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Background    Folsomia candida  is a model in soil biology, belonging to the family of Isotomidae, subclass Collembola. It reproduces parthenogenetically in the presence of  Wolbachia , and exhibits remarkable physiological adaptations to stress. To better understand these features and adaptations to life in the soil, we studied its genome in the context of its parthenogenetic lifestyle.    Results  We applied Pacific Bioscience sequencing and assembly to generate a reference genome for  F. candida  of 221.7 Mbp, comprising only 162 scaffolds. The complete genome of its endosymbiont  Wolbachia , was also assembled and turned out to be the largest strain identified so far. Substantial gene family expansions and lineage-specific gene clusters were linked to stress response. A large number of genes (809) were acquired by horizontal gene transfer. A substantial fraction of these genes are involved in lignocellulose degradation. Also, the presence of genes involved in antibiotic biosynthesis was confirmed. Intra-genomic rearrangements of collinear gene clusters were observed, of which 11 were organized as palindromes. The  Hox  gene cluster of  F. candida  showed major rearrangements compared to arthropod consensus cluster, resulting in a disorganized cluster.    Conclusions  The expansion of stress response gene families suggests that stress defense was important to facilitate colonization of soils. The large number of HGT genes related to lignocellulose degradation could be beneficial to unlock carbohydrate sources in soil, especially those contained in decaying plant and fungal organic matter. Intra- as well as inter-scaffold duplications of gene clusters may be a consequence of its parthenogenetic lifestyle. This high quality genome will be instrumental for evolutionary biologists investigating deep phylogenetic lineages among arthropods and will provide the basis for a more mechanistic understanding in soil ecology and ecotoxicology.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3852-x) contains supplementary material, which is available to authorized users.

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida