Fig. 1: Diverse Starships populate the Verticillium genus.

a The tree in black shows the phylogeny of the 56 strains used in this study across the Verticillium genus, divided into the Flavexudans (FE) and Flavnonexudans (FNE) clades²⁸, based on whole-genome sequence alignments. Circle colors indicate the ten Verticillium spp. while the label comprises species abbreviation followed by strain name. The tree in gray shows only the V. dahliae strains at increased resolution. Scale bars indicate phylogenetic distances expressed as nucleotide substitutions per site. b Repertoires of Starship haplotypes (hap.) per strain. Starships were classified according to previous studies^5,6. Columns indicate Starship haplotypes defined by k-mer similarity and named according to captain navis and family (Supplementary Fig. S1b), whereas heatmap colors show haplotype member counts. “Id” refers to identical Starships (coverage and nucleotide sequence identity >98%) within a haplotype. c Size of the different Verticillium Starships. Points indicate individual Starships listed in Supplementary Data 3. Gray crossbars and error bars indicate the median and 95% confidence interval range of Starship lengths for each navis. d Captain/captain-like tyrosine recombinase (YR) navis repertoires in Starships with multiple YR genes. e Captain/captain-like YR gene classification per strain where “Starship (captain)” indicates YR genes located as the first gene at the 5’-terminus of a Starship for which both borders could reliably be identified with the Starfish tool⁶, “Starship (non-captain)” refers to YR genes located at other sites in a Starship, suggesting nested Starships with unidentified boundaries. Furthermore, “other Starship region” indicates YR gene presence in regions that could not reliably be identified as Starship with Starfish, but that are syntenic to reference Starships. Finally, “unaffiliated” refers to YR genes that cannot reliably be affiliated with a Starship region.