Fig. 4

Synteny of the accessory genomes of Foa race 4 and other strains. Circos plot comparisons of “reciprocal best BLAST hits” (RBBH) homologs of genes in non-core (=accessory) regions of the F. oxysporum genome in F. oxysporum f. sp. apii (Foa) race 4 on the right side and on the left side Foa race 3 (a), Foci3–2 (b), Foa race 2 (c) and Fol 4287 (d). Contigs less than 150kbp are not shown. Non-core regions were determined using progressiveMauve with Fol4287 as a reference. Tic marks on ring a are 500 kb. Within ring a, red lines indicate miniature impala transposable elements (mimps), and blue lines indicate all genes with significantly (adjusted P < 0.05) increased expression in planta in celery crowns that were infected with Foa race 4 compared to Foa race 4 grown in vitro. In ring b, the solid colors within the upper portion denote a region with homology to one of the Fol core chromosomes. Genes within these regions are part of the core genome. Blue shows the density of repetitive elements with a full scale of 120 per 100 kb increment. In ring c, dark grey shows the density of gene models with a full scale of 50 per 100 kb increment. In ring d, the grey lines show genes in the accessory genome that have an RBBH with a > 80% identity over > 80% of the predicted nucleotide sequence. In the center, lines connect the RBBH in the accessory genome; genes connected by black lines are in accessory contigs and genes connected with other colors are in non-core regions of core chromosomes. The plots illustrate the most synteny between Foa races 4 and 3 in the accessory genome, less synteny between Foa race 4 and the F. oxysporum f. sp. coriandrii (Foci) strain 3–2, and the least synteny between Foa race 4 and either Foa race 2 or the f. sp. lycopersici reference Fol4287. Quantification of the number of homologs and their synteny are in Additional File 1