Statistical parsimony haplotype network for <i>FpAH1</i>/<i>PnAH1</i> in <i>Fusarium pseudograminearum</i> and <i>Phaeosphaeria</i> spp. Haplotype bubbles are proportional to sample size shown in parentheses.

<p>Dots on line segments indicate single point mutations.</p

Examples of <i>Fusarium pseudograminearum</i> genes that may be of fungal origin and are candidates for roles in cereal pathogenicity.

<p>Numbers indicate BLASTp bit scores from the reciprocal best blast hits.</p>†<p>Cereal pathogen</p

Summary of BLASTp analysis of FpAH1 versus the non-redundant protein database (nr) at NCBI.

†<p>BLASTp performed 18-May-2012.</p

Summary of the <i>F. pseudograminearum</i> genome sequence assembly in comparison to selected fungal genome sequences obtained by short-read sequencing and the reference genome for <i>F. graminearum</i>.

*<p>not provided.</p>†<p>85× coverage with Illumina and 10× with 454.</p

Virulence assay of the <i>Fusarium pseudograminearum dienelactone hydrolase 1</i> mutant (ΔFpDLH1) mutant towards wheat cultivar Kennedy in crown rot (A and B) and root rot (C and D) assays.

<p>For A and B N = 3 with each biological replicate consisting of 4 paper towel rolls consisting of 7–8 plants per roll. For C and D N = 15–16 plants. Error bars represent the standard error of the mean. Letters indicate statistically significant differences at <i>P</i><0.05. CS3096 and CS3427 are the parental strains for the FpDLH1 mutants, 96T926 and 27T892 respectively. Mock treatments are inoculations performed with agar plugs that have not been colonized by <i>Fusarium</i>.</p

Fusarium root-rot virulence assay of the <i>Fusarium pseudograminearum</i> amidohydrolase 1 mutant (ΔFpAH1) towards wheat cultivar Kennedy (A and B) and barley cultivar Golden Promise (C and D).

<p>N = 16 individual plants. CS3096 is the parental strain for the FpAH1 mutant (96T492), which was complemented with <i>FpAH1</i> driven by the <i>TrpC</i> promoter (96T681). Error bars represent the standard error of the mean. Different letters on A and C indicate statistically significant differences (<i>P</i><0.05) in pair-wise t-tests. B and D are the plants used to score the shoot length shown in A and C.</p

Phylogram of fungal amidohydrolases found in <i>F. pseudograminearum</i> that appear to be of bacterial origin and a number of bacterial amidohydrolases.

<p>Fungal sequences are highlighted in grey boxes. Numbers on branches indicate approximate likelihood ratio test branch support values.</p

Alignment between <i>F. graminearum</i> and <i>F. pseudograminearum</i>.

<p><i>F. graminearum</i> chromosomes are ordered in decreasing size. (A) Dot-plot representing a whole genome alignment between <i>F. graminearum</i> isolate Ph1 and <i>F. pseudograminearum</i> isolate CS3096. The alignment was generated with NUCmer, part of the MUMmer 3 comparative sequence analysis package. Sequences were pre-masked for known repetitive elements and simple repeats using RepeatMasker. The dot plot represents the best 1∶1 alignment between the two genomes. Dots closest to the diagonal represent co-linearity between the two genomes. Red represents matches in the forward direction and blue is indicative of inversions in part of the mapped contig relative to the <i>F. graminearum</i> genome. (B) Distribution of gaps in the alignment between <i>F. pseudograminearum</i> and <i>F. graminearum</i>, relative to the <i>F. graminearum</i> genome. <i>F. graminearum</i> chromosomes were divided into 100 Kbp non-overlapping windows and the unaligned nucleotides in each window summed and expressed as a percentage.</p

Virulence assay of the <i>Fusarium pseudograminearum</i> amidohydrolase 1 mutants (ΔFpAH1) compared to the parental strain towards barley cultivar Golden Promise at 21 days post inoculation (dpi) (A–B).

<p>(A) Survival of plants in the assay 21 dpi. N = 3 with each replicate consisting of 13–15 plants divided between two paper towel rolls and maintained in separate vessels. The difference between wild type and each mutant was highly statistically significant (P-value <0.01). (B) Representative rolls of plants from the assay. (C–D). Complementation of ΔFpAH1 (strains 96T681 and 96T682) restores virulence towards barley cultivar Golden Promise. (C) Proportion of plants surviving at 13 dpi. The total number of plants in each case was 30. (D) Photograph of assays at 13 dpi.</p

Nucleotide alignment of the end of <i>F. graminearum</i> chromosome 1 (top) and the <i>F. pseudograminearum</i> contig containing <i>FpAH1</i> (bottom).

<p>Clear orthologous relationships were evident between regions joined by grey shaded boxes. <i>FpAH1</i> is indicated in red. The genes surrounding <i>FpAH1</i> in the <i>F. pseudograminearum</i> genome that do not have clear orthologous relationships in <i>F. graminearum</i> are blown up and the putative function and species of the closest match in GenBank is indicated.</p