Fig. 1

FOSC Helitrons divide into two groups and 5 subgroups. The phylogeny inferred from a multiple sequence alignment of the (predicted) protein sequences of FOSC Helitrons shows that they are separated into two major groups that can be further subdivided into 5 subgroups in total. These subgroups are designated FoHeli1 – FoHeli5. All except three branches have 100% bootstrap support, the bootstrap support (based on 100 replicates) of those three is indicated in red adjacent to the respective branch. Nodes are coloured according to the fungal strain the Helitron was found in. FoHeli1 is distinct from the other 4 subgroups because the protein sequences are nearly identical, because this subgroup is only found in the most completely assembled genome, that of Fol4287, and because this subgroups is also found on core chromosomes of Fol4287. Copies on core chromosomes are indicated with an *. In the genomes of strains F. oxysporum f. sp. radicis-lycopersici CL57 and F. oxysporum f.sp. cubense II5 no genes encoding proteins with a Rep-Hel domain architecture were detected. This is most likely due to deficiencies in genome assembly and gene annotation as we do find partial Helitron copies in these genomes, albeit in small numbers (Additional file 5: Table S5)