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

A - Papers appearing in refereed journals

King, R., Brown, N. A., Urban, M. and Hammond-Kosack, K. E. 2018. Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. BMC Genomics. 19, p. 269. https://doi.org/10.1186/s12864-018-4612-2

AuthorsKing, R., Brown, N. A., Urban, M. and Hammond-Kosack, K. E.
Abstract

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.
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.
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.

KeywordsFusarium graminearum; Comparative genome analyses; Fusarium venenatum; Secondary metabolite clusters; Secretome; PHI-base genes; Species-specific genes
Year of Publication2018
JournalBMC Genomics
Journal citation19, p. 269
Digital Object Identifier (DOI)https://doi.org/10.1186/s12864-018-4612-2
PubMed ID29673315
Open accessPublished as ‘gold’ (paid) open access
FunderBiotechnology and Biological Sciences Research Council
Funder project or code20:20 Wheat [ISPG]
[20:20 Wheat] Protecting yield potential of wheat
Designing Future Wheat (DFW) [ISPG]
DFW - Designing Future Wheat - Work package 2 (WP2) - Added value and resilience
BB/J/004383/1
BB/1000488/1
PhytoPath, an infrastructure for hundreds of plant pathogen genomes [2014-2017]
Do G-protein coupled receptors regulate pathogenesis and mycotoxin biosynthesis in filamentous phytopathogenic fungi?
Publisher's version
Output statusPublished
Publication dates
Online19 Apr 2018
Publication process dates
Accepted20 Mar 2018
PublisherBiomed Central Ltd
Copyright licenseCC BY
ISSN1471-2164
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