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Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cellcell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

Fundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown 1 , 2 . Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo. The heterochromatin protein HP1 has an essential role in establishing several features of the 3D nuclear organization of the genome during early embryonic development in Drosophila .

Consumption of edible insects is a potential solution to the growing need for protein. However, the wild harvested edible insects’ value chain faces several challenges including limited knowledge on indigenous practices in the harvesting and processing and lack of information on roles of the different actors in the chain. A case study of Gonimbrasia belina , colloquially referred to as the ’mopane worm’, was conducted to understand and identify determinants of participation in the value chain of the edible caterpillar. A cross sectional study was conducted in Gwanda (a rural district in Zimbabwe) to (a) understand the indigenous knowledge on harvesting and processing methods, (b) explore value addition and the traditional beliefs surrounding the utilisation of the mopane worm. Results showed that consumers (81.7%), and harvesters (76.6%) were the main actors in the mopane worm value chain. Using the Ordinary Least Squares (OLS) model, the following were shown to be determinants of participation in the mopane worm value chain: (a) gender (b) household size (c) marital status (d) religion and (e) household assets. Two primary processing methods of harvested mopane worm were distinguished i.e., boiling and roasting on ambers. Results showed lack of diversity in mopane worm-based products. Current culturally acceptable processing techniques need improvement and standardization to support sustainable mopane worm processing while optimising nutrient bio-accessibility.

A high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis shows that although local regulatory interactions are frequent, long-range interactions are also very common; unexpectedly, most interactions appear unchanged between tissues and across development and are formed prior to gene expression, indicating that transcription initiates from preformed enhancer–promoter loops, which are associated with paused polymerase. Enhancer activity during embryogenesis Two papers in this issue of Nature examine the role of developmental enhancers in Drosophila melanogaster , an ideal model for the purpose, as it takes just 18 hours from egg laying to completion of embryogenesis and involves marked changes in transcription linked to changes in enhancer activity. Evgeny Kvon et al . systematically assayed the activity of more than 7,000 candidate enhancers. Nearly half of the tested genomic fragments are active in the embryo and display dynamic spatial patterns during development. Enhancer activity is matched to expression patterns of putative target genes and predictive cis -regulatory motifs are identified. Yad Ghavi-Helm et al . present a high-resolution map of enhancer three-dimensional contacts. They find that although there are many local regulatory interactions, long-range interactions are more common. Surprisingly, most interactions appear unchanged between tissues and across development. Thus, transcription initiates from preformed enhancer–promoter loops through release of paused polymerase. The study also implies that the general topology governing enhancer contacts is conserved from flies to humans. Developmental enhancers initiate transcription and are fundamental to our understanding of developmental networks, evolution and disease. Despite their importance, the properties governing enhancer–promoter interactions and their dynamics during embryogenesis remain unclear. At the β-globin locus, enhancer–promoter interactions appear dynamic and cell-type specific 1 , 2 , whereas at the HoxD locus they are stable and ubiquitous, being present in tissues where the target genes are not expressed 3 , 4 . The extent to which preformed enhancer–promoter conformations exist at other, more typical, loci and how transcription is eventually triggered is unclear. Here we generated a high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis, covering two developmental stages and tissue contexts, at unprecedented resolution. Although local regulatory interactions are common, long-range interactions are highly prevalent within the compact Drosophila genome. Each enhancer contacts multiple enhancers, and promoters with similar expression, suggesting a role in their co-regulation. Notably, most interactions appear unchanged between tissue context and across development, arising before gene activation, and are frequently associated with paused RNA polymerase. Our results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer–promoter loops through release of paused polymerase.

Pheromone communication is a key mechanism by which the reproductive division of labor is maintained within insect communities. Understanding how pheromones evolved to regulate social behavior requires knowledge of the molecular regulation of their production. However, even in cases where pheromones were identified, our understanding of their biosynthesis and molecular regulation remains limited. Bumble bees provide a unique system to explore pheromone biosynthesis since workers produce ester sterility signals in their Dufour’s gland that differ from gyne-specific esters and are not produced by queens. These esters are hypothesized to be produced in the exocrine gland where they are stored, and indeed queens, gynes and workers differ significantly in the expression of Dufour’s gland genes coding to enzymes involved in the biosynthesis of esters. However, a previous transcriptome analysis revealed no gene expression differences in the Dufour’s gland of workers despite differences in both ester production and ovarian activation, suggesting that ester production may be regulated lower down. Proteomics of the Dufour’s gland of queens, gynes, and workers recovered over 2400 proteins and broadly matched the previous RNAseq data. However, more than 100 differentially expressed proteins were found between the worker groups, including key enzymes in fatty acid biosynthesis, indicating that the regulation of reproductive signal biosynthesis in workers is done post-transcription. Overall, our data provide evidence that pheromone biosynthesis in the Dufour’s gland is caste specific, that gynes and workers are likely using different enzymes to make their respective wax esters, and that the regulation on pheromone production in queens, gynes and workers is likely done at different regulatory levels, with workers signals being subjected to regulation at the protein level.

Genome sequencing analyses from 765 specimens of Anopheles gambiae and Anopheles coluzzii from 15 locations across Africa characterize patterns of gene flow and variations in population size, and provide a resource for studying the evolution of natural malaria vector populations. Mosquito genetic diversity dataset Anopheles gambiae is the primary mosquito vector responsible for the transmission of malaria in most of sub-Saharan Africa. Alistair Miles, Dominic Kwiatkowski and colleagues report analyses from the Anopheles gambiae 1000 Genomes Project (Ag1000G), including low-coverage genome sequences of 765 specimens of Anopheles gambiae and Anopheles coluzzii , caught in the wild at 15 locations across 8 countries in Africa. The authors analyse genetic variation, finding a high level of genetic diversity in these populations, and characterize patterns of gene flow and variations in population size. These datasets provide a resource for studies into the evolution of malaria vector populations that could guide control strategies and be used to address problems such as the evolution of insecticide resistance. The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease 1 . To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa, and identified over 50 million single nucleotide polymorphisms within the accessible genome. These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size. Strong signals of recent selection were observed in insecticide-resistance genes, with several sweeps spreading over large geographical distances and between species. The design of new tools for mosquito control using gene-drive systems will need to take account of high levels of genetic diversity in natural mosquito populations.

Pesticide exposure and queen loss are considered to be major causes of honey bee colony mortality, yet little is known regarding the effects of regularly encountered agrochemicals on honey bee reproduction. Here, we present the results of a two-generational study using specialized cages to expose queens to commonly used insect growth disrupting pesticides (IGDs) via their retinue of worker bees. Under IGD exposure, we tracked queen performance and worker responses to queens, then the performance of the exposed queens’ offspring was assessed to identify patterns that may contribute to the long-term health and stability of a social insect colony. The positive control, novaluron, resulted in deformed larvae hatching from eggs laid by exposed queens, and methoxyfenozide, diflubenzuron, and novaluron caused a slight decrease in daily egg laying rates, but this was not reflected in the total egg production over the course of the experiment. Curiously, eggs laid by queens exposed to pyriproxyfen exhibited increased hatching rates, and those larvae developed into worker progeny with increased responsiveness to their queens. Additionally, pyriproxyfen and novaluron exposure affected the queen ovarian protein expression, with the overwhelming majority of differentially expressed proteins coming from the pyriproxyfen exposure. We discuss these results and the potential implications for honey bee reproduction and colony health.

Wolbachia used to counter dengue fever The mosquito-borne viral disease dengue fever is an increasing problem in tropical and subtropical regions. Traditional control measures aimed at reducing populations of the main transmission vector, Aedes aegypti , have had little success. Two papers in this issue report an alternative approach to mosquito population control using the bacterium Wolbachia pipientis , natural insect symbionts that facilitate their own transmission through a process called cytoplasmic incompatibility. In the first paper, Scott O'Neill and colleagues describe a Wolbachia strain derived from fruitflies that significantly reduces dengue virus carriage in mosquitoes without imposing a fitness cost. In the second paper, they demonstrate in a controlled field trial that the release of colonized mosquitoes leads to successful invasion of natural mosquito populations. These results suggest a viable strategy to control dengue fever. Dengue fever is the most important mosquito-borne viral disease of humans with more than 50 million cases estimated annually in more than 100 countries 1 , 2 . Disturbingly, the geographic range of dengue is currently expanding and the severity of outbreaks is increasing 2 , 3 , 4 . Control options for dengue are very limited and currently focus on reducing population abundance of the major mosquito vector, Aedes aegypti 5 , 6 . These strategies are failing to reduce dengue incidence in tropical communities and there is an urgent need for effective alternatives. It has been proposed that endosymbiotic bacterial Wolbachia infections of insects might be used in novel strategies for dengue control 7 , 8 , 9 . For example, the w MelPop-CLA Wolbachia strain reduces the lifespan of adult A. aegypti mosquitoes in stably transinfected lines 8 . This life-shortening phenotype was predicted to reduce the potential for dengue transmission. The recent discovery that several Wolbachia infections, including w MelPop-CLA, can also directly influence the susceptibility of insects to infection with a range of insect and human pathogens 9 , 10 , 11 has markedly changed the potential for Wolbachia infections to control human diseases. Here we describe the successful transinfection of A. aegypti with the avirulent w Mel strain of Wolbachia , which induces the reproductive phenotype cytoplasmic incompatibility with minimal apparent fitness costs and high maternal transmission, providing optimal phenotypic effects for invasion. Under semi-field conditions, the w Mel strain increased from an initial starting frequency of 0.65 to near fixation within a few generations, invading A. aegypti populations at an accelerated rate relative to trials with the w MelPop-CLA strain. We also show that w Mel and w MelPop-CLA strains block transmission of dengue serotype 2 (DENV-2) in A. aegypti , forming the basis of a practical approach to dengue suppression 12 .