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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  ( w Fex), 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.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5665-6) contains supplementary material, which is available to authorized users.

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