of gene expression. While recent years has seen an increased emphasis on understanding the role of miRNAs in host-virus associations, existing literature on the interaction between insects and their arthropod-borne viruses (arboviruses) is largely restricted to miRNA abundance profiling. Here we analyse the commonalities and contrasts between miRNA abundance profiles with different host-arbovirus combinations and outline a suggested pipeline and criteria for functional analysis of the contribution of miRNAs to the insect vector-virus interaction. Finally, we discuss the potential use of the model organism, Drosophila melanogaster, in complementing research on the role of miRNAs in insect vector-virus interaction.

Leishmania, microbiota and sand fly immunity

In this review, we explore the state-of-the-art of sand fly relationships with microbiota, viruses and Leishmania, with particular emphasis on the vector immune responses. Insect-borne diseases are a major public health problem in the world. Phlebotomine sand flies are proven vectors of several aetiological agents including viruses, bacteria and the trypanosomatid Leishmania, which are responsible for diseases such as viral encephalitis, bartonellosis and leishmaniasis, respectively. All metazoans in nature coexist intimately with a community of commensal microorganisms known as microbiota. The microbiota has a fundamental role in the induction, maturation and function of the host immune system, which can modulate host protection from pathogens and infectious diseases. We briefly review viruses of public health importance present in sand flies and revisit studies done on bacterial and fungal gut contents of these vectors. We bring this information into the context of sand fly development and immune responses. We highlight the immunity mechanisms that the insect utilizes to survive the potential threats involved in these interactions and discuss the recently discovered complex interactions among microbiota, sand fly, Leishmania and virus. Additionally, some of the alternative control strategies that could benefit from the current knowledge are considered.

A comparative analysis of corpora allata-corpora cardiaca microRNA repertoires revealed significant changes during mosquito metamorphosis

The corpora allata (CA) are a pair of endocrine glands with neural connections to the brain and close association with another neuroendocrine organ, the corpora cardiaca (CC). The CA from adult female Aedes aegypti mosquitoes synthesize fluctuating levels of juvenile hormone (JH), which have been linked to the ovarian development and are influenced by nutritional signals. In this study, we investigated the potential involvement of microRNAs (miRNAs), a type of small non-coding RNAs, in the regulation of gene expression in CA-CC complexes during mosquito reproductive development, at stages with distinct JH biosynthesis patterns. We analyzed the miRNA repertoires expressed in the CA-CC of pupae, sugar-fed and blood-fed female Ae. aegypti. In total, 156 mature miRNAs were detected in the CA-CC, with 84 displaying significant differences in expression among the three CA-CC developmental stages. There were more miRNAs that were expressed in pupae, and decreased or were absent after adult emergence, when compared with changes between CA-CC of sugar and blood-fed females. Analysis of the genes identified as potential targets for the CA-CC miRNA repertoires classified them into the broad categories of metabolism, information storage and processing, and cellular processes and signaling; with genes involved in cellular processes and signaling representing the largest portion. Among them, the signal-transduction mechanisms and intracellular trafficking, secretion and vesicular transport contained almost 55% of the genes' targets. A substantial number of miRNAs were differentially abundant in the libraries of the three developmental stages, and those changes were much more notable when pupae and adult stages were compared. We detected putative binding sites for some of the most abundant miRNAs on genes encoding JH biosynthetic enzymes and CC neuropeptides. These studies should help us to gain a better understanding of the regulation of CA-CC activity mediated by miRNAs during major developmental stages in mosquitoes.

Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT-resistance in the Drosophila melanogaster strain 91-R

Dichloro-diphenyl-trichloroethane (DDT) resistance among arthropod species is a model for understanding the molecular adaptations in response to insecticide exposures. Previous studies reported that DDT resistance may involve one or multiple detoxification genes, such as cytochrome P450 monooxygenases (P450s), glutathione S-transferases (GSTs), esterases, and ATP binding cassette (ABC) transporters, or changes in the voltage-sensitive sodium channel. However, the possible involvement of microRNAs (miRNAs) in the post-transcriptional regulation of genes associated with DDT resistance in the Drosophila melanogaster strain 91-R remains poorly understood. In this study, the majority of the resulting miRNAs discovered in small RNA libraries from 91-R and the susceptible control strain, 91-C, ranged from 16-25 nt, and contained 163 precursors and 256 mature forms of previously-known miRNAs along with 17 putative novel miRNAs. Quantitative analyses predicted the differential expression of ten miRNAs between 91-R and 91-C, and, based on Gene Ontology and pathway analysis, these ten miRNAs putatively target transcripts encoding proteins involved in detoxification mechanisms. RT-qPCR validated an inverse correlation between levels of differentially-expressed miRNAs and their putatively targeted transcripts, which implies a role of these miRNAs in the differential regulation of detoxification pathways in 91-R compared to 91-C. This study provides evidence associating the differential expression of miRNAs in response to multigenerational DDT selection in Drosophila melanogaster and provides important clues for understanding the possible roles of miRNAs in mediating insecticide resistance traits.

Host miRNAs are involved in hormonal regulation of HaSNPV-triggered climbing behaviour in Helicoverpa armigera

Baculoviruses manipulate host climbing behaviour to ensure that the hosts die at elevated positions on host plants to facilitate virus proliferation and transmission, which is a process referred to as tree-top disease. However, the detailed molecular mechanism underlying tree-top disease has not been elucidated. Using transcriptome analysis, we showed that two hormone signals, juvenile hormone (JH) and 20-hydroxyecdysone (20E), are key components involved in HaSNPV-induced tree-top disease in Helicoverpa armigera larvae. RNAi-mediated knockdown and exogenous hormone treatment assays demonstrated that 20E inhibits virus-induced tree-top disease, while JH mediates tree-top disease behaviour. Knockdown of BrZ2, a downstream signal of JH and 20E, promoted HaSNPV-induced tree-top disease. We also found that two miRNAs target BrZ2 and are involved in the cross-talk regulation between 20E and JH manipulating HaSNPV replication, time to death and HaSNPV-induced tree-top disease.

The Importance of ncRNAs as Epigenetic Mechanisms in Phenotypic Variation and Organic Evolution

Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic information, in terms of genes and chromosomes, was considered the cornerstone of evolution at the level of natural populations. This predominant view excluded both alternative explanations and phenomenologies that did not fit its paradigm. With the discovery of non-coding RNAs (ncRNAs) and their role in the control of genetic expression, new mechanisms arose providing heuristic power to complementary explanations to evolutionary processes overwhelmed by mainstream genocentric views. Viruses, epimutation, paramutation, splicing, and RNA editing have been revealed as paramount functions in genetic variations, phenotypic plasticity, and diversity. This article discusses how current epigenetic advances on ncRNAs have changed the vision of the mechanisms that generate variation, how organism-environment interaction can no longer be underestimated as a driver of organic evolution, and how it is now part of the transgenerational inheritance and evolution of species.

Multiple miRNAs jointly regulate the biosynthesis of ecdysteroid in the holometabolous insects, Chilo suppressalis

The accurate rise and fall of active hormones is important for insect development. The ecdysteroids must be cleared in a timely manner. However, the mechanism of suppressing the ecdysteroid biosynthesis at the right time remains unclear. Here, we sequenced a small RNA library of Chilo suppressalis and identified 300 miRNAs in this notorious rice insect pest. Microarray analysis yielded 54 differentially expressed miRNAs during metamorphosis development. Target prediction and in vitro dual-luciferase assays confirmed that seven miRNAs (two conserved and five novel miRNAs) jointly targeted three Halloween genes in the ecdysteroid biosynthesis pathway. Overexpression of these seven miRNAs reduced the titer of 20-hydroxyecdysone (20E), induced mortality, and retarded development, which could be rescued by treatment with 20E. Comparative analysis indicated that the miRNA regulation of metamorphosis development is a conserved process but that the miRNAs involved are highly divergent. In all, we present evidence that both conserved and lineage-specific miRNAs have crucial roles in regulating development in insects by controlling ecdysteroid biosynthesis, which is important for ensuring developmental convergence and evolutionary diversity.

MicroRNAs are differentially abundant during Aedes albopictus diapause maintenance but not diapause induction

Diapause is a programmed dormancy that allows organisms to tolerate predictable periods of unfavourable conditions by temporarily halting development and reducing metabolism. Diapause is widespread amongst insects and is crucial for allowing organisms to coordinate their growth and reproduction with favourable environmental conditions. Although the adaptive significance of diapause is well understood, the molecular mechanisms underpinning diapause remain unresolved. We performed high-throughput sequencing to investigate the role of microRNAs (miRNAs) in the diapause of the Asian tiger mosquito, Aedes albopictus. We first investigated miRNAs in diapause induction by characterizing maternally provisioned miRNAs in mature oocytes of Ae. albopictus under diapause-inducing and diapause-averting conditions. Second, we investigated miRNAs in diapause maintenance by characterizing miRNAs in diapause and nondiapause pharate larvae. We identified 162 miRNAs, 152 previously known and 10 putatively novel. We identified no differentially abundant miRNAs in mature oocytes and seven differentially abundant miRNAs in pharate larvae. The predicted targets of differentially abundant miRNAs include genes affecting several processes related to diapause maintenance including ecdysone regulation, immune response, lipid metabolism and regulation of development. Our results suggest that Ae. albopictus does not maternally provision a unique set of miRNAs during diapause induction but miRNAs are a component of diapause maintenance in this species.

Insect RNAi: Integrating a New Tool in the Crop Protection Toolkit

Protecting crops against insect pests is a major focus area in crop protection. Over the past two decades, biotechnological interventions, especially Bt proteins, have been successfully implemented across the world and have had major impacts on reducing chemical pesticide applications. As insects continue to adapt to insecticides, both chemical and protein-based, new methods, molecules, and modes of action are necessary to provide sustainable solutions. RNA interference (RNAi) has emerged as a significant tool to knock down or alter gene expression profiles in a species-specific manner. In the past decade, there has been intense research on RNAi applications in crop protection. This chapter looks at the current state of knowledge in the field and outlines the methodology, delivery methods, and precautions required in designing targets. Assessing the targeting of specific gene expression is also an important part of a successful RNAi strategy. The current literature on the use of RNAi in major orders of insect pests is reviewed, along with a perspective on the regulatory aspects of the approach. Risk assessment of RNAi would focus on molecular characterization, food/feed risk assessment, and environmental risk assessment. As more RNAi-based products come through regulatory systems, either via direct application or plant expression based, the impact of this approach on crop protection will become clearer.

Zika virus alters the microRNA expression profile and elicits an RNAi response in Aedes aegypti mosquitoes

Zika virus (ZIKV), a flavivirus transmitted primarily by Aedes aegypti, has recently spread globally in an unprecedented fashion, yet we have a poor understanding of host-microbe interactions in this system. To gain insights into the interplay between ZIKV and the mosquito, we sequenced the small RNA profiles in ZIKV-infected and non-infected Ae. aegypti mosquitoes at 2, 7 and 14 days post-infection. ZIKA induced an RNAi response in the mosquito with virus-derived short interfering RNAs and PIWI-interacting RNAs dramatically increased in abundance post-infection. Further, we found 17 host microRNAs (miRNAs) that were modulated by ZIKV infection at all time points. Strikingly, many of these regulated miRNAs have been reported to have their expression altered by dengue and West Nile viruses, while the response was divergent from that induced by the alphavirus Chikungunya virus in mosquitoes. This suggests that conserved miRNA responses occur within mosquitoes in response to flavivirus infection. This study expands our understanding of ZIKV-vector interactions and provides potential avenues to be further investigated to target ZIKV in the mosquito host.

The overexpression of insect endogenous small RNAs in transgenic rice inhibits growth and delays pupation of striped stem borer (Chilo suppressalis)

BACKGROUND

The striped stem borer (SSB), Chilo suppressalis Walker, is a major rice insect pest worldwide. RNA interference (RNAi) has become a promising strategy for developing insect-resistant crops. In a previous study, five double-stranded RNAs (dsRNAs) targeting important SSB housekeeping genes were overexpressed in rice, but none of the acquired dsRNA-transgenic rice plants showed significant effects on SSB.

RESULTS

Thirteen selected SSB endogenous small RNAs, predicted as SSB novel microRNAs (miRNAs), were overexpressed in rice using artificial miRNA (amiRNA) expression technology. Feeding tests showed that two out of 13 selected SSB novel miRNAs caused significant growth inhibition for feeding SSB larvae based on transgenic rice expression. Pupation was delayed 4 days when SSB larvae consecutively fed on transgenic rice expressing the SSB novel miRNA candidate csu-novel-miR15 (csu-15 rice). Gene expression analysis confirmed that the expression levels of at least six SSB unigenes significantly changed (i.e., were up- or down-regulated) after feeding on csu-15 rice.

CONCLUSIONS

Our research demonstrated a novel RNAi strategy using SSB endogenous small RNAs to develop RNAi crops for pest management; this strategy is different from the common RNAi resulting from transgenic dsRNAs or amiRNAs targeting certain insect endogenous genes. © 2016 Society of Chemical Industry.

Significantly altered expression of miR-511-3p and its target AKT3 has negative prognostic value in human prostate cancer

PURPOSE

In this study, we assessed the expression and functions of microRNA-511-3p (miR-511-3p) in human prostate cancer (CaP).

METHODS

Gene expressions of miR-511-3p in CaP cells and human CaP tumors were assessed by qPCR. In VCaP and PC3 cells, miR-511-3p was overexpressed by lentivirus. The functions of miR-511-3p upregulation in regulating in vitro cancer proliferation, migration and in vivo cancer growth were assessed by MTT, transwell and transplantation assays, respectively. Downstream target gene of miR-511-3p, AKT3, was verified by dual-luciferase activity and qPCR assays. AKT3 was then overexpressed in miR-511-3p-upregulated CaP cells to assess its functions in miR-511-3p-mediated cancer regulation.

RESULTS

MiR-511-3p is significantly downregulated in CaP cell lines, and human CaP tumors. MiR-511-3p was further downregulated in T3/T4-staged CaP tumors and closely correlated with shorter overall survival among CaP patients. In VCaP and PC3 cells, lentiviral-induced miR-511-3p upregulation was acting as a tumor suppressor by inhibiting in vitro cancer proliferation, migration and in vivo transplantation. Human AKT3 gene was confirmed to be the downstream target of miR-511-3p in CaP. In miR-511-3p-upregulated VCaP and PC3 cells, forced-overexpression of AKT3 reversed the tumor suppressive effects of miR-511-3p in CaP.

CONCLUSION

MiR-511-3p may serve as a prognostic factor and tumor suppressor in CaP, very likely through inverse regulation of its downstream target gene of AKT3.

Experimental evolution of resistance against Bacillus thuringiensis in the insect model host Galleria mellonella results in epigenetic modifications

Epigenetic mechanisms have been proposed to translate environmental stimuli into heritable transgenerational phenotypic variations that can significantly influence natural selection. An intriguing example is exposure to pathogens, which imposes selection for host resistance. To test this hypothesis, we used larvae of the greater wax moth Galleria mellonella as model host to experimentally select for resistance to Bacillus thuringiensis (Bt), the most widely used bacterial agent for the biological control of pest insects. To determine whether epigenetic mechanisms contribute to the evolution of resistance against pathogens, we exposed G. mellonella larvae over 30 generations to spores and crystals mix of Bt and compared epigenetic markers in this selected line, exhibiting almost 11-fold enhanced resistance against Bt, to those in a non-selected control population. We found that experimental selection influenced acetylation of specific histones and DNA methylation as well as transcription of genes encoding the enzymatic writers and erasers of these epigenetic mechanisms. Using microarray analysis, we also observed differences in the expression of conserved miRNAs in the resistant and susceptible larvae, resulting in the repression of candidate genes that confer susceptibility to Bt. By combining in silico minimum free energy hybridization with RT-PCR experiments, we identified the functions and biological processes associated with the mRNAs targeted by these miRNAs. Our results suggest that epigenetic mechanisms operating at the pre-transcriptional and post-transcriptional levels contribute to the transgenerational inherited transcriptional reprogramming of stress and immunity-related genes, ultimately providing a mechanism for the evolution of insect resistance to pathogen.

RNA interference of Dicer-1 and Argonaute-1 increasing the sensitivity of Aphis gossypii Glover (Hemiptera: Aphididae) to plant allelochemical

Plant allelochemicals are a group of important defensive agents of plants, which have been documented to be deleterious to insect herbivores. In the present study, we found that the expression level of Dicer-1 was significantly increased when Aphis gossypii adults fed on plant allelochemicals (tannic acid and gossypol) incorporated artificial diets. Consider that miRNAs play great regulatory roles in various biological processes, this suggested that miRNAs may be related to the regulation of enzymes involved in metabolism of plant allelochemicals in A. gossypii. To further reveal the roles of miRNAs in the response of A. gossypii against plant allelochemicals, both Dicer-1 and Argonaute-1, an important component of the RNA-induced silencing complex (RISC) in miRNA pathway, were silenced using systemic RNA interference (RNAi). The results indicated that silence of Dicer-1 reduced the expression of miRNAs, and resulted in a high mortality of A. gossypii when fed on both tannic acid and gossypol. The silencing of Argonaute-1 resulted in the mortality of A. gossypii by the treatment of tannic acid significantly increased compared with control, however, the sensitivity of A. gossypii to gossypol was not significantly changed. It suggested that miRNAs play potential regulatory roles in the response of A. gossypii to plant allelochemicals. These results should be useful to understand the molecular mechanisms of the cotton aphid adaption to plant allelochemicals.

Infections of virulent and avirulent viruses differentially influenced the expression of dicer-1, ago-1, and microRNAs in Bombus terrestris

The microRNA (miRNA) pathway is well established to be involved in host-pathogen interactions. As key insect pollinators, bees are suffering from widely spreading viruses, especially honeybees and bumblebees. In order to better understand bee-virus interaction, we comparatively analyzed the involvement of the bumblebee miRNA pathway upon infection by two different viruses. In our setup, an avirulent infection is induced by slow bee paralysis virus (SBPV) and a virulent infection is induced by Israeli acute paralysis virus (IAPV). Our results showed the increased expressions of dicer-1 and ago-1 upon SBPV infection. There were 17 and 12 bumblebee miRNAs differentially expressed upon SBPV and IAPV infections, respectively. These results may indicate the involvement of the host miRNA pathway in bumblebee-virus interaction. However, silencing of dicer-1 did not influence the genome copy number of SBPV. Target prediction for these differentially expressed miRNAs showed their possible involvement in targeting viral genomic RNA and in the regulation of networks in bumblebee. Our study opens a new insight into bee-virus interaction meditated by host miRNAs.

Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae)

BACKGROUND

MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects.

RESULTS

We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals. Using Illumina sequencing, a total of 73.27 million clean reads was obtained, and 292 miRNAs were identified from A. gossypii. Comparative analysis of read counts indicated that both conserved and novel miRNAs were differently expressed among the five libraries, and the differential expression was validated via qRT-PCR. We found that the transcript levels of several miRNAs were increased or decreased in all of the allelochemical treatment libraries compared to the control. The putative target genes of the miRNAs were predicted using in silico tools, and the target genes of several miRNAs were presumed to be involved in the metabolism of xenobiotic compounds. Furthermore, the target prediction results were confirmed using dual luciferase reporter assay, and Ago-miR-656a-3p was demonstrated to regulate the expression of CYP6J1 post-transcriptionally through binding to the 3' UTR of CYP6J1.

CONCLUSION

Our research results indicate that miRNAs may be involved in the metabolism of plant allelochemicals in A. gossypii, and these results also represent an important new small RNA genomics resource for further studies on this topic.

De novo characterization of microRNAs in oriental fruit moth Grapholita molesta and selection of reference genes for normalization of microRNA expression

MicroRNAs (miRNAs) are a group of endogenous non-coding small RNAs that have critical regulatory functions in almost all known biological processes at the post-transcriptional level in a variety of organisms. The oriental fruit moth Grapholita molesta is one of the most serious pests in orchards worldwide and threatens the production of Rosacea fruits. In this study, a de novo small RNA library constructed from mixed stages of G. molesta was sequenced through Illumina sequencing platform and a total of 536 mature miRNAs consisting of 291 conserved and 245 novel miRNAs were identified. Most of the conserved and novel miRNAs were detected with moderate abundance. The miRNAs in the same cluster normally showed correlated expressional profiles. A comparative analysis of the 79 conserved miRNA families within 31 arthropod species indicated that these miRNA families were more conserved among insects and within orders of closer phylogenetic relationships. The KEGG pathway analysis and network prediction of target genes indicated that the complex composed of miRNAs, clock genes and developmental regulation genes may play vital roles to regulate the developmental circadian rhythm of G. molesta. Furthermore, based on the sRNA library of G. molesta, suitable reference genes were selected and validated for study of miRNA transcriptional profile in G. molesta under two biotic and six abiotic experimental conditions. This study systematically documented the miRNA profile in G. molesta, which could lay a foundation for further understanding of the regulatory roles of miRNAs in the development and metabolism in this pest and might also suggest clues to the development of genetic-based techniques for agricultural pest control.

Identification and characterization of microRNAs in the screwworm flies Cochliomyia hominivorax and Cochliomyia macellaria (Diptera: Calliphoridae)

MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression through post-transcriptional regulation. Here, we report the identification and characterization of miRNAs in two closely related screwworm flies with different feeding habits: Cochliomyia hominivorax and Cochliomyia macellaria. The New World screwworm, C. hominivorax, is an obligatory parasite of warm-blooded vertebrates, whereas the secondary screwworm, C. macellaria, is a free-living organism that feeds on decaying organic matter. Here, the small RNA transcriptomes of adults and third-instar larvae of both species were sequenced. A total of 110 evolutionarily conserved miRNAs were identified, and 10 putative precursor miRNAs (pre-miRNAs) were predicted. The relative expression of six selected miRNAs was further investigated, including miRNAs that are related to reproduction and neural processes in other insects. Mature miRNAs were also characterized across an evolutionary time scale, suggesting that the majority of them have been conserved since the emergence of the Arthropoda [540 million years ago (Ma)], Hexapoda (488 Ma) and Brachycera (195 Ma) lineages. This study is the first report of miRNAs for screwworm flies. We also performed a comparative analysis with the hereby predicted miRNAs from the sheep blowfly, Lucilia cuprina. The results presented may advance our understanding of parasitic habits within Calliphoridae and assist further functional studies in blowflies.

Molecular Evolution of Insect Sociality: An Eco-Evo-Devo Perspective

The evolution of eusociality is a perennial issue in evolutionary biology, and genomic advances have fueled steadily growing interest in the genetic changes underlying social evolution. Along with a recent flurry of research on comparative and evolutionary genomics in different eusocial insect groups (bees, ants, wasps, and termites), several mechanistic explanations have emerged to describe the molecular evolution of eusociality from solitary behavior. These include solitary physiological ground plans, genetic toolkits of deeply conserved genes, evolutionary changes in protein-coding genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes. Despite this proliferation of ideas, there has been little synthesis, even though these ideas are not mutually exclusive and may in fact be complementary. We review available data on molecular evolution of insect sociality and highlight key biotic and abiotic factors influencing social insect genomes. We then suggest both phylogenetic and ecological evolutionary developmental biology (eco-evo-devo) perspectives for a more synthetic view of molecular evolution in insect societies.

MicroRNAs and the Evolution of Insect Metamorphosis

MicroRNAs (miRNAs) are involved in the regulation of a number of processes associated with metamorphosis, either in the less modified hemimetabolan mode or in the more modified holometabolan mode. The miR-100/let-7/miR-125 cluster has been studied extensively, especially in relation to wing morphogenesis in both hemimetabolan and holometabolan species. Other miRNAs also participate in wing morphogenesis, as well as in programmed cell and tissue death, neuromaturation, neuromuscular junction formation, and neuron cell fate determination, typically during the pupal stage of holometabolan species. A special case is the control of miR-2 over Kr-h1 transcripts, which determines adult morphogenesis in the hemimetabolan metamorphosis. This is an elegant example of how a single miRNA can control an entire process by acting on a crucial mediator; however, this is a quite exceptional mechanism that was apparently lost during the transition from hemimetaboly to holometaboly.

Global identification of microRNAs associated with chlorantraniliprole resistance in diamondback moth Plutella xylostella (L.)

The diamondback moth (DBM), Plutella xylostella (L.), is one of the most serious cruciferous pests and has developed high resistance to most insecticides, including chlorantraniliprole. Previous studies have reported several protein-coding genes that involved in chlorantraniliprole resistance, but research on resistance mechanisms at the post-transcription level is still limited. In this study, a global screen of microRNAs (miRNAs) associated with chlorantraniliprole resistance in P. xylostella was performed. The small RNA libraries for a susceptible (CHS) and two chlorantraniliprole resistant strains (CHR, ZZ) were constructed and sequenced, and a total of 199 known and 30 novel miRNAs were identified. Among them, 23 miRNAs were differentially expressed between CHR and CHS, and 90 miRNAs were differentially expressed between ZZ and CHS, of which 11 differentially expressed miRNAs were identified in both CHR and ZZ. Using miRanda and RNAhybrid, a total of 1,411 target mRNAs from 102 differentially expressed miRNAs were predicted, including mRNAs in several groups of detoxification enzymes. The expression of several differentially expressed miRNAs and their potential targets was validated by qRT-PCR. The results may provide important clues for further study of the mechanisms of miRNA-mediated chlorantraniliprole resistance in DBM and other target insects.

Identification and Evaluation of Suitable Reference Genes for Normalization of MicroRNA Expression in Helicoverpa armigera (Lepidoptera: Noctuidae) Using Quantitative Real-Time PCR

More and more studies have focused on microRNAs (miRNAs) expression in the pest Helicoverpa armigera (Lepidoptera: Noctuidae) recently. Quantitative real-time PCR (qRT-PCR) is being widely used in miRNA expression studies. Suitable reference genes are necessary for the correct analysis of results. In this study, 10 candidate genes of H. armigera were selected and analyzed for their expression stability under different biotic and abiotic conditions with 3 statistical methods, including geNorm, NormFinder, and Bestkeeper. Combination the best number of reference genes was calculated by geNorm. One target gene, let-7, was used to validate the selection of reference genes. The suitable candidate reference genes were shown as follows: miR-9 and U6 snRNA for developmental stages, miR-100 and U6 snRNA for larval tissues, miR-100 and miR-305 for adult tissues, miR-9 and miR-279 for parasitic treatment, miR-998 and U6 snRNA for nuclear polyhedrosis virus infection, miR-9 and U6 snRNA for insecticide treatment, miR-92a, miR-100, and miR-279 for temperature treatment, miR-92a, miR-305, and miR-998 for starvation treatment, miR-9 and miR-279 for light treatment, miR-305 and miR-998 for hormone treatment, and there was not one reference gene suitable for all samples. This study could promote future research on miRNAs expression in H. armigera with optimal reference genes under different experimental conditions.

Identification and characterization of microRNAs expressed in antennae of Holotrichia parallela Motschulsky and their possible roles in olfactory regulation

MicroRNAs (miRNAs) are small noncoding RNAs that play posttranscriptional, regulatory roles in various biological processes. However, there has been limited investigation into the potential function of miRNAs in olfaction. The coleopteran Holotrichia parallela is an economically important pest, and miRNAs have been identified in only one coleopteran (Tribolium castaneum). Therefore, this study was conducted to identify miRNAs expressed in the antennae of H. parallela and obtain insights into their possible roles in olfaction. By combining deep sequencing and miRDeep2 software, a total of 99 miRNAs, including 76 conserved miRNAs and 23 novel miRNAs, were identified from H. parallela antennae. The 76 conserved miRNAs belong to 63 families and the other 23 may be species specific or tissue specific. The identified miRNAs have many conserved features of miRNAs. Evaluation of the conservation of the identified miRNA families across different species revealed that most of the families are insect specific. The prediction and annotation of targets suggested that 13 of the identified miRNAs participate in olfactory regulation. Gender differences in antennal expression of nine of the olfactory-related miRNAs were confirmed by quantitative real-time PCR.

miR-276 and miR-3016-modulated expression of acetyl-CoA carboxylase accounts for spirotetramat resistance in Aphis gossypii Glover

Acetyl-coenzyme A carboxylase (acetyl-CoA carboxylase, ACC) catalyses the carboxylation of acetyl-CoA to produce malonyl-CoA during de novo fatty acid synthesis. A laboratory-selected spirotetramat-resistant strain (SR) of cotton aphid was used in this study. RT-qPCR results demonstrated significant increases in the levels of ACC transcript in the resistant strain compared to the susceptible strain. Depletion of overexpressed ACC transcripts by RNAi also significantly enhanced the sensitivity of the resistant aphid to spirotetramat. We hypothesized that ACC gene expression is subject to post-transcriptional regulation. To investigate the underlying mechanism, the 66 known miRNAs of Aphis gossypii were used for target prediction, eight of which were predicted to target ACC. Validation identified two miRNAs, miR-276 and miR-3016, with abundance levels that were highly inversely correlated with ACC transcript levels. This result suggests that the miRNAs miR-276 and miR-3016 may play major roles in the post-transcriptional regulation of the ACC gene. Modulation of the abundance of miR-276 and miR-3016 through addition of inhibitors/mimics of miR-276 or miR-3016 to the artificial diet significantly altered both ACC transcript levels and the tolerance of A. gossypii to spirotetramat, thus confirming the roles of these two miRNAs in the regulation of spirotetramat resistance.

Chapter 6. Comparative genomic approaches to investigate molecular traits specific to social insects

Ageing is a feature of nearly all known organisms and, by its connection to survival, appears to trade off with fecundity. However, in some organisms such as in queens of social insects, this negative relation appears reversed and individuals live long and reproduce much. Since new experimental techniques, transcriptomes and genomes of many social insects have recently become available, a comparison of these data in a phylogenetic framework becomes feasible. This allows the study of general trends, species specific oddities and evolutionary dynamics of the molecular properties and changes which underlie ageing, fecundity and the reversal of this negative association. In the framework of social insect evolution, we review the most important recent insights, computational methods, their applications and data resources which are available.

Reduced abundance of the CYP6CY3-targeting let-7 and miR-100 miRNAs accounts for host adaptation of Myzus persicae nicotianae

Nicotine is one of the most abundant and toxic secondary plant metabolites in nature and is defined by high toxicity to plant-feeding insects. Studies suggest that increased expression of cytochrome P450 (CYP6CY3) and the homologous CYP6CY4 genes in Myzus persicae nicotianae is correlated with tolerance to nicotine. Indeed, through expression analyses of the CYP6CY3 and CYP6CY4 genes of different M. persicae subspecies, we determined that the mRNA levels of these two genes were much higher in M. persicae nicotianae than in M. persicae sensu stricto. We hypothesized that the expression of these two genes is subject to post-transcriptional regulation. To investigate the underlying mechanism, the miRNA profile of M. persicae nicotianae was sequenced, and twenty-two miRNAs were predicted to target CYP6CY3. Validation of these miRNAs identified two miRNAs, let-7 and miR-100, whose abundance was highly inversely correlated with the abundance of the CYP6CY3 gene. This result implies that the let-7 and miR-100 miRNAs play a major role in the post-transcriptional regulation of the CYP6CY3 gene. Modulation of the abundance of let-7 and miR-100 through the addition of inhibitors/mimics of let-7 or miR-100 to artificial diet significantly altered the tolerance of M. persicae nicotianae to nicotine, further confirming the regulatory role of these two miRNAs. Interestingly, after decreasing the transcript levels of CYP6CY3 by modulating regulatory miRNAs, the transcript levels of the homologous isozyme CYP6CY4 were significantly elevated, suggesting a compensatory mechanism between the CYP6CY3 gene and its homologous CYP6CY4 gene. Our findings provide insight into the molecular drivers of insect host shifts and reveal an important source of genetic variation for adaptive evolution in insect species.

Mammalian African trypanosome VSG coat enhances tsetse's vector competence

Tsetse flies are biological vectors of African trypanosomes, the protozoan parasites responsible for causing human and animal trypanosomiases across sub-Saharan Africa. Currently, no vaccines are available for disease prevention due to antigenic variation of the Variant Surface Glycoproteins (VSG) that coat parasites while they reside within mammalian hosts. As a result, interference with parasite development in the tsetse vector is being explored to reduce disease transmission. A major bottleneck to infection occurs as parasites attempt to colonize tsetse's midgut. One critical factor influencing this bottleneck is the fly's peritrophic matrix (PM), a semipermeable, chitinous barrier that lines the midgut. The mechanisms that enable trypanosomes to cross this barrier are currently unknown. Here, we determined that as parasites enter the tsetse's gut, VSG molecules released from trypanosomes are internalized by cells of the cardia-the tissue responsible for producing the PM. VSG internalization results in decreased expression of a tsetse microRNA (mir-275) and interferes with the Wnt-signaling pathway and the Iroquois/IRX transcription factor family. This interference reduces the function of the PM barrier and promotes parasite colonization of the gut early in the infection process. Manipulation of the insect midgut homeostasis by the mammalian parasite coat proteins is a novel function and indicates that VSG serves a dual role in trypanosome biology-that of facilitating transmission through its mammalian host and insect vector. We detail critical steps in the course of trypanosome infection establishment that can serve as novel targets to reduce the tsetse's vector competence and disease transmission.

pol-miR-731, a teleost miRNA upregulated by megalocytivirus, negatively regulates virus-induced type I interferon response, apoptosis, and cell cycle arrest

Megalocytivirus is a DNA virus that is highly infectious in a wide variety of marine and freshwater fish, including Japanese flounder (Paralichthys olivaceus), a flatfish that is farmed worldwide. However, the infection mechanism of megalocytivirus remains largely unknown. In this study, we investigated the function of a flounder microRNA, pol-miR-731, in virus-host interaction. We found that pol-miR-731 was induced in expression by megalocytivirus and promoted viral replication at the early infection stage. In vivo and in vitro studies revealed that pol-miR-731 (i) specifically suppresses the expression of interferon regulatory factor 7 (IRF7) and cellular tumor antigen p53 in a manner that depended on the integrity of the pol-miR-731 complementary sequences in the 3′ untranslated regions of IRF7 and p53, (ii) disrupts megalocytivirus-induced Type I interferon response through IRF7, (iii) inhibits megalocytivirus-induced splenocyte apoptosis and cell cycle arrest through p53. Furthermore, overexpression of IRF7 and p53 abolished both the inhibitory effects of pol-miR-731 on these biological processes and its stimulatory effect on viral replication. These results disclosed a novel evasion mechanism of megalocytivirus mediated by a host miRNA. This study also provides the first evidence that a virus-induced host miRNA can facilitate viral infection by simultaneously suppressing several antiviral pathways.

Epigenetic code and insect behavioural plasticity

Although the nature of the genetic control of adaptive behaviours in insects is a major unresolved problem it is now understood that epigenetic mechanisms, bound by genetic constraints, are prime drivers of brain plasticity arising from both developmental and experience-dependent events. With the recent advancements in methylomics and emerging analyses of histones and non-protein-coding RNAs, insect epigenetics is well positioned to ask more direct questions and importantly, address them experimentally. To achieve rapid progress, insect epigenetics needs to focus on mechanistic explanations of epigenomic dynamics and move beyond low-depth genome-wide analyses to cell-type specific epigenomics. One topic of a high priority is the impact of sequence variants on generating differential methylation patterns and their contribution to behavioural plasticity.

Identification of Differentially Expressed microRNAs between the Fenpropathrin Resistant and Susceptible Strains in Tetranychus cinnabarinus

The carmine spider mite (Tetranychus cinnabarinus) is one of the most serious pests on crops and its control mainly depends on chemical acaricides. The excessive and improper acaricides use has resulted in mite resistance to many acaricides, including fenpropathrin. Previous studies have indicated fenpropathrin resistance is a complex development process involving many genes, but information on resistance mechanism of post-transcription regulation is rare. Using Illumina sequencing, several categories of sRNAs were identified from susceptible (TS) and fenpropathrin-resistant strains (TR) of T. cinnabarinus, including 75 known microRNAs (miRNAs) and 64 novel miRNAs, whose target genes containing 78592 miRNA-target pairs were predicted by 6 algorithms. Also, 12 significantly differently expressed miRNAs were identified between the TS and TR libraries and RT-qPCR validation also performed a well consistency with sequencing. The targets of significantly differentially expressed miRNAs included 7 glutathione S-transferase, 7 cytochrome P450 and 16 carboxyl/choline esterase genes, their function in fenpropathrin resistance were further analyzed. The present study provides the firstly large-scale characterization of miRNAs in T. cinnabarinus and the comparison between TS and TR strains gives a clue on how miRNA involves in fenpropathrin resistance.

Polydnaviruses: Nature's Genetic Engineers

Virus-host associations are usually viewed as parasitic, but several studies in recent years have reported examples of viruses that benefit host organisms. The Polydnaviridae are of particular interest because these viruses are all obligate mutualists of insects called parasitoid wasps. Parasitoids develop during their immature stages by feeding inside the body of other insects, which serve as their hosts. Polydnaviruses are vertically transmitted as proviruses through the germ line of wasps but also function as gene delivery vectors that wasps rely upon to genetically manipulate the hosts they parasitize. Here we review the evolutionary origin of polydnaviruses, the organization and function of their genomes, and some of their roles in parasitism.

miR-8-3p regulates mitoferrin in the testes of Bactrocera dorsalis to ensure normal spermatogenesis

Genetics-enhanced sterile insect techniques (SIT) are promising novel approaches to control Bactrocera dorsalis, the most destructive horticultural pest in East Asia and the Pacific region. To identify novel genetic agents to alter male fertility of B. dorsalis, previous studies investigated miRNA expression in testes of B. dorsalis. One miRNA, miR-8-3p was predicted to bind the 3'UTR of putative B. dorsalis mitoferrin (bmfrn). The ortholog of bmfrn in D. melanogaster is essential for male fertility. Here we show that bmfrn has all conserved amino acid residues of known mitoferrins and is most abundantly expressed in B. dorsalis testes, making miR-8-3p and mitoferrin candidates for genetics-enhanced SIT. Furthermore, using a dual-luciferase reporter system, we show in HeLa cells that miR-8-3p interacts with the 3'UTR of bmfrn. Dietary treatments of adult male flies with miR-8-3p mimic, antagomiR, or bmfrn dsRNA, altered mitoferrin expression in the testes and resulted in reduced male reproductive capacity due to reduced numbers and viability of spermatozoa. We show for the first time that a mitoferrin is regulated by a miRNA and we demonstrate miR-8-3p as well as bmfrn dsRNA to be promising novel agents that could be used for genetics-enhanced SIT.

Diet-delivered RNAi in Helicoverpa armigera--Progresses and challenges

Helicoverpa armigera (the cotton bollworm) is a significant agricultural pest endemic to Afro-Eurasia and Oceania. Gene suppression via RNA interference (RNAi) presents a potential avenue for management of the pest, which is highly resistant to traditional insecticide sprays. This article reviews current understanding on the fate of ingested double-stranded RNA in H. armigera. Existing in vivo studies on diet-delivered RNAi and their effects are summarized and followed by a discussion on the factors and hurdles affecting the efficacy of diet-delivered RNAi in H. armigera.

Identification, characterization and target gene analysis of testicular microRNAs in the oriental fruit fly Bactrocera dorsalis

MicroRNAs (miRNAs) are small noncoding RNAs that regulate various diverse biological processes including insect spermatogenesis. The oriental fruit fly, Bactrocera dorsalis, is one of the most destructive horticultural pests in East Asia and the Pacific region. Although developmental miRNA profiles of B. dorsalis have enriched our knowledge, specific testicular miRNAs in this dipteran species are unexplored. In this study, we identified miRNAs from B. dorsalis testes by deep sequencing, which provided an overview of miRNA expression during spermatogenesis. Small RNA libraries were constructed from the testes of fully mature (FM), immature (IM) and middle-aged (MA) adult flies of B. dorsalis. Small RNA sequencing and data analysis revealed 172 known and 78 novel miRNAs amongst these libraries. Pairwise comparisons of libraries led to the identification of 24, 15 and 14 differentially expressed miRNAs in FM vs. IM, FM vs. MA and IM vs. MA insects, respectively. Using a bioinformatic approach, we predicted 124 target genes against the 13 most differentially expressed miRNAs. Furthermore, the expression patterns of six randomly selected miRNAs (from the 13 most differentially expressed miRNAs) and their putative target genes (from the 124 predicted target genes) were analysed in the testis of B. dorsalis by quantitative real-time PCR, which showed that out of six, four tested miRNAs-mRNAs had an inverse expression pattern and are probably co-regulated. This study is the first comparative profile of the miRNA transcriptome in three developmental stages of the testis, and provides a useful resource for further studies on the role of miRNAs in spermatogenesis in B. dorsalis.

MicroRNAs in Honey Bee Caste Determination

The cellular mechanisms employed by some organisms to produce contrasting morphological and reproductive phenotypes from the same genome remains one of the key unresolved issues in biology. Honeybees (Apis mellifera) use differential feeding and a haplodiploid sex determination system to generate three distinct organismal outcomes from the same genome. Here we investigate the honeybee female and male caste-specific microRNA and transcriptomic molecular signatures during a critical time of larval development. Both previously undetected and novel miRNAs have been discovered, expanding the inventory of these genomic regulators in invertebrates. We show significant differences in the microRNA and transcriptional profiles of diploid females relative to haploid drone males as well as between reproductively distinct females (queens and workers). Queens and drones show gene enrichment in physio-metabolic pathways, whereas workers show enrichment in processes associated with neuronal development, cell signalling and caste biased structural differences. Interestingly, predicted miRNA targets are primarily associated with non-physio-metabolic genes, especially neuronal targets, suggesting a mechanistic disjunction from DNA methylation that regulates physio-metabolic processes. Accordingly, miRNA targets are under-represented in methylated genes. Our data show how a common set of genetic elements are differentially harnessed by an organism, which may provide the remarkable level of developmental flexibility required.