Correction: The Genomes of the Fungal Plant Pathogens <i>Cladosporium fulvum</i> and <i>Dothistroma septosporum</i> Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

<p>Correction: The Genomes of the Fungal Plant Pathogens <i>Cladosporium fulvum</i> and <i>Dothistroma septosporum</i> Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry</p

Syntenic and non-syntenic regions between <i>C. fulvum</i> and <i>D. septosporum</i> are unevenly distributed over the <i>C. fulvum</i> scaffolds.

a<p>Number of repeat regions on syntenic vs. non-syntenic scaffolds.</p>b<p>A syntenic scaffold is one that contains at least a single syntenic block, but may not be syntenic along its entire length. Total syntenic scaffold size (37.4-Mb) is therefore larger than total syntenic size in whole genome (22.3-Mb).</p>c<p>Summed repeat length on syntenic <i>versus</i> non-syntenic scaffolds.</p

Repetitive regions flanking known effectors of <i>Cladosporium fulvum</i>.

<p>Scaffolds harboring sequenced <i>C. fulvum</i> effector genes with flanking repeats. Repeat regions longer than 200-bp are shown, with different types indicated in different color code. Red arrows depict the effector genes and sizes are in kb. The sizes of scaffolds range from 8 to 213-kb but some are shortened to fit the figure due to differences in size.</p

Arrangement of predicted dothistromin genes in <i>Dothistroma septosporum</i> and <i>Cladosporium fulvum</i>.

<p>A) Predicted dothistromin genes within the labeled clusters (left to right) are: <i>Ver1, DotC</i> (<i>Ver1</i> cluster); <i>PksA, CypX, AvfA, MoxY</i> (<i>PksA</i> cluster); <i>AflR, AflJ</i> (<i>AflR/J</i> cluster); <i>OrdB</i>, <i>AvnA, HexB, HexA, HypC, VbsA</i> (<i>VbsA</i> cluster); <i>Nor1, AdhA, VerB</i> (<i>Nor1</i> cluster). Positions of mini-clusters are approximate and they are not drawn to scale. Dothistromin genes within the published <i>D. septosporum PksA</i> and <i>VbsA</i> clusters <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen.1003088-Bradshaw3" target="_blank">[36]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen.1003088-Zhang1" target="_blank">[38]</a> and the newly discovered <i>AflR/J</i> and <i>Nor-1</i> clusters are found in the same order and orientation in <i>C. fulvum</i>. B) Expression of dothistromin biosynthetic genes (<i>Ver1, PksA, VbsA</i>) and regulatory gene (<i>AflR</i>) was determined in <i>D. septosporum</i> by quantitative PCR. Mean expression and standard deviations are shown for at least 3 biological replicates relative to β-tubulin expression. In <i>D. septosporum</i> all genes but <i>DsVbsA</i> are expressed more highly <i>in planta</i> (late-stage sporulating lesions from a forest sample) than in culture (PDB or B5 media) as highlighted by the dashed-grey line. C) Expression of <i>C. fulvum</i> genes is shown as for (B), revealing that expression is not higher during tomato infection than in culture (dashed-grey line). Note the different scales for expression, which reveal a much lower level of transcription both <i>in planta</i> and in PDB medium compared to <i>D. septosporum</i>.</p

Organization of repeats and pathogenicity-related genes in the <i>Dothistroma septosporum</i> genome.

<p>The fourteen chromosomes from the <i>D. septosporum</i> genome assembly are shown as GC (dark grey line) and AT (pale grey line) content (%) plots made from a 500-bp sliding window using Geneious (<a href="http://www.geneious.com" target="_blank">www.geneious.com</a>). All chromosomes have telomere sequence at both ends except chromosomes 2, 11 and 14 which have telomere sequences only at the left end as shown in the figure. Chromosome 1 has been split into two parts in the figure (L, R) because of its length, and the GC/AT content scale is shown beside the right arm of this chromosome. The positions of putative <i>Avr</i> and <i>Ecp</i> effector, secondary metabolite, dothistromin biosynthesis, and mating type genes are shown above the GC/AT content plot, while the positions of repeats (>200-bp) are shown below the plot. Color-coding of the gene and repeat types is indicated in the legend. Most chromosomes have repeat clusters at one or two sites that coincide with regions of high AT content. The chromosome sizes are to scale, as indicated by the vertical pale grey lines, with the values (in kb) shown at the bottom; neither the genes nor the repeats are drawn to scale.</p

Key secondary metabolism genes in Ascomycete genomes.

<p>Numbers of predicted polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), hybrid PKS-NRPS (Hybrid), terpene cyclase (TC) and dimethylallyl tryptophan synthase (DMATS) genes are shown. Data are from this study and from Collemare et al. 2008 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen.1003088-Collemare2" target="_blank">[105]</a>.</p

Recognition of <i>Dothistroma septosporum</i> effectors by tomato Cf receptors.

<p>A) <i>DsEcp2-1</i>, the <i>D. septosporum</i> ortholog of <i>CfEcp2-1</i>, was cloned into <i>pSfinx</i>. Tomato plants were inoculated with <i>Agrobacterium tumefaciens</i> transformants expressing <i>pSfinx::DsEcp2-1</i>. A hypersensitive response (HR) was induced in the tomato line carrying the <i>Cf-Ecp2</i> resistance gene (MM-Cf-Ecp2). Empty vector was used as a negative control and caused only mosaic symptoms. Pictures were taken at four weeks post inoculation. B) The <i>C. fulvum</i> avirulence gene <i>Avr4</i> (<i>CfAvr4</i>) and its ortholog in <i>D. septosporum (DsAvr4)</i> were heterologously expressed in <i>Cf-4</i> transgenic <i>Nicotiana benthamiana</i> using the <i>A. tumefaciens</i> transient transformation assay (ATTA). Expression of <i>CfAvr4</i> and <i>DsAvr4</i> results in an HR demonstrating that the tomato Cf-4 receptor recognizes DsAvr4. Picture was taken at six days post inoculation.</p

<i>C. fulvum</i> and <i>D. septosporum</i> genome statistics.

a<p>For details see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen.1003088.s007" target="_blank">Protocol S1</a>.</p>b<p>L50 is defined as the smallest number of scaffolds that make up 50% of the genome; N50 is defined as the size (Mb) of the smallest of the L50 scaffolds.</p

Location of gene models of <i>C. fulvum</i> in regions syntenic or non-syntenic with the <i>D. septosporum</i> genome.

a<p>Values are numbers of gene models located in regions of the <i>C. fulvum</i> genome syntenic or non-syntenic with the <i>D. septosporum</i> genome as described in Materials and Methods.</p>b<p>For all proteins the percentage of gene models represents the fraction of all gene models present in the <i>C. fulvum</i> genome; for other categories (BDBH, secreted proteins, secreted Cys-rich proteins) the percentage of gene models represents the fraction of gene models present in syntenic and non-syntenic regions.</p>c<p>All proteins encoded by predicted gene models in the <i>C. fulvum</i> genome.</p>d<p>Bi-directional best BLAST hit between <i>C. fulvum</i> and <i>D. septosporum</i> proteins with at least 50% (global) pairwise amino acid similarity and at least 60% coverage by overlap-corrected blastp HSPs.</p>e<p>Gene models predicted to encode secreted proteins.</p>f<p>Secreted small cysteine-rich proteins contain less than 300 amino acids of which at least four are cysteines.</p>g<p>The mean amino acid similarities of all protein gene models in syntenic regions and non-syntenic regions are 85.2% and 65.1%, respectively.</p>h<p>The mean amino acid similarities of secreted protein gene models in syntenic regions and non-syntenic regions are 81.1% and 60.7%, respectively.</p

Occurrence of Repeat-Induced Point Mutation (RIP) signatures and repeats in <i>C. fulvum</i> and <i>D. septosporum</i>.

a<p>Number of loci, defined as consecutive blocks of sequence assigned as repeats or RIP'd regions.</p>b<p>Percentage of the genome is indicated in brackets.</p>c<p>Only classified repeats (as shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen-1003088-t002" target="_blank">Table 2</a>) were considered.</p>d<p>Repeated sequence ≥500 nt that (at least partially) overlaps with RIP'd sequence.</p>e<p>Percentage of classified repeats is indicated in brackets.</p