Fig. 2: Starships are hotspots of genomic rearrangements.

a Circular plots showing the locations of Starship regions, adaptive genomic regions (AGRs), and genomic rearrangements between V. dahliae strains JR2 (upper eight chromosomes) and VdLs17 (lower eight chromosomes). Tracks are filled with colors representing either core, AGR, or centromeric regions, overlaid with bold lines and arrows representing Starship regions and Starships colored by haplotype. Overlapping arrows in a single region indicate that the Starship orientation is not determined due to the presence of captains at the 5’ end of both strands. Regular triangles point to the captain and captain-like tyrosine recombinase (YR) genes, colored by family and annotated with navis identification (ID). The overlaps among these elements and rearrangement breakpoints are shown in Supplementary Fig. S2 at a higher resolution. Colored bands at the inner edge of tracks represent genetic elements grouped into protein coding sequence (CDS) and transposable element (TE). Ribbons connect syntenic regions (>80% nucleotide sequence identity over 10 kb). b Total length of genomic compartments in V. dahliae strains JR2 and VdLs17. c Violin plots depicting the sequence alignment coverage determined by comparing JR2 genomic compartments against 35 V. dahliae genomes (Supplementary Fig. S3). Points indicate the coverage, and the color represents genome-wide average nucleotide identity (ANI) for each genome alignment (n = 35), while blue crossbars indicate the median values. Different letter labels indicate significant differences (two-sided Dunn’s test, adjusted p < 0.05). d Violin plots depicting the fold-enrichment of structural variations (SVs) (insertion and deletion (INDEL) without size definition, translocation (TRA), inversion (INV), and duplication (DUP)) in the three genomic compartments compared with the genome-wide average. SVs were determined by comparing the genome of V. dahliae strain JR2 against the 35 V. dahliae genomes. Points indicate the fold-enrichment determined for each genome (n = 35), while blue crossbars indicate the median values. Different letter labels indicate significant differences for each genetic variation (two-sided Dunn’s test, adjusted p < 0.05). e Violin plots depicting length of unaligned regions accompanied by SVs in JR2 genomic compartments. Points indicate the length of every gap (n = 644 in Starship regions, n = 1163 in other AGRs, and n = 8877 in core regions) found between the JR2 genome and 35 V. dahliae genomes in a color and shape representing SV type, while blue crossbars indicate the median values. Different letter labels indicate significant differences (two-sided Dunn’s test, adjusted p < 0.05). f Starship rearrangements between the genomes of V. dahliae strains JR2 (X-axis) and GF1192 (Y-axis). Diagonal lines indicate synteny, while the color represents nucleotide sequence identity. Bars and triangles aligned to the plots indicate the positions of Starships and YR genes. The left and right plots are superimposed in Supplementary Fig. S4b to make the breakpoints of inter-chromosomal rearrangements clearer.