The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism

Abstract

Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6-43.1 MB, with 13217-13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.

Figure 1. Sliding window map with numbers of SNP's and indels per 20 kb in the three F. avenaceum strains Fa05001, FaLH03 and FaLH27 on the 11 supercontigs.

Locations of the polyketide synthase and non-ribosomal peptide synthetase genes in the strain FaLH27 are plotted on the supercontigs.

Figure 2. Molecular phylogenetic analysis of Fusarium species based on 69 orthologous proteins.

The evolutionary history was inferred by using the Maximum Likelihood method and the tree with the highest log likelihood (−152577,9625) is shown. Bootstrap values, as percentages, are shown next to the individual branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions containing gaps and missing data were eliminated prior to the ML analysis and the final data set contained 25535 positions.

Figure 3. Shared gene homology map between Fa05001 and F. graminearum PH-1 has been created using the four defined F. graminearum chromosomes as templates.

Genes in F. graminearum are coloured according to whether genes have corresponding orthologs in Fa05001, with one gene being one strip. Regions of the same color match to the same supercontigs (Figure S2 in File S1) in F. avenaceum. White regions represent lack of orthologs in Fa05001.

Figure 4. Functional analysis of Fa05001 and other sequenced Fusaria based on InterPro visualizing similarities and differences between the fungi.

Categories with most differences between Fa05001 and others are presented with the number of proteins in each category. All details are listed in File S4. FA  =  F. avenaceum Fa05001, FG  =  F. graminearum PH-1, FO  =  F. oxysporum f. sp. lycopersici 4287, FV  =  F. verticillioides, FS  =  F. solani.

Figure 5. Shared and unique polyketide synthase (PKS), non-ribosomal peptide synthetases (NRPS) and terpene cyclase (TC) encoding genes in public available Fusaria genomes.

Green and yellow boxes are the number of shared and unique genes, respectively. Fg  =  F. graminearum, Fv  =  F. verticillioides, Fo  =  F. oxysporum, Fs  =  F. solani, Fp  =  F. pseudograminearum, Ff  =  F. fujikuroi and Fa05001, FaLH03 and FaLH27  =  F. avenaceum.

Figure 6. Apicidin-like gene cluster (oNRPS31) in the three F. avenaceum strains (Fa05001_Scaffold14, FaLH03_contig11, FaLH27_contig13) compared to the characterized apicidin gene cluster from F. incarnatum and the HC-toxin gene clusters from Cochliobolus carbonum, Pyrenophora tritici-repentis and Setosphaeria turcica (A).

The genes are colored based on homology across the species. Chemical structure of apicidin and HC-toxin (B). See Table S8 in File S1 for further details.

Figure 7. Architecture of the gibberellic acid (GA) gene clusters from F. fujikuroi MP-A, F. avenaceum and Sphaceloma manihoticola.

The gene cluster and surrounding genes are identical in the three F. avenaceum strains and only Fa05001 is shown (FaLH03 cluster: FAVG2_04186 - FAVG2_04192 and FaLH27 cluster: FAVG3_04219 - FAVG3_04224). The mVista trace shows the similarity over a 100 bp sliding windows (Shuffle-LAGAN plot) between the F. avenaceum and F. fujikuroi clusters, bottom line  = 50% and second line  = 75% identity. Genes: gss2  =  geranylgeranyldiphosphate synthase, cps/ks  =  copalyldiphosphate/ent-kaurene synthase, P450-4  =  ent-kaurene oxidase, P450-1  =  GA₁₄ synthase, P450-2  =  C20-oxidase, P450-3  =  13-hydroxylase and DES  =  desaturase. Note that the intergenic regions are unknown for the S. manihoticola GA cluster, while the size of these regions is not to drawn to size.