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Background  The soil dwelling saprotrophic non-pathogenic fungus  Fusarium venenatum , routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen  F. graminearum . This study aimed to sequence, assemble and annotate the  F. venenatum  (strain A3/5) genome, and compare this genome with  F. graminearum .    Results  Using shotgun sequencing, a 38,660,329 bp  F. venenatum  genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome. In comparison to  F. graminearum , the predicted gene count of 13,946 was slightly lower. The  F. venenatum  centromeres were found to be 25% smaller compared to  F. graminearum . Chromosome length was 2.8% greater in  F. venenatum,  primarily due to an increased abundance of repetitive elements and transposons, but not transposon diversity. On chromosome 3 a major sequence rearrangement was found, but its overall gene content was relatively unchanged. Unlike homothallic  F. graminearum , heterothallic  F. venenatum  possessed the  MAT1–1  type locus, but lacked the  MAT1–2  locus. The  F. venenatum  genome has the type A trichothecene mycotoxin  TRI5  cluster, whereas  F. graminearum  has type B. From the  F. venenatum  gene set, 786 predicted proteins were species-specific versus NCBI. The annotated  F. venenatum  genome was predicted to possess more genes coding for hydrolytic enzymes and species - specific genes involved in the breakdown of polysaccharides than  F. graminearum . Comparison of the two genomes reduced the previously defined  F. graminearum- specific gene set from 741 to 692 genes. A comparison of the  F. graminearum  versus  F. venenatum  proteomes identified 15 putative secondary metabolite gene clusters (SMC), 109 secreted proteins and 38 candidate effectors not found in  F. venenatum . Five of the 15  F. graminearum-specific  SMCs that were either absent or highly divergent in the  F. venenatum  genome showed increased in planta expression. In addition, two predicted  F. graminearum  transcription factors previously shown to be required for fungal virulence on wheat plants were absent or exhibited high sequence divergence.    Conclusions  This study identifies differences between the  F. venenatum  and  F. graminearum  genomes that may contribute to contrasting lifestyles, and highlights the repertoire of  F. graminearum -specific candidate genes and SMCs potentially required for pathogenesis.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4612-2) contains supplementary material, which is available to authorized users.

Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum