Comparison of genomic differences between eFp and pathogenic Fusarium spp.: A time-calibrated phylogeny of nine representative pathogenic Fusarium species, including the outgroup Neonectria ditissima; B, C comparison of the number of carbohydrate-activating enzyme genes and the number of clusters of secondary metabolite genes in the genomes of eFp and the eight pathogenic Fusarium species; D intra-species macro-synteny and re-arrangement plot depicting chromosome comparison between CS3096 and eFp using SyRI software. Syntenic blocks are indicated in grey. CS3096 chromosomes are shown in blue and eFp chromosomes are shown in orange. The four chromosomes were proportional to size; E whole-genome comparison of CS3096 and eFp. The black histogram bars represent the reference gene sequences of the four chromosomes of CS3096; the blue, orange, grey and red histogram bars represent the linear relationship between the gene sequences of the four chromosomes of eFp; the blue broken line (repeat) and the green folded line (SNP) represent the length proportion of the repeated sequences and the single-nucleotide polymorphisms in the reference genome CS3096 with a window of 20 kb, respectively; and the black dots (lost genes) are the missing genes relative to CS3096. SNPs located in the sub-telomeric regions of chromosomes were biased toward the ends of the chromosomes.