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 Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host–microbe symbioses

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

The developmental basis of caste evolution in ants

Phenotypic plasticity is the ability for a single genotype to give rise to alternative adaptive phenotypes in response to environmental conditions facilitating their survival. In some cases, environmental conditions can influence the course of development of an organism, leading to the induction of novel phenotypic variation, the raw materials for selection in evolution. Although this fact has the potential to unify the disparate fields of ecology, development and evolution, we have only begun to investigate the underlying molecular mechanisms that translate the environment into phenotypic diversity. Ants are highly plastic; during development a single genotype can give rise to an array of alternative phenotypes related to dramatic differences in morphology, longevity, reproduction and behavior. This environmental sensitivity is the basis for the diversity of complex ant caste systems. Here, I used ant development of the hyperdiverse genera Pheidole and Camponotus as models to investigate my major goal, which is to understand how ecology (environment) acts on development, generating morphological variation, which can then lead to morphological diversification and evolution. The first specific goal (Chapter 2) of my thesis is to investigate the hormonal and developmental genetic basis underlying the evolution of novel worker ant subcastes. Specifically, the genus Pheidole is composed of over 1000 species, all of which comprise a complex worker caste system of minor workers and soldiers. In a hand full of these species, there exists an additional novel worker subcaste, the supersoldier. Through phylogenetic and developmental genetic analysis, I determined that this subcaste has evolved in parallel in different species. I then discovered through field observations and hormonal manipulations that there exists an ancestral developmental potential in this group: all Pheidole species have the hidden capacity to produce supersoldiers through environmental induction, the recurrence of which can lead to their evolution. The second specific goal of my thesis (Chapter 4) is to investigate the epigenetic mechanisms that translate environmental conditions into morphological variation within castes. Specifically, I investigated the involvement of DNA methylation in generating continuous sizing in the worker caste of the genus Camponotus. I discovered that DNA methylation is responsible for generating a continuous distribution of worker size and that one of its primary targets is the gene Egfr. Furthermore, the methylation level of Egfr is associated with quantitative variation in worker size and pharmacological inhibition of EGFR signaling demonstrated that this pathway is capable of generating the continuous distribution of size found within this caste. DNA methylation is an epigenetic mechanism that is known to cause transgenerational inheritance and therefore it can facilitate the evolution of environmentally generated quantitative variation. Collectively, the results of my thesis show how the environment acts on development through the integration of hormones, genes and epigenetic mechanisms to generate phenotypic variation for selection to act on. Perhaps we are coming closer to a point in time in evolutionary theory when we can say that the environment is as important in generating phenotypic variation as it is in the process of selection.La plasticité phénotypique est l'habileté d'un génotype unique de produire des phénotypes adaptatifs alternes en réponse à des conditions environnementales facilitant leur survie. Dans certains cas, les conditions environnementales peuvent influencer le cours du développement d'un organisme, menant à l'induction d'une variation phénotypique nouvelle, qui est la matière brute pour la sélection en évolution. Bien que ce fait ait le potentiel d'unifier les champs distincts de l'écologie, du développement et de l'évolution, on commence seulement à étudier les mécanismes moléculaires fondamentaux qui traduisent l'environnement en diversité phénotypique. Les fourmis démontrent une grande plasticité phénotypique; durant le développement, un génotype unique peut produire une diversité de phénotypes adaptatifs qui démontrent des différences dramatiques de morphologie, de longévité, de reproduction et de comportement. Cette sensibilité environnementale est à la base de la diversité des systèmes complexes de castes chez les fourmis. Ici, j'ai utilisé le développement des genres hyperdiversifiés Pheidole et Camponotus comme modèles pour investiguer mon but principal, qui est de comprendre comment l'écologie (l'environnement) agit sur le développement, en générant de la variation morphologique qui peut par la suite mener à une évolution morphologique. Le premier objectif spécifique de ma thèse (Chapitre 2) est d'investiguer les bases hormonales et du développement des nouvelles sous-castes ouvrières chez les fourmis. Plus spécifiquement, le genre Pheidole est composé de plus de 1000 espèces, toutes démontrant un système de castes ouvrières complexe comprenant des ouvrières mineurs et des soldates. Chez un petit groupe de ces espèces, il existe une caste ouvrière additionnelle, la supersoldate. En utilisant des analyses phylogénétiques et de génétique du développement, j'ai déterminé que cette sous-caste a évolué en parallèle chez les différentes espèces. J'ai par la suite découvert, par des observations sur le terrain et des manipulations hormonales, qu'il existe un potentiel ancestral de développement dans ce groupe: toutes les espèces de Pheidole ont une capacité cachée de produire des supersoldates par induction environnementale, cette récurrence pouvant mener à leur évolution. Le second objectif spécifique de ma thèse (Chapitre 4) est d'investiguer les mécanismes épigénétiques qui traduisent les conditions environnementales en variation morphologique entre les castes. Plus spécifiquement, j'ai investigué le rôle de la méthylation de l'ADN dans l'élaboration d'une distribution de taille continue chez la caste ouvrière de Camponotus. J'ai découvert que la méthylation de l'ADN génère une distribution continue de taille chez la caste ouvrière et que l'une de ses cibles principales est le gène Egfr. D'ailleurs, le niveau de méthylation de Egfr est associé à une variation quantitative de la taille des ouvrières et une inhibition pharmacologique de la signalisation EGFR a démontré que cette voie de signalisation est capable de générer la distribution continue des tailles dans cette caste. La méthylation de l'ADN est un mécanisme épigénétique qui est connu pour causer une héritabilité transgénérationelle et donc, elle peut faciliter l'évolution d'une variation quantitative générée par l'environnement. Collectivement, les résultats de ma thèse montrent comment l'environnement agit sur le développement par l'intégration des hormones, des gènes et des mécanismes épigénétiques pour générer de la variation phénotypique sur laquelle la sélection naturelle peut agir par la suite. Peut-être que nous nous rapprochons d'un moment où la théorie de l'évolution peut proposer que l'environnement soit également important pour générer de la variation phénotypique qu'il peut l'être au cours du processus de sélection

Interruption points in the wing gene regulatory network underlying wing polyphenism evolved independently in male and female morphs in Cardiocondyla ants

Wing polyphenism in ants, which produces a winged female queen caste and a wingless female worker caste, evolved approximately 150 million years ago and has been key to the remarkable success of ants. Approximately 20 million years ago, the myrmicine ant genus Cardiocondyla evolved an additional wing polyphenism among males producing two male morphs: wingless males that fight to enhance mating success and winged males that disperse. Here we show that interruption of rudimentary wing-disc development in larvae of the ant Cardiocondyla obscurior occurs further downstream in the network in wingless males as compared with wingless female workers. This pattern is corroborated in C. kagutsuchi, a species from a different clade within the genus, indicating that late interruption of wing development in males is conserved across Cardiocondyla. Therefore, our results show that the novel male wing polyphenism was not developmentally constrained by the pre-existing female wing polyphenism and evolved through independent alteration of interruption points in the wing gene network. Furthermore, a comparison of adult morphological characters in C. obscurior reveals that developmental trajectories lead to similar morphological trait integration between winged and wingless females, but dramatically different integration between winged and wingless males. This suggests that the alternative sex-specific developmental routes to achieve winglessness in the genus Cardiocondyla may have evolved through different selection regimes acting on wingless males and females

Draft genome of the red harvester ant \u3ci\u3ePogonomyrmex barbatus\u3c/i\u3e

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences betweenthe queenandworker castes (e.g.,wingsandovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps inparallel with the development of the North American deserts

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses