Inter-genome comparison of the Quorn fungus <italic>Fusarium venenatum</italic> and the closely related plant infecting pathogen <italic>Fusarium graminearum</italic>.

Background: The soil dwelling saprotrophic non-pathogenic fungus <italic>Fusarium venenatum</italic>, routinely used in the commercial fermentation industry, is phylogenetically closely related to the globally important cereal and non-cereal infecting pathogen <italic>F. graminearum</italic>. This study aimed to sequence, assemble and annotate the <italic>F. venenatum</italic> (strain A3/5) genome, and compare this genome with <italic>F. graminearum</italic>. Results: Using shotgun sequencing, a 38,660,329 bp <italic>F. venenatum</italic> genome was assembled into four chromosomes, and a 78,618 bp mitochondrial genome. In comparison to <italic>F. graminearum</italic>, the predicted gene count of 13,946 was slightly lower. The <italic>F. venenatum</italic> centromeres were found to be 25% smaller compared to <italic>F. graminearum</italic>. Chromosome length was 2.8% greater in <italic>F. venenatum,</italic> 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 <italic>F. graminearum</italic>, heterothallic <italic>F. venenatum</italic> possessed the <italic>MAT1–1</italic> type locus, but lacked the <italic>MAT1–2</italic> locus. The <italic>F. venenatum</italic> genome has the type A trichothecene mycotoxin <italic>TRI5</italic> cluster, whereas <italic>F. graminearum</italic> has type B. From the <italic>F. venenatum</italic> gene set, 786 predicted proteins were species-specific versus NCBI. The annotated <italic>F. venenatum</italic> genome was predicted to possess more genes coding for hydrolytic enzymes and species<italic>-</italic>specific genes involved in the breakdown of polysaccharides than <italic>F. graminearum</italic>. Comparison of the two genomes reduced the previously defined <italic>F. graminearum-</italic>specific gene set from 741 to 692 genes. A comparison of the <italic>F. graminearum</italic> versus <italic>F. venenatum</italic> proteomes identified 15 putative secondary metabolite gene clusters (SMC), 109 secreted proteins and 38 candidate effectors not found in <italic>F. venenatum</italic>. Five of the 15 <italic>F. graminearum-specific</italic> SMCs that were either absent or highly divergent in the <italic>F. venenatum</italic> genome showed increased in planta expression. In addition, two predicted <italic>F. graminearum</italic> 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 <italic>F. venenatum</italic> and <italic>F. graminearum</italic> genomes that may contribute to contrasting lifestyles, and highlights the repertoire of <italic>F. graminearum</italic>-specific candidate genes and SMCs potentially required for pathogenesis. [ABSTRACT FROM AUTHOR]