Fig. 5

Synteny of gene models in four selected Foa race 4 accessory superscaffolds that have the most up-expressed genes in planta compared to in vitro. These four accessory contigs are shown on the top right, and contigs with homologous genes from the strain indicated in the top left are to the left and below in Foa race 3 (a), Foci3–2 (b), Foa race 2 (c) and Fol 4287 (d). Rings a-c are described in the legend for Fig. 4; the blue lines in ring a 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 the center, lines connect each “reciprocal best BLAST hit” (RBBH) with a > 80% identity over > 80% of the predicted nucleotide sequence. There are the following number of genes in each of the selected accessory Foa race 4 superscaffolds (SS): SS2, 523; SS17, 480; SS19, 320; and SS14, 204. In these selected accessory contigs, Foa race 3 (A) has homologs of 59 to 73% of these Foa race 4 gene models, depending on the contig (Additional file 14). Foci3–2 (B) has 70 and 58% of the homologs in the lineage-specific SS 2 and SS19 and only 8 and 25% of the homologs of the host-specific SS 17 and SS 14. Both Foa race 2 (C) and Fol 4287 (D), which are in FOSC Clade 3, have the fewest homologs, with only a total of 11 to 12% of the homologs in the four accessory contigs in Foa race 4