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Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensyl- vanica). Our chromosome-level Vespula assemblies each contain 176–179 Mb of total sequence assembled into 25 scaffolds, with 10–200 unanchored scaffolds, and 16,566–18,948 genes. We annotated gene sets relevant to the applied management of invasive wasp populations, including genes associated with spermatogenesis and development, pesticide resistance, olfactory receptors, immunity and venom. These genomes provide evidence for active DNA methylation in Vespidae and tandem duplications of venom genes. Our genomic resources will contribute to the development of next-generation control strategies, and monitoring potential resistance to chemical control.

Eusocial insect societies are defined by the reproductive division of labour, a social structure that is generally enforced by the reproductive dominant or ‘queen’. Reproductive dominance is maintained through behavioural dominance in some species as well as production of queen pheromones in others, or a mixture of both. Queen mandibular pheromone (QMP) is produced by honeybee (Apis mellifera) queens and has been characterised chemically. How QMP acts to repress worker reproduction, and how it has evolved this activity, remains less well understood. Surprisingly, QMP is capable of repressing reproduction in non-target arthropods which have not co-evolved with QMP, are never exposed to QMP in nature, and are up to 530 million years diverged from the honeybee. Here we show that, in Drosophila melanogaster, QMP treatment mimics nutrient limiting conditions, leading to disrupted reproduction. Exposure to QMP induces an increase in food consumption, consistent with that observed in D. melanogaster in response to starvation conditions. This response induces the activation of two checkpoints within the ovary that inhibit oogenesis. The first is the 2a/b ovarian checkpoint in the germarium, which reduces the flow of presumptive oocytes. A stage 9 ovarian checkpoint is also activated, causing degradation of oocytes. The magnitude of activation of both checkpoints is indistinguishable between QMP treated and starved individuals. As QMP seems to trigger a starvation response in an insect highly diverged from honeybees, we propose that QMP originally evolved by co-opting nutrition signalling pathways to regulate reproduction, a key step in the evolution of eusociality.

Insect segmentation is a well-studied and tractable system with which to investigate the genetic regulation of development. Though insects segment their germband using a variety of methods, modelling work implies that a single gene regulatory network can underpin the two main types of insect segmentation. This means limited genetic changes are required to explain significant differences in segmentation mode between different insects. Evidence for this idea is limited toDrosophila melanogaster, Tribolium castaneum, and the spiderParasteatoda tepidariorum, and the nature of the gene regulatory network (GRN) underlying this model has not been tested. Some insects, for exampleNasonia vitripennisandApis melliferasegment progressively, a pattern not examined in studies of this segmentation model, producing stripes at different times throughout the embryo, but not from a segment addition zone.Here we aim to understand the GRNs patterningNasoniausing a simulation-based approach. We found that an existing model ofDrosophilasegmentation (Clark, 2017) can be used to recapitulateNasonia’s progressive segmentation, if provided with altered inputs in the form of expression of the timer genesNν-caudalandNν-odd paired. We also predict limited topological changes to the pair rule network. Together this implies that very limited changes to theDrosophilanetwork are required to simulateNasoniasegmentation, despite the differences in segmentation modes, implying thatNasoniause a very similar version of an ancestral GRN also used byDrosophila.

CRISPR gene drives have potential for widespread and cost-efficient pest control, but are highly controversial. We examined a potential gene drive targeting spermatogenesis to control the invasive common wasp (Vespula vulgaris) in New Zealand. Vespula wasps are haplodiploid. Their life cycle makes gene drive production challenging, as nests are initiated by single fertilized queens in spring followed by several cohorts of sterile female workers and the production of reproductives in autumn. We show that different spermatogenesis genes have different levels of variation between introduced and native ranges, enabling a potential ‘precision drive’ that could target the reduced genetic diversity and genotypes within the invaded range. In vitro testing showed guide-RNA target specificity and efficacy that was dependent on the gene target within Vespula, but no cross-reactivity in other Hymenoptera. Mathematical modelling incorporating the genetic and life history traits of Vespula wasps identified characteristics for a male sterility drive to achieve population control. There was a trade-off between drive infiltration and impact: a drive causing complete male sterility would not spread, while partial sterility could be effective in limiting population size if the homing rate is high. Our results indicate that gene drives may offer viable suppression for wasps and other haplodiploid pests.

Eusociality is characterised by the reproductive division of labour; a dominant female (queen) or females are responsible for the majority of reproduction, and subordinate females are reproductively constrained. Reproductive constraint can be due to behavioural aggression and/or chemical cues, so-called queen pheromones, produced by the dominant females. In the honeybee, Apis mellifera, this repressive queen pheromone is queen mandibular pheromone (QMP). The mechanism by which honeybee workers are susceptible to QMP is not yet completely understood, however it is thought to be through olfaction via the antennae and/or gustation via trophallaxis. We have investigated whether olfaction is key to sensing of QMP, using both Drosophila melanogaster- a tractable non-eusocial insect which is also reproductively repressed by QMP- and the target species, A. mellifera worker honeybees. D. melanogaster are still capable of sensing and responding to QMP without their antenna and maxillary palps, and therefore without olfactory receptors. When worker honeybees were exposed to QMP but unable to physically interact with it, therefore required to use olfaction, they were similarly not reproductively repressed. Combined, these findings support either a non-olfactory based mechanism for the repression of reproduction via QMP, or redundancy via non-olfactory mechanisms in both D. melanogaster and A. mellifera. This study furthers our understanding of how species are susceptible to QMP, and provides insight into the mechanisms governing QMP responsiveness in these diverse species.

Modified, agricultural landscapes are susceptible to damage by insect pests. Biological control of pests is typically successful once a control agent has established, but this depends on the agent&rsquo, s capacity to co-evolve with the host. Theoretical studies have shown that different levels of genetic variation between the host and the control agent will lead to rapid evolution of resistance in the host. Although this has been reported in one instance, the underlying genetics have not been studied. To address this, we measured the genetic variation in New Zealand populations of the pasture pest, Argentine stem weevil (Listronotus bonariensis), which is controlled with declining effectiveness by a parasitoid wasp, Microctonus hyperodae. We constructed a draft reference genome of the weevil, collected samples from a geographical survey of 10 sites around New Zealand, and genotyped them using a modified genotyping-by-sequencing approach. New Zealand populations of Argentine stem weevil have high levels of heterozygosity and low population structure, consistent with a large effective population size and frequent gene flow. This implies that Argentine stem weevils were able to evolve more rapidly than their biocontrol agent, which reproduces asexually. These findings show that monitoring genetic diversity in biocontrol agents and their targets is critical for long-term success of biological control.

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

The longhorned tick, Haemaphysalis longicornis, feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand. A New Zealand-USA consortium was established to sequence, assemble, and annotate the genome of this tick, using ticks obtained from New Zealand's North Island. In New Zealand, the tick is considered exclusively parthenogenetic and this trait was deemed useful for genome assembly. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq4000 and the long-read Pac Bio Sequel platforms. Twenty-eight SMRT cells produced a total of 21.3 million reads which were assembled with Canu on a reserved supercomputer node with access to 12 TB of RAM, running continuously for over 24 days. The final assembly dataset consisted of 34,211 contigs with an average contig length of 215,205 bp. The quality of the annotated genome was assessed by BUSCO analysis, an approach that provides quantitative measures for the quality of an assembled genome. Over 95% of the BUSCO gene set was found in the assembled genome. Only 48 of the 1066 BUSCO genes were missing and only 9 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information. Keywords: Tick genome, Pac Bio de novo assembly, Genome annotation, Cattle tick

Invasive insect species can act as a plague across the globe, capable of vast expansion and rapid, proliferate reproduction. The spread of pathogens of serious diseases such as malaria and Zika virus and damages to agricultural crops number some of the afflictions invasive insects provide to humans alone. Additionally, an escape from predators can fail to keep invasive insects in check, providing potential threats such as extra resource competition to native species when insects invade. A variety of methods are employed to combat these invasive species, each with their own varying levels of success. Here, we explore the more traditional methods of invasive insect pest control, such as pesticides and biological control. In lieu of several unintended consequences resulting from such practices, we suggest some should be abandoned. We evaluate the potential of new techniques, in particular, those with a genetic component, regarding the costs, benefits and possible consequences of implementing them. And finally, we consider which techniques should be the focus of future research, if we truly wish to manage or even eradicate invasive insects in their introduced lands.

Axis specification is a fundamental developmental process. Despite this, the mechanisms by which it is controlled across insect taxa are strikingly different. An excellent example of this is terminal patterning, which in Diptera such as Drosophila melanogaster occurs via the localized activation of the receptor tyrosine kinase Torso. In Hymenoptera, however, the same process appears to be achieved via localized mRNA. How these mechanisms evolved and what they evolved from remains largely unexplored. Here, we show that torso-like, known for its role in Drosophila terminal patterning, is instead required for the integrity of the vitelline membrane in the hymenopteran wasp Nasonia vitripennis. We find that other genes known to be involved in Drosophila terminal patterning, such as torso and Ptth, also do not function in Nasonia embryonic development. These findings extended to orthologues of Drosophila vitelline membrane proteins known to play a role in localizing Torso-like in Drosophila; in Nasonia these are instead required for dorso–ventral patterning, gastrulation and potentially terminal patterning. Our data underscore the importance of the vitelline membrane in insect development, and implies phenotypes caused by knockdown of torso-like must be interpreted in light of its function in the vitelline membrane. In addition, our data imply that the signalling components of the Drosophila terminal patterning systems were co-opted from roles in regulating moulting, and co-option into terminal patterning involved the evolution of a novel interaction with the vitelline membrane protein Torso-like. This article has an associated First Person interview with the first author of the paper., Summary: In the parasitic wasp Nasonia, Tsl, a key component of the process that defines the termini of the embryo of Drosophila, has a function in the structure of the vitelline membrane.

We de novo assembled a transcriptome for early life-stages of the Aotearoa-New Zealand crayfish, Paranephrops zealandicus, establishing the first genetic resource for this under-developed aquaculture species and for the Paranephrops genus. Mining of this transcriptome for neuropeptides and their putative cognate G protein-coupled receptors (GPCRs) yielded a comprehensive catalogue of neuropeptides, but few putative neuropeptide GPCRs. Of the neuropeptides commonly identified from decapod transcriptomes, only crustacean female sex hormone and insulin-like peptide were absent from our trinity de novo transcriptome assembly, and also RNA-sequence reads. We identified 63 putative neuropeptide precursors from 43 families, predicted to yield 122 active peptides. Transcripts encoding 26 putative neuropeptide GPCRs were identified but were often incomplete. Putative GPCRs for 15 of the neuropeptides identified here were absent from our transcriptome and RNAseq reads. These data highlight the diverse neuropeptide systems already present at the early development life stages sampled here for P. zealandicus.

Queen pheromones effect the reproductive division of labour, a defining feature of eusociality. Reproductive division of labour ensures that one, or a small number of, females are responsible for the majority of reproduction within a colony. Much work on the evolution and function of these pheromones has focussed on Queen Mandibular Pheromone (QMP) which is produced by the Western or European honeybee (Apis mellifera). QMP has phylogenetically broad effects, repressing reproduction in a variety of arthropods, including those distantly related to the honeybee such as the fruit fly Drosophila melanogaster. QMP is highly derived and has little chemical similarity to the majority of hymenopteran queen pheromones which are derived from cuticular hydrocarbons. This raises the question of whether the phylogenetically widespread repression of reproduction by QMP also occurs with more basal saturated hydrocarbon-based queen-pheromones. Using D. melanogaster we show that saturated hydrocarbons, are incapable of repressing reproduction, unlike QMP. We also show no interaction between the four saturated hydrocarbons tested or between the saturated hydrocarbons and QMP, implying that there is no conservation in the mechanism of detection or action between these compounds. We propose that the phylogenetically broad reproductive repression seen in response to QMP is not a feature of all queen pheromones, but unique to QMP itself, which has implications for our understanding of how queen pheromones act and evolve.

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos

Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso‐activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and prothoracicotropic hormone (PTTH), and the spatially restricted protein Torso‐like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. In order to trace the evolutionary history of the TAC we determined the presence or absence of TAC components in the genomes of arthropods. Our analyses reveal that Torso, Trunk and PTTH are evolutionarily labile components of the TAC with multiple individual or combined losses occurring in the arthropod lineages leading to and within the insects. These losses are often correlated, with both ligands and receptor missing from the genome of the same species. We determine that the PTTH gene evolved in the common ancestor of Hemiptera and Holometabola, and is missing from the genomes of a number of species with experimentally demonstrated PTTH activity, implying another molecule may be involved in ecdysis in these species. In contrast, the torso‐like gene is a common component of pancrustacean genomes.

Wing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stonefly Zelandoperla fenestrata species group (Z. fenestrata, Z. tillyardi, Z. pennulata) contains populations ranging from fully winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n = 62) and vestigial-winged (n = 34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. While we found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, we did detect several outlier loci that strongly differentiated morphotypes across independent tests. These findings indicate that small regions of the genome are likely to be highly differentiated between morphotypes, suggesting a genetic basis for wing reduction. Our results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.

Wing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stoneflyZelandoperla fenestrataspecies group (Z. fenestrata, Z. tillyardi, Z. pennulata) contains populations ranging from long-winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n=62) and vestigial-winged (n=34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. We found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, however we did detect several outlier loci that strongly differentiated morphotypes across independent tests. This indicates small regions of the genome are likely to be highly differentiated between morphotypes, indicating a genetic basis for morphotype differentiation. These results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.

We report the complete mitogenome of Sitona obsoletus, an agricultural pest in New Zealand and some European countries. Like other Sitona mitogenomes, the 6 tRNA gene box is ordered RNSAEF, support...

The Developmental Origins of Health and Disease (DOHaD) hypothesis predicts that early-life environmental exposures can be detrimental to later-life health, and that mismatch between the pre- and postnatal environment may contribute to the growing non-communicable disease (NCD) epidemic. Within this is an increasingly recognised role for epigenetic mechanisms; epigenetic modifications can be influenced by, e.g., nutrition, and can alter gene expression in mothers and offspring. Currently, there are no whole-genome transcriptional studies of response to nutritional alteration. Thus, we sought to explore how nutrition affects the expression of genes involved in epigenetic processes in Drosophila melanogaster. We manipulated Drosophila food macronutrient composition at the F0 generation, mismatched F1 offspring back to a standard diet, and analysed the transcriptome of the F0 – F3 generations by RNA-sequencing. At F0, the altered (high protein, low carbohydrate, HPLC) diet increased expression of genes involved in epigenetic processes, with coordinated downregulation of genes involved in immunity, neurotransmission and neurodevelopment, oxidative stress and metabolism. Upon reversion to standard nutrition, mismatched F1 and F2 generations displayed multigenerational inheritance of altered gene expression. By the F3 generation, gene expression had reverted to F0 (matched) levels. These nutritionally-induced gene expression changes demonstrate that dietary alteration can upregulate epigenetic genes, which may influence the expression of genes with broad biological functions. Further, the multigenerational inheritance of the gene expression changes in F1 and F2 mismatched generations suggests a predictive adaptive response (PAR) to maternal nutrition. Our findings may help to understand the interaction between maternal diet and future offspring health, and have direct implications for the current NCD epidemic.

Empty-spiracle class homeodomain proteins have similar roles in anterior and head development in many animal species. We have identified a honeybee empty-spiracles gene and examined its expression in honeybee ovaries and embryos. The expression of honeybee empty-spiracles in embryos is similar to that reported for Drosophila and Tribolium, implying broad conservation of the role of this gene in insect embryogenesis. We also identify expression in somatic and germ-line cells of the ovary, not previously seen in other insect species.

The Torso receptor tyrosine kinase has two crucial roles in Drosophila melanogaster development. One is in the control of insect moulting, which is regulated by the neuropeptide hormone PTTH (prothoracicotropic hormone). PTTH activates ERK signalling via Torso in the prothoracic gland to stimulate ecdysone secretion. Torso also has a role in control of one of the earliest events in embryogenesis in Drosophila; patterning of the embryonic termini. Here Torso is activated by a different, but related, peptide called Trunk. During terminal patterning another protein, Torso-like, has a key role in mediating activation of Torso by Trunk. Torso-like is also expressed in the prothoracic gland and null-mutants have defective developmental timing in Drosophila. This function, however, has been recently shown to be independent of Torso and PTTH. We refer to these proteins, Trunk, PTTH, Torso and Torso-like, as the Torso-activation module. Outside Drosophila we see that the genes encoding the Torso-activation module have a complex phylogenetic history, with different origins and multiple losses of components of this signalling pathway during arthropod evolution. This, together with expression and functional data in a range of insects, leads us to propose that the terminal patterning pathway in Drosophila and Tribolium arose through co-option of PTTH/Trunk and Torso, which has a role in developmental timing, into a new context, and that Torso-like was recruited specifically in the ovary to modulate the specificity of this pathway.

The pea aphid (Acyrthosiphon pisum) can reproduce either sexually or asexually (parthenogenetically), giving rise, in each case, to almost identical adults. These two modes of reproduction are accompanied by differences in ovarian morphology and the developmental environment of the offspring, with sexual forms producing eggs that are laid, whereas asexual development occurs within the mother. Here we examine the effect each mode of reproduction has on the expression of key maternal and axis patterning genes; orthodenticle (otd), hunchback (hb), caudal (cad) and nanos (nos). We show that three of these genes (Ap-hb, Ap-otd and Ap-cad) are expressed differently between the sexually and asexually produced oocytes and embryos of the pea aphid. We also show, using immunohistochemistry and cytoskeletal inhibitors, that Ap-hb RNA is localized differently between sexually and asexually produced oocytes, and that this is likely due to differences in the 3′ untranslated regions of the RNA. Furthermore, Ap-hb and Ap-otd have extensive expression domains in early sexually produced embryos, but are not expressed at equivalent stages in asexually produced embryos. These differences in expression likely correspond with substantial changes in the gene regulatory networks controlling early development in the pea aphid. These data imply that in the evolution of parthenogenesis a new program has evolved to control the development of asexually produced embryos, whilst retaining the existing, sexual, developmental program. The patterns of modification of these developmental processes mirror the changes that we see in developmental processes between species, in that early acting pathways in development are less constrained, and evolve faster, than later ones. We suggest that the evolution of the novel asexual development pathway in aphids is not a simple modification of an ancestral system, but the evolution of two very different developmental mechanisms occurring within a single species.

Summary Development of the symbiotic association in the bipartite lichen Pseudocyphellaria crocata was investigated by characterizing two regions of the thallus. Thallus organization was examined using microscopy. A HIP1-based differential display technique was modified for use on Nostoc strains, including lichenized strains. Northern hybridization and quantitative real-time polymerase chain reaction were used to confirm differential display results, and determine expression levels of key cyanobacterial genes. Photosystem II yield across the thallus was measured using pulse-amplitude modulated fluorescence. Microscopy revealed structural differences in the thallus margins compared with the centre and identified putative heterocysts in both regions. Differential display identified altered transcript levels in both Nostoc punctiforme and a lichenized Nostoc strain. Transcript abundance of cox2, atpA, and ribA was increased in the thallus margin compared with the centre. Expression of cox2 is heterocyst specific and expression of other heterocyst-specific genes (hetR and nifK) was elevated in the margin, whereas, expression of psbB and PSII yield were not. Structural organization of the thallus margin differed from the centre. Both regions contained putative heterocysts but gene expression data indicated increased heterocyst differentiation in the margins where photosystem II yield was decreased. This is consistent with a zone of heterocyst differentiation within the thallus margin.

Aphids exhibit unique attributes, such as polyphenisms and specialized cells to house endosymbionts, that make them an interesting system for studies at the interface of ecology, evolution and development. Here we present a comprehensive characterization of the developmental genes in the pea aphid, Acyrthosiphon pisum, and compare our results to other sequenced insects. We investigated genes involved in fundamental developmental processes such as establishment of the body plan and organogenesis, focusing on transcription factors and components of signalling pathways. We found that most developmental genes were well conserved in the pea aphid, although many lineage-specific gene duplications and gene losses have occurred in several gene families. In particular, genetic components of transforming growth factor beta (TGFβ) Wnt, JAK/STAT (Janus kinase/signal transducer and activator of transcription) and EGF (Epidermal Growth Factor) pathways appear to have been significantly modified in the pea aphid.

Background The New Zealand glowworm is the larva of a carnivorous fungus gnat that produces bioluminescence to attract prey. The bioluminescent system of the glowworm is evolutionarily distinct from other well-characterised systems, especially that of the fireflies, and the molecules involved have not yet been identified. We have used high throughput sequencing technology to produce a transcriptome for the glowworm and identify transcripts encoding proteins that are likely to be involved in glowworm bioluminescence. Results Here we report the sequencing and annotation of the first transcriptome of the glowworm, and a differential analysis of expression from the glowworm light organ compared with non-light organ tissue. The analysis identified six transcripts encoding proteins that are potentially involved in glowworm bioluminescence. Three of these proteins are members of the ANL superfamily of adenylating enzymes, with similar amino acid sequences to that of the luciferase enzyme found in fireflies (31 to 37 % identical), and are candidate luciferases for the glowworm bioluminescent system. The remaining three transcripts encode putative aminoacylase, phosphatidylethanolamine-binding and glutathione S-transferase proteins. Conclusions This research provides a basis for further biochemical studies into how the glowworm produces light, and a source of genetic information to aid future ecological and evolutionary studies of the glowworm. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2006-2) contains supplementary material, which is available to authorized users.

In honeybees, the haplodiploid sex determination system promotes a unique embryogenesis process wherein females develop from fertilized eggs and males develop from unfertilized eggs. However, the developmental strategies of honeybees during early embryogenesis are virtually unknown. Similar to most animals, the honeybee oocytes are supplied with proteins and regulatory elements that support early embryogenesis. As the embryo develops, the zygotic genome is activated and zygotic products gradually replace the preloaded maternal material. The analysis of small RNA and mRNA libraries of mature oocytes and embryos originated from fertilized and unfertilized eggs has allowed us to explore the gene expression dynamics in the first steps of development and during the maternal-to-zygotic transition (MZT). We localized a short sequence motif identified as TAGteam motif and hypothesized to play a similar role in honeybees as in fruit flies, which includes the timing of early zygotic expression (MZT), a function sustained by the presence of the zelda ortholog, which is the main regulator of genome activation. Predicted microRNA (miRNA)-target interactions indicated that there were specific regulators of haploid and diploid embryonic development and an overlap of maternal and zygotic gene expression during the early steps of embryogenesis. Although a number of functions are highly conserved during the early steps of honeybee embryogenesis, the results showed that zygotic genome activation occurs earlier in honeybees than in Drosophila based on the presence of three primary miRNAs (pri-miRNAs) (ame-mir-375, ame-mir-34 and ame-mir-263b) during the cleavage stage in haploid and diploid embryonic development.

Made available in DSpace on 2015-10-21T20:31:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-04-24. Added 1 bitstream(s) on 2015-10-22T09:48:01Z : No. of bitstreams: 1 WOS000353676700001.pdf: 2518339 bytes, checksum: d1f8d18bd059b76504f3fcd9aa639a74 (MD5) National Institutes of Health (NIH) Agriculture and Food Research Initiative Competitive grant from the USDA National Institute of Food and Agriculture Research Council of Norway (NFR) PEW Charitable Trust University of East Anglia, UK Israel Science Foundation (ISF) Biotechnology and Biological Sciences Research Council, UK University of East Anglia University of Alabama College of Arts and Sciences Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Marie Curie International Outgoing Fellowship Swiss National Science Foundation New Faculty Initiative Grant (NFIG) from Illinois State University College of Arts and Sciences DFG Instituto Nacional de Bioinformatica (INB) from ISCIII in Spain Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation. Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA ETH, Inst Integrat Biol, Expt Ecol, CH-8092 Zurich, Switzerland E Carolina Univ, Dept Biol, Greenville, NC 27858 USA Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Ecol Evolut &Behav, Jerusalem, Israel Univ Ghent, Fac Sci, Lab Zoophysiol, B-9000 Ghent, Belgium Univ Otago, Dept Biochem, Labo Evolut &Dev Genet, Dunedin 9054, New Zealand Univ Otago, Dept Biochem, Natl Res Ctr Growth &Dev, Dunedin 9054, New Zealand Univ Missouri, Div Plant Sci, Div Anim Sci, Columbia, MO 65211 USA Univ Missouri, MU Informat Inst, Columbia, MO 65211 USA Georgetown Univ, Dept Biol, Washington, DC 20057 USA Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA Univ Copenhagen, Dept Biol, Ctr Funct &Comparat Insect Gen, Copenhagen, Denmark Univ Hohenheim, Inst Anim Sci, D-70599 Stuttgart, Germany Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA Univ Illinois, Dept Entomol, Urbana, IL 61801 USA Univ Ghent, Fac Biosci Engn, Dept Crop Protect, Lab Agrozool, B-9000 Ghent, Belgium Univ Halle Wittenberg, Inst Biol, Wittenberg, Germany Univ Geneva, Sch Med, Dept Genet Med &Dev, CH-1211 Geneva, Switzerland Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland MIT, Comp Sci &Artificial Intelligence Lab, Cambridge, MA 02139 USA MIT &Harvard, Broad Inst, Cambridge Ctr 7, Cambridge, MA 02142 USA Univ Munster, Inst Evolut &Biodivers, D-48149 Munster, Germany Ctr Genom Regulat CRG, Barcelona 08003, Spain UPF, Barcelona, Spain Ernst Moritz Arndt Univ Greifswald, Inst Math &Comp Sci, D-17487 Greifswald, Germany Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA Natl Lib Med, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA Norwegian Univ Food Sci, Dept Chem Biotechnol &Food Sci, N-1432 As, Norway Univ E Anglia, Sch Comp Sci, Norwich NR4 7TJ, Norfolk, England Univ Dusseldorf, Inst Evolut Genet, D-40225 Dusseldorf, Germany Univ Cologne, Inst Genet, Cologne, Germany Univ Sao Paulo, Dept Biol, Fac Filosofia Ciencias &Letras Ribeirao Preto, BR-14040901 Ribeirao Preto, Brazil Univ Edinburgh, Ashworth Labs, Inst Evolutionary Biol &Edinburgh Gen, Edinburgh EH9 3FL, Midlothian, Scotland Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England Royal Holloway Univ London, Sch Biol Sci, London, England Maynooth Univ, Dept Biol, Co, Kildare, Ireland Univ Bristol, Sch Biol Sci, Bristol BS8 1TQ, Avon, England CSIRO, Land &Water Flagship, Canberra, ACT, Australia Trin Coll Dublin, Sch Nat Sci, Dept Zool, Dublin, Ireland Zool Soc London, Inst Zool, London NW1 4RY, England ETH, Inst Integrat Biol, Theoret Biol, CH-8092 Zurich, Switzerland Swiss Inst Bioinformat, Lausanne, Switzerland Swiss Fed Inst Technol, Dept Biosyst Sci &Engn, Computat Evolut, Basel, Switzerland USDA ARS, Bee Res Lab, Washington, DC 20250 USA Univ Sao Paulo, Dept Genet, Fac Med Ribeirao Preto, BR-14040900 Ribeirao Preto, Brazil N Carolina State Univ, Ctr Res Sci Computat, Raleigh, NC 27695 USA Kyoto Univ, Grad Sch Agr, Lab Insect Ecol, Kyoto, Japan Univ Sao Paulo, Dept Biol Celular &Mol &Bioagentes Patogen, Fac Med Ribeirao Preto, BR-14040900 Ribeirao Preto, Brazil Inst Fed Educ Ciencia &Tecnol Sao Paulo, BR-15991502 Matao, Brazil Ohio State Univ, Dept Entomol, Wooster, OH 44791 USA Oxford Brookes Univ, Fac Hlth &Life Sci, Dept Biol &Med Sci, Oxford OX3 0BP, England Xian Jiaotong Liverpool Univ, Dept Biol Sci, Suzhou, Peoples R China Univ Hosp Halle Saale, Dept Lab Med, Halle, Germany German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany Univ Southampton, Southampton, Hants, England Univ Leicester, Dept Biol, Leicester, Leics, England Univ Fed Sao Carlos, Ctr Ciencias Biol &Saude, Dept Genet &Evolucao, BR-13565905 Sao Carlos, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr &Vet, Dept Tecnol, BR-14884900 Jaboticabal, Brazil Univ N Carolina, Dept Biol, Greensboro, NC 27403 USA Natl Ctr Sci Res Demokritos, Inst Biosci &Applicat, Athens, Greece Univ Munich, Munich, Germany Baylor Coll Med, Dept Mol &Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA Univ Illinois, Roy J Carver Biotechnol, Urbana, IL 61801 USA Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA MD Anderson Canc Ctr, Sch Hlth Profess, Mol Genet Technol Program, Unit 2, Houston, TX 77025 USA Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA Univ Ghent, Dept Biochem &Microbiol, Lab Prot Biochem &Biomol Engn, B-9000 Ghent, Belgium Queen Mary Univ London, Sch Biol &Chem Sci, Dept Biol &Expt Psychol, London E1 4NS, England Guangzhou Univ, Sch Life Sci, Guangzhou, Guangdong, Peoples R China Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Ctr Computat Biol, Baltimore, MD 21205 USA Univ Illinois, Neurosci Program, Dept Entomol, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, 14884-900, Brazi National Institutes of Health (NIH): DP1 OD006416 National Institutes of Health (NIH): U54 HG003273 Agriculture and Food Research Initiative Competitive grant from the USDA National Institute of Food and Agriculture: 2010-65106-21301 FAPESP: 11/03171-5 Marie Curie International Outgoing Fellowship: PIOF-GA-2011-303312 Swiss National Science Foundation: 31003A-125350 Swiss National Science Foundation: 31003A-143936

TGF-β signalling plays a key role in the patterning of metazoan body plans and growth. It is widely regarded as a 'module' capable of co-option into novel functions. The TGF-β pathway arose in the Metazoan lineage, and while it is generally regarded as well conserved across evolutionary time, its components have been largely studied in the Ecdysozoa and Deuterostomia. The recent discovery of the Nodal molecule in molluscs has underlined the necessity of untangling this signalling network in lophotrochozoans in order to truly comprehend the evolution, conservation and diversification of this key pathway. Three novel genome resources, the mollusc Patella vulgata, annelid Pomatoceros lamarcki and rotifer Brachionus plicatilis, along with other publicly available data, were searched for the presence of TGF-β pathway genes. Bayesian and Maximum Likelihood analyses, along with some consideration of conserved domain structure, was used to confirm gene identity. Analysis revealed conservation of key components within the canonical pathway, allied with extensive diversification of TGF-β ligands and partial loss of genes encoding pathway inhibitors in some lophotrochozoan lineages. We fully describe the TGF-β signalling cassette of a range of lophotrochozoans, allowing firm inference to be drawn as to the ancestral state of this pathway in this Superphylum. The TGF-β signalling cascade's reputation as being highly conserved across the Metazoa is reinforced. Diversification within the activin-like complement, as well as potential wide loss of regulatory steps in some Phyla, hint at specific evolutionary implications for aspects of this cascade's functionality in this Superphylum.

Embryo segmentation has been studied extensively in the fruit fly,Drosophila. These studies have demonstrated that a mechanism acting with dual segment periodicity is required for correct patterning of the body plan in this insect, but the evolutionary origin of the mechanism, the pair-rule system, is unclear. We have examined the expression of the homologues of two Drosophila pair-rule genes, runt andpaired (Pax Group III), in segmenting embryos of the two-spotted spider mite (Tetranychus urticae Koch). Spider mites are chelicerates, a group of arthropods that diverged from the lineage leading toDrosophila at least 520 million years ago. In T. urticae,the Pax Group III gene Tu-pax3/7 was expressed during patterning of the prosoma, but not the opisthosoma, in a series of stripes which appear first in even numbered segments, and then in odd numbered segments. The miterunt homologue (Tu-run) in contrast was expressed early in a circular domains that resolved into a segmental pattern. The expression patterns of both of these genes also indicated they are regulated very differently from their Drosophila homologues. The expression pattern of Tu-pax3/7 lends support to the possibility that a pair-rule patterning mechanism is active in the segmentation pathways of chelicerates.

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.

The C termini of N-methyl-d-aspartate (NMDA) receptor NR2 subunits are thought to play a major role in the molecular establishment of memory across the Bilateria, via the phenomenon known as long-term potentiation (LTP). Despite their long history of use as models in the study of memory, the expression and structure of the NR2 subunit in the Lophotrochozoa has remained uncategorized. Here, we report the phylogenic relationships of NR subunits across the Bilateria, and the cloning and in situ analysis of expression of NMDA NR1 and NR2 subunits in the monogont rotifer Brachionus plicatilis. RNA in situ hybridization suggests expression of NMDA receptor subunits in B. plicatilis is neural, consistent with expression observed in other species, and ours is the first report confirming NR2 expression in the lophotrochozoan clade. However, the single NR2 subunit identified in B. plicatilis was found to lack the long C terminal domain found in vertebrates, which is believed to modulate LTP. Further investigation revealed that mollusc and annelid NR2 subunits possess long intracellular C terminal domains. As data from molluscs (and particularly Aplysia californica) are the basis for much of our understanding of LTP, understanding how these diverse lophotrochozoan C termini function in vivo will have many implications for how we consider the evolution of the molecular control of learning and memory across the Metazoa as a whole and interpret the results of experiments into this vital component of cognition.

Pair-rule genes are a class of segmentation genes first identified in Drosophila melanogaster. In Drosophila, these genes act to translate non-periodic information produced by the overlapping patterns of gap gene expression into patterns of gene expression in every other segment. While pair-rule genes are, for the most part, conserved in metazoans, their function in pair-rule patterning is not. Many of these genes do, however, regulate segmentation in arthropods and do so with dual-segment periodicity. Here we examine the expression and function of honeybee orthologues of Drosophila pair-rule genes. Knockdown of the expression of these genes leads to extensive patterning defects, implying that they act in early patterning, as well as segmentation in honeybee embryos. We show that these pair-rule gene orthologues indeed regulate the expression of honeybee maternal and gap genes implying roles in maternal patterning of the honeybee embryo.

In Drosophila, the maternal Torso terminal signaling pathway activates expression of the gene tailless (tll), which is required for the patterning of anterior and posterior termini. We cloned the honeybee orthologue of tll (Am-tll) and found that embryonic expression of Am-tll resembles that of Drosophila, with expression in triangular anterior dorsal–lateral domains and a posterior cap. Functional studies revealed that Am-tll has an essential role in patterning the posterior terminal segments and the brain, similar to the activity of tll in other insects. As the honeybee genome lacks many of the components of the Torso pathway required for terminal patterning, we investigated the regulation of honeybee tailless (Am-tll). Am-tll is expressed maternally and, in the honeybee ovary, Am-tll mRNA becomes localized to the dorsal side of the oocyte, a process requiring the actin cytoskeleton. This RNA becomes redistributed in early embryos to a posterior domain. We also show that the activation of the anterior domain of Am-tll is dependent on honeybee orthodenticle-1. Together these findings indicate major differences in post-transcriptional regulation of tailless in the honeybee compared to other insects but that this regulation leads to a conserved expression pattern. These results provide an example of an early event in development evolving and yet still producing a conserved output for the rest of development to build upon.

Background Gene clusters, such as the Hox gene cluster, are known to have critical roles in development. In eukaryotes gene clusters arise primarily by tandem gene duplication and divergence. Genes within a cluster are often co-regulated, providing selective pressure to maintain the genome organisation, and this co-regulation can result in temporal or spatial co-linearity of gene expression. It has been previously noted that in Drosophila melanogaster, three of the four runt-domain (RD) containing genes are found in a relatively tight cluster on chromosome 1, raising the possibility of a putative functional RD gene cluster in D. melanogaster. Results To investigate the possibility of such a gene cluster, orthologues of the Drosophila melanogaste r RD genes were identified in several endopterygotan insects, two exopterygotan insects and two non-insect arthropods. In all insect species four RD genes were identified and orthology was assigned to the Drosophila sequences by phylogenetic analyses. Although four RD genes were found in the crustacean D. pulex, orthology could not be assigned to the insect sequences, indicating independent gene duplications from a single ancestor following the split of the hexapod lineage from the crustacean lineage. In insects, two chromosomal arrangements of these genes was observed; the first a semi-dispersed cluster, such as in Drosophila, where lozenge is separated from the core cluster of three RD genes often by megabases of DNA. The second arrangement was a tight cluster of the four RD genes, such as in Apis mellifera. This genomic organisation, particularly of the three core RD genes, raises the possibility of shared regulatory elements. In situ hybridisation of embryonic expression of the four RD genes in Drosophila melanogaster and the honeybee A. mellifera shows no evidence for either spatial or temporal co-linearity of expression during embryogenesis. Conclusion All fully sequenced insect genomes contain four RD genes and orthology can be assigned to these genes based on similarity to the D. melanogaster protein sequences. Examination of the genomic organisation of these genes provides evidence for a functional RD gene cluster. RD genes from non-insect arthropods are also clustered, however the lack of orthology between these and insect RD genes suggests this cluster is likely to have resulted from a duplication event independent from that which created the insect RD gene cluster. Analysis of embryonic RD gene expression in two endopterygotan insects, A. mellifera and D. melanogaster, did not show evidence for coordinated gene expression, therefore while the functional significance of this gene cluster remains unknown its maintenance during insect evolution implies some functional significance to the cluster.

The current insect genome sequencing projects provide an opportunity to extend studies of the evolution of developmental genes and pathways in insects. In this paper we examine the conservation and divergence of genes and developmental processes between Drosophila and the honey bee; two holometabolous insects whose lineages separated ∼300 million years ago, by comparing the presence or absence of 308 Drosophila developmental genes in the honey bee. Through examination of the presence or absence of genes involved in conserved pathways (cell signaling, axis formation, segmentation and homeobox transcription factors), we find that the vast majority of genes are conserved. Some genes involved in these processes are, however, missing in the honey bee. We have also examined the orthology of Drosophila genes involved in processes that differ between the honey bee and Drosophila. Many of these genes are preserved in the honey bee despite the process in which they act in Drosophila being different or absent in the honey bee. Many of the missing genes in both situations appear to have arisen recently in the Drosophila lineage, have single known functions in Drosophila, and act early in developmental pathways, while those that are preserved have pleiotropic functions. An evolutionary interpretation of these data is that either genes with multiple functions in a common ancestor are more likely to be preserved in both insect lineages, or genes that are preserved throughout evolution are more likely to co-opt additional functions.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history., Author Summary Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.

Pax group III genes are involved in a number of processes during insect segmentation. In Drosophila melanogaster, three genes, paired, gooseberry and gooseberry-neuro, regulate segmental patterning of the epidermis and nervous system. Paired acts as a pair-rule gene and gooseberry as a segment polarity gene. Studies of Pax group III genes in other insects have indicated that their expression is a good marker for understanding the underlying molecular mechanisms of segmentation. We have cloned three Pax group III genes from the honeybee (Apis mellifera) and examined their relationships to other insect Pax group III genes and their expression patterns during honeybee segmentation. The expression pattern of the honeybee homologue of paired is similar to that of paired in Drosophila, but its expression is modulated by anterior-posterior temporal patterning similar to the expression of Pax group III proteins in Tribolium. The expression of the other two Pax group III genes in the honeybee indicates that they also act in segmentation and nervous system development, as do these genes in other insects.

Although the molecular pathways that pattern the early embryo of Drosophila melanogaster are well understood, how these pathways differ in other types of insect embryo remains largely unknown. We have examined the expression of three markers of early patterning in the embryo of the African plague locust Schistocerca gregaria, an orthopteran insect that displays a mode of embryogenesis very different from that of Drosophila. Transcripts of the caudal gene are expressed maternally and are present in all cells that aggregate to form the early embryonic rudiment. First signs of a posterior-to-anterior gradient in the levels of caudal transcript appear in the early heart-stage embryo, shortly before gastrulation. This gradient rapidly resolves to a defined expression domain marking segment A11. The decapentaplegic (dpp) gene, which encodes a transforming growth factor β family ligand, is first expressed in a circle of cells that delimit the margins of the embryonic primordium, where embryonic and extra-embryonic tissues abut. Patterned transcription of wingless reveals that the first segments are delineated in the Schistocerca embryo substantially earlier than previously thought, at least 14-16 hours before the onset of engrailed expression. By the late heart-stage, gnathal and thoracic segments are all defined. Thus, with respect to the molecular patterning of segments, the short germ Schistocerca embryo differs little from intermediate germ embryos. The expression of these marker genes suggests that embryonic pattern formation in the grasshopper occurs as cells move together to form the blastodisc.

In insects, a key step in the early patterning of the egg is to distinguish the primordium of the embryo proper from those regions that will form extra-embryonic membranes. In Drosophila, where these processes are well understood, the structure of the extra-embryonic membranes is highly derived. The distinct amnion and serosa typical of lower insects is replaced by a single, fused, and much reduced membrane, the amnioserosa, which never secretes an embryonic cuticle. We have used the Zen gene as a marker to study the formation of the extra-embryonic membranes, and other aspects of early embryonic patterning, in the grasshopper Schistocerca gregaria (African Plague Locust). Zen genes are derived from Hox genes, but in Drosophila they appear to have lost any role in patterning the A/P axis of the embryo; instead, they are involved in D/V patterning and the specification of the extra-embryonic membranes. We show that the Schistocerca zen gene is expressed during embryogenesis in three distinct phases. The first of these is during cleavage, when Sgzen is transiently expressed in all energids that reach the cell surface. The second phase of expression initiates in a ring of "necklace cells" that surround the forming embryo, and demarcate the boundary between the amnion and serosa. This leads to expression throughout the serosa. The final phase of expression is in the amnion, after this has separated from the serosa. This complex pattern implies that the role of Sgzen in Schistocerca is not limited solely to the specification of cell identity in the extra-embryonic membranes. We also report that the Schistocerca zen gene is expressed maternally, unlike its Drosophila and Tribolium counterparts. A distinct maternal transcript, and maternal Zen protein, accumulate in the developing oocyte from early post-meiotic stages. They remain uniformly distributed in the oocyte cytoplasm until late vitellogenic stages, when the protein and RNA become somewhat concentrated at the egg cortex and in the posterior polar cap of the oocyte, probably by passive exclusion from the yolk. The cytoplasmic localization of Sgzen protein in the oocyte, and at some stages during embryogenesis, implies that nuclear exclusion of this transcription factor is specifically controlled.

Studies of somitogenesis in vertebrates have identified a number of genes that are regulated by a periodic oscillator that patterns the pre-somitic mesoderm. One of these genes, hairy, is homologous to a Drosophila segmentation gene that also shows periodic spatial expression. This, and the periodic expression of a zebrafish homologue of hairy during somitogenesis, has suggested that insect segmentation and vertebrate somitogenesis may use similar molecular mechanisms and possibly share a common origin. In chicks and mice expression of the lunatic fringe gene also oscillates in the presomitic mesoderm. Fringe encodes an extracellular protein that regulates Notch signalling. This, and the finding that mutations in Notch or its ligands disrupt somite patterning, suggests that Notch signalling plays an important role in vertebrate somitogenesis. Although Notch signalling is not known to play a role in the formation of segments in Drosophila, we reasoned that it might do so in other insects such as the grasshopper, where segment boundaries form between cells, not between syncytial nuclei as they do in Drosophila. Here we report the cloning of a single fringe gene from the grasshopper Schistocerca. We show that it is not detectably expressed in the forming trunk segments of the embryo until after segment boundaries have formed. We conclude that fringe is not part of the mechanism that makes segments in Schistocerca. Thereafter it is expressed in a pattern which shows that it is a downstream target of the segmentation machinery and suggests that it may play a role in segment morphogenesis. Like its Drosophila counterpart, Schistocerca fringe is also expressed in the eye, in rings in the legs, and during oogenesis, in follicle cells.

Aphids are the leading pests in agricultural crops. A large-scale sequencing of 40,904 ESTs from the pea aphid Acyrthosiphon pisum was carried out to define a catalog of 12,082 unique transcripts. A strong AT bias was found, indicating a compositional shift between Drosophila melanogaster and A. pisum. An in silico profiling analysis characterized 135 transcripts specific to pea-aphid tissues (relating to bacteriocytes and parthenogenetic embryos). This project is the first to address the genetics of the Hemiptera and of a hemimetabolous insect.

Background The Enhancer of split complex is an unusual gene complex found in Arthropod genomes. Where known this complex of genes is often regulated by Notch cell signalling and is critically important for neurogenesis. The Enhancer of split complex is made up of two different classes of genes, basic helix-loop-helix-orange domain transcription factors and bearded class genes. The association of these genes has been detected in the genomes of insects and crustaceans. Results Tracing the evolution of the Enhancer of split complex in recently sequenced Arthropod genomes indicates that enhancer of split basic helix-loop-helix orange domain genes arose before the common ancestor of insects and Crustacea, and before the formation of the complex. Throughout insect and crustacean evolution, a four-gene cluster has been present with lineage specific gene losses and duplications. The complex can be found in the vast majority of genomes, but appears to be missing from the genomes of chalcid wasps, raising questions as to how they carry out neurogenesis in the absence of these crucial genes. Conclusions The enhancer of split complex arose in the common ancestor of Crustacea and insects, probably through the linkage of a basic helix-loop-helix orange domain gene and a bearded class gene. The complex has been maintained, with variations, throughout insect and crustacean evolution indicating some function of the complex, such as coordinate regulation, may maintain its structure through evolutionary time. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1926-1) contains supplementary material, which is available to authorized users.

The specification of germ cells is an important process during the development of all animals. Expression of an evolutionarily conserved gene such as vasa can be used as a marker for germ cell fate. We have isolated a vasa-related gene from the two-spotted spider mite (Tetranychus urticae) and used it to examine the segregation of germ cells in this animal. In spider mites, vasa expression first appears in a group of cells that do not join the initial blastoderm surface. Instead, these cells remain in the interior of the blastoderm and then migrate to posterior regions of the embryo, where they form a cluster that appears in regions of the embryo consistent with the gonads. The expression pattern of this spider mite vasa homologue implies a novel process acts to specify germ cells in this species and that the specification of germ cells is an evolutionarily labile process.

Background The Sox gene family of transcriptional regulators have essential roles during development and have been extensively studied in vertebrates. The mouse, human and fugu genomes contain at least 20 Sox genes, which are subdivided into groups based on sequence similarity of the highly conserved HMG domain. In the well-studied insect Drosophila melanogaster, eight Sox genes have been identified and are involved in processes such as neurogenesis, dorsal-ventral patterning and segmentation. Results We examined the available genome sequences of Apis mellifera, Nasonia vitripennis, Tribolium castaneum, Anopheles gambiae and identified Sox family members which were classified by phylogenetics using the HMG domains. Using in situ hybridisation we determined the expression patterns of eight honeybee Sox genes in honeybee embryo, adult brain and queen ovary. AmSoxB group genes were expressed in the nervous system, brain and Malphigian tubules. The restricted localization of AmSox21b and AmSoxB1 mRNAs within the oocyte, suggested a role in, or that they are regulated by, dorsal-ventral patterning. AmSoxC, D and F were expressed ubiquitously in late embryos and in the follicle cells of the queen ovary. Expression of AmSoxF and two AmSoxE genes was detected in the drone testis. Conclusion Insect genomes contain between eight and nine Sox genes, with at least four members belonging to Sox group B and other Sox subgroups each being represented by a single Sox gene. Hymenopteran insects have an additional SoxE gene, which may have arisen by gene duplication. Expression analyses of honeybee SoxB genes implies that this group of genes may be able to rapidly evolve new functions and expression domains, while the combined expression pattern of all the SoxB genes is maintained.