Genome Sequence of Fusarium graminearum ITEM 124 (ATCC 56091), a Mycotoxigenic Plant Pathogen.

Fusarium graminearum is among the main causal agents of Fusarium head blight (FHB), or scab, of wheat and other cereals, caused by a complex of Fusarium species, worldwide. Besides causing economic losses in terms of crop yield and quality, F. graminearum poses a severe threat to animal and human health. Here, we present the first draft whole-genome sequence of the mycotoxigenic Fusarium graminearum strain ITEM 124, also providing useful information for comparative genomics studies.

GENOME ANNOUNCEMENT

Fusarium head blight (FHB) of wheat is a major disease worldwide, with Fusarium graminearum being the main causal agent of the species complex (1). Notably, F. graminearum was recently ranked fourth in a top 10 fungal plant pathogen list (2). FHB not only directly affects the grain production but also poses a severe threat to plant, animal, and human health due to the accumulation of mycotoxins on kernels and wheat products.

F. graminearum ITEM 124 (http://server.ispa.cnr.it/ITEM/Collection/), also known as ATCC 56091, was isolated in 1976 from rice harvested in Vercelli, Piemonte, Italy. F. graminearum ITEM 124 is able to produce deoxynivalenol (DON), the best-known mycotoxin belonging to trichothecenes (3). This class of mycotoxins acts as an inhibitor of cell protein synthesis (4). The ability of F. graminearum ITEM 124 to produce DON on wheat and rice kernels has been assessed previously (5, 6). Molecular chemotype detection, performed according to Somma et al. (7), identified the strain F. graminearum ITEM 124 as chemotype 15-acetyl DON (15ADON). Chemical analyses confirmed the production of DON by ultraperformance liquid chromatography (UPLC) with a photodiode array (PDA) assay (8).

A competition test on rice kernels inoculated with F. graminearum ITEM 124 and the beneficial fungus Trichoderma gamsii T6085 highlighted a reduction of the amount of DON to almost 92% as a direct consequence of a decreased biomass of the pathogen. Moreover, the growth of F. graminearum ITEM 124 has been reduced by the presence of T. gamsii T6085 in dual confrontation assays. F. graminearum ITEM 124 is overgrown by T. gamsii T6085 under in vitro conditions, and the latter produces short loops and coilings on pathogen hyphae, which are typical mycoparasitic traits (5, 6, 9).

The genome of F. graminearum ITEM 124 was sequenced using Illumina paired-end sequencing technology by BMR Genomics (Padua, Italy). Paired reads of 300 bp (3.16 Gbp; average coverage, 38×) were assembled using SPAdes v3.8.2 (10). The nuclear genome of F. graminearum ITEM 124 consists of 67 sequence scaffolds with a total assembly length of 36.88 Mbp (N50, 1,518,396; L50, 6), 48.18% GC content, and a maximum scaffold size of 7,305,194 bp. The completeness of the assembly was assessed using BUSCO v12 (11), which estimated the genome sequence to be 99.86% complete. The nuclear genome was annotated using the MAKER2 pipeline (12). Overall, 11,827 protein-coding gene models were predicted. Analysis with SignalP 4.1 (13) revealed that 1,288 predicted proteins (10.9% of the proteome) contain a secretion signal peptide.

The genome sequence of the mycotoxigenic F. graminearum ITEM 124 provides a novel source for comparative genomics studies and also represents a useful platform to study fungal-fungal interactions, such as the mycoparasitic relationship established with the beneficial isolate T. gamsii T6085, whose genome is also available (14).

Accession number(s).

This whole-genome shotgun project has been deposited in GenBank under accession number NQOC00000000 (BioProject PRJNA397367; BioSample SAMN07455307). The version described in this paper is NQOC01000000.