Transcriptomic responses to location learning by honeybee dancers are partly mirrored in the brains of dance-followers

Open Access via the Royal Society agreement This research was funded by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant no. 638873 to E.L.). This funding also supported F.M. for the whole duration of the project.Peer reviewedPublisher PD

GeneValidator: identify problems with protein-coding gene predictions

This work was supported by the Sciruby community, NESCent Google Summer of Code, the NESCent “Building non-model species genome curation communities” working group, Biotechnology and Biological Sciences Research Council [BB/K004204/1], Natural Environment Research Council [NE/L00626X/1, EOS Cloud] and QMUL Apocrita Midplus (EP/K000128/1)

Visualization and quality assessment of de novo genome assemblies

Summary: Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds. Contact: [email protected]; [email protected] Availability: Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet. Supplementary Information: Supplementary data are available at Bioinformatics onlin

Social Isolation and Group Size are Associated with Divergent Gene Expression in the Brain of Ant Queens

ACKNOWLEDGEMENTS The authors would like to thank members of the Shoemaker’s Lab at the USDA-ARS in Gainesville for support during field experiments and sample collections: special thanks to Eileen Carroll who coordinated all activities associated with field experiments and arranged the shipment of samples to the UK. The authors would also like to thank all members of the Leadbeater Lab at Royal Holloway for providing feedback on an early draft of this manuscript, and the two anonymous reviewers who provided constructive criticism that helped improving the manuscript. This work was supported by a Marie Curie International Incoming Fellowship (FP7-PEOPLE-2013-IIF-625487) to F.M. and M.J.F.B. which also supported F.M. salary for two years. The Natural Environment Research Council supported the salaries of C.M.R. (NE/L002485/1) and Y.W. (NE/L00626X/1). The authors declare that they have no conflict of interest. Open access via Wiley agreementPeer reviewedPublisher PD

An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta

Ants display a range of fascinating behaviors, a remarkable level of intra-species phenotypic plasticity and many other interesting characteristics. Here we present a new tool to study the molecular mechanisms underlying these traits: a tentatively annotated expressed sequence tag (EST) resource for the fire ant Solenopsis invicta. From a normalized cDNA library we obtained 21,715 ESTs, which represent 11,864 putatively different transcripts with very diverse molecular functions. All ESTs were used to construct a cDNA microarray

The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host

Abstract Background Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict. Results In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7 Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes. Conclusion We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization

Fourmidable: a database for ant genomics

BACKGROUND: Fourmidable is an infrastructure to curate and share the emerging genetic, molecular, and functional genomic data and protocols for ants. DESCRIPTION: The Fourmidable assembly pipeline groups nucleotide sequences into clusters before independently assembling each cluster. Subsequently, assembled sequences are annotated via Interproscan and BLAST against general and insect-specific databases. Gene-specific information can be retrieved using gene identifiers, searching for similar sequences or browsing through inferred Gene Ontology annotations. The database will readily scale as ultra-high throughput sequence data and sequences from additional species become available. CONCLUSION: Fourmidable currently houses EST data from two ant species and microarray gene expression data for one of these. Fourmidable is publicly available at http://fourmidable.unil.ch

Convergent evolution of a labile nutritional symbiosis in ants

Ants are among the most successful organisms on Earth. It has been suggested that forming symbioses with nutrient-supplementing microbes may have contributed to their success, by allowing ants to invade otherwise inaccessible niches. However, it is unclear whether ants have evolved symbioses repeatedly to overcome the same nutrient limitations. Here, we address this question by comparing the independently evolved symbioses in Camponotus, Plagiolepis, Formica and Cardiocondyla ants. Our analysis reveals the only metabolic function consistently retained in all of the symbiont genomes is the capacity to synthesise tyrosine. We also show that in certain multi-queen lineages that have co-diversified with their symbiont for millions of years, only a fraction of queens carry the symbiont, suggesting ants differ in their colony-level reliance on symbiont-derived resources. Our results imply that symbioses can arise to solve common problems, but hosts may differ in their dependence on symbionts, highlighting the evolutionary forces influencing the persistence of long-term endosymbiotic mutualisms.Peer reviewe