The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water.

BACKGROUND: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. RESULTS: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. CONCLUSIONS: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Background: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. Results: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. Conclusions: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders

Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome.

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

Genome Architecture and Phenotypic Plasticity: Is the Lethal (2) Essential for Life cluster epigenetically regulated during ovary activation in the honeybee, Apis mellifera?

Phenotypic plasticity is the ability of an organism to alter its phenotype, without altering its genome, in response to environmental cues. There is mounting evidence it is involved in human development, where it has been implicated in the risk of developing noncommunicable adult diseases. Studying the molecular basis of this in mammals can be difficult, particularly separating out single influences from complex environmental interactions. The honey bee, Apis mellifera, provides a useful model in which to study plasticity because of its well-controlled, easily triggered plastic responses. Queen bees are normally the only reproductively active females within a hive, but workers can activate their ovaries in response to the loss of the queen. During this process, over a third of the genome shows altered gene expression, implying that coordinated gene regulation within a chromatin domain may play a role. We have identified a candidate cluster for investigating this hypothesis, the Lethal (2) Essential for Life (L(2)efl) group. The genes of which are down-regulated as the workers undergo ovary activation. The findings of this study show that the original boundaries of the chromatin domain had been underestimated, and that the CTCF insulator element binding sites which flank the genes of the Lethal(2)efl cluster, LOC100576174 and Gmap, appear to be the boundaries of the coordinated regulation. All of the genes within these sites show co-ordinated regulation, with expression occurring in the terminal filament cells of the ovary in queens, workers and active workers. As ovary activation is a phenotypically plastic response to an environmental cue, it was hypothesised that the mechanisms which underlie it are epigenetic in nature, with previous work identifying the repressive histone mark H3K27me3 as likely playing a role in ovary activation. Potential binding sites for the ecdysteroid-regulated transcription factors BR-C Z1 and Z4 were found for all of the genes within the CTCF binding sites, and none directly outside it (LOC411452 and LOC412824). The proposed model for the coordinated regulation of the genes within the chromatin domain containing the L(2)efl group is through an interaction of both histone modifications and ecdysteroid-regulated transcription factors. This work provides evidence for large scale, coordinated changes in gene expression leading to phenotypic plasticity in response to an environmental influence

Genome Architecture and Phenotypic Plasticity: Is the Lethal (2) Essential for Life cluster epigenetically regulated during ovary activation in the honeybee, Apis mellifera?

Phenotypic plasticity is the ability of an organism to alter its phenotype, without altering its genome, in response to environmental cues. There is mounting evidence it is involved in human development, where it has been implicated in the risk of developing noncommunicable adult diseases. Studying the molecular basis of this in mammals can be difficult, particularly separating out single influences from complex environmental interactions. The honey bee, Apis mellifera, provides a useful model in which to study plasticity because of its well-controlled, easily triggered plastic responses. Queen bees are normally the only reproductively active females within a hive, but workers can activate their ovaries in response to the loss of the queen. During this process, over a third of the genome shows altered gene expression, implying that coordinated gene regulation within a chromatin domain may play a role. We have identified a candidate cluster for investigating this hypothesis, the Lethal (2) Essential for Life (L(2)efl) group. The genes of which are down-regulated as the workers undergo ovary activation. The findings of this study show that the original boundaries of the chromatin domain had been underestimated, and that the CTCF insulator element binding sites which flank the genes of the Lethal(2)efl cluster, LOC100576174 and Gmap, appear to be the boundaries of the coordinated regulation. All of the genes within these sites show co-ordinated regulation, with expression occurring in the terminal filament cells of the ovary in queens, workers and active workers. As ovary activation is a phenotypically plastic response to an environmental cue, it was hypothesised that the mechanisms which underlie it are epigenetic in nature, with previous work identifying the repressive histone mark H3K27me3 as likely playing a role in ovary activation. Potential binding sites for the ecdysteroid-regulated transcription factors BR-C Z1 and Z4 were found for all of the genes within the CTCF binding sites, and none directly outside it (LOC411452 and LOC412824). The proposed model for the coordinated regulation of the genes within the chromatin domain containing the L(2)efl group is through an interaction of both histone modifications and ecdysteroid-regulated transcription factors. This work provides evidence for large scale, coordinated changes in gene expression leading to phenotypic plasticity in response to an environmental influence

Sentencing and public confidence: Results from a national Australian survey on public opinions towards sentencing

This paper examines the critical issue of public confidence in sentencing, and presents findings from Phase I of an Australia-wide sentencing and public confidence project. Phase I comprised a nationally representative telephone survey of 6005 participants. The majority of respondents expressed high levels of punitiveness and were dissatisfied with sentences imposed by the courts. Despite this, many were strongly supportive of the use of alternatives to imprisonment for a range of offences. These nuanced views raise questions regarding the efficacy of gauging public opinion using opinion poll style questions; indeed the expected outcome from this first phase of the four phase sentencing and public confidence project. The following phases of this project, reported on elsewhere, examined the effects of various interventions on the robustness and nature of these views initially expressed in a standard ‘top of the head’ opinion poll

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus

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 pensylvanica). 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