The RIP index (TpA/ApT) of genes as a function of the distance from a transposable element.

<p>The RIP index is highest near the transposable elements and levels off after approximately 2000 bp, signifying that these regions are subjected to repeat induced point mutations.</p

Estimated phylogeny and divergence times of <i>Dothideomycetes</i>, based on sequences of three protein-coding genes.

<p>Species with a sequenced genome that are included in this study are highlighted in dark blue. Vertical lines in blue and green indicate minimum and maximum ages for specific nodes, respectively. The age ranges for highlighted taxa are indicated by blocks with different shades of gray. Horizontal green lines indicate bootstrap recovery for specific nodes – thickened branches represent more than 70%, normal branches, 50–70% and less than 50% are indicated with dashed lines. In some cases relevant horizontal lines were stylistically extended to highlight node labels. Only families with multiple genomes are indicated. Orders, suborders and families that contain important plant-pathogenic species are colored brown and those containing majority lichenized species are green. Brown squares indicate plant pathogenic and green triangles lichenized species. Saprotrophs and fungi with other nutritional modes are not labeled.</p

Heat map of CAZY families in the <i>Dothideomycetes</i>.

<p>Both the CAZY families and the organisms are hierarchically clustered. The clustering of organisms largely follows the phylogeny in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003037#ppat-1003037-g002" target="_blank">Figure 2A</a>. Notable exceptions are the observation that the biotroph <i>C. fulvum</i> clusters as an outgroup to the hemibiotrophs and saprotroph within the <i>Capnodiales</i>, and the observation that the two pathogens of <i>Brassica</i> spp. (<i>L. maculans</i> and <i>A. brassicicola</i>) cluster together.</p

Species used in this comparative study.

a<p>Additional genome-centric papers are planned.</p><p>Taxonomy and lifestyle of the 18 <i>Dothideomycetes</i> used in this study, as well as the outgroups for comparative purposes.</p

Phylogeny and genome characteristics of the 18 studied <i>Dothideomycetes</i>.

<p><b>A.</b> Genome-based phylogenetic tree of 18 <i>Dothideomycetes</i> computed using 51 conserved protein families. Bootstrap values are indicated on the branches. Lifestyles and strategies of pathogenesis (green circle for necrotrophs, orange circle for saprotrophs and blue circle for [hemi]biotrophs) are indicated. <i>Aspergillus nidulans</i> was used as an outgroup and its branch on the tree is not drawn to scale. <b>B.</b> Genome size and repeat content. Repeat content varies widely among <i>Dothideomycetes</i>, but in general the largest part consists of long terminal repeats. Asterisks indicate genomes that were sequenced exclusively with Illumina technology. Repeat content in these genomes is likely an underestimate. <b>C.</b> Number of predicted genes, broken down by level of conservation. <b>D.</b> Gene counts of classes that have been implicated in plant pathogenesis. Members of <i>Capnodiales</i> have fewer genes in these classes than <i>Pleosporales</i> and <i>Hysteriales</i> (with the exception of <i>Cladosporium fulvum</i>). This trend is also illustrated by the estimated gene counts for the last common ancestors of the indicated taxa (below the x-axis), which correspond to the taxa in (A). See also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003037#ppat.1003037.s003" target="_blank">Figure S3</a>. Bars on all graphs (B, C, and D) correspond to the organisms on the tree in (A).</p

Summary of gene classes that are over-represented in repeat regions (i.e., the 2000 bp flanking predicted transposable elements).

<p>See also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003037#ppat.1003037.s036" target="_blank">Table S27</a> for more information. Genomes labeled with an asterisk (*) have been sequenced exclusively using Illumina technology.</p

Potential core and dispensable chromosomes in the genomes of <i>Dothideomycetes</i>.

<p><i>Mycosphaerella graminicola</i> has been shown previously to contain dispensable (i.e., not necessary for survival) chromosomes <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003037#ppat.1003037-Goodwin1" target="_blank">[24]</a>. These chromosomes are smaller, less gene-dense and more repeat-rich than the core chromosomes. Proteins encoded by genes on these chromosomes less frequently contain a PFAM domain. Scaffolds with similar characteristics are also present in five other <i>Dothideomycetes</i>. Additional statistics for these scaffolds are given in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003037#ppat.1003037.s021" target="_blank">Table S12</a>.</p

The full and core proteomes of the 18 <i>Dothideomycetes</i>.

<p><b>A.</b> The full proteome of the <i>Dothideomycetes</i> contains 215,225 proteins and for the majority of these the function according to KOG <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003037#ppat.1003037-Koonin1" target="_blank">[93]</a> is unknown or poorly characterized. <b>B.</b> The core proteome contains the 66,761 proteins from multi-gene families that had at least one member in each <i>Dothideomycete</i>. Relative to (A), this set of proteins has more KOG annotations than the full proteome. In particular genes involved in metabolism are over-represented.</p

Simulation of chromosome evolution leading to mesosynteny.

<p><b>A.</b> Two identical sequences show perfect macrosynteny. <b>B.</b> This is also the case for scaffold_1 of <i>Cochliobolus heterostrophus</i> C4 and scaffold_2 of <i>C. heterostrophus</i> C5, reflecting their close relationship as progeny. <b>C.</b> The two sequences from (A) have each undergone one random inversion. <b>D.</b> Scaffold_4 of <i>C. heterostrophus</i> C5 and scaffold_9 of <i>C. sativus</i> show a very similar pattern as in (C). <b>E.</b> The two sequences in (A) have each undergone 25 random inversions. <b>F.</b> Scaffold_8 of <i>Setosphaeria turcica</i> and part of scaffold_10 of <i>C. heterostrophus</i> C5 show a pattern of syntenic regions progressively spreading across the scaffolds similar to that in (E) <b>G.</b> The two sequences from (A) have each undergone 500 random inversions. Syntenic regions are short and spread homogeneously across the two scaffolds. <b>H.</b> Scaffold_1 of <i>Dothistroma septosporum</i> and scaffold_1 of <i>Mycosphaerella populorum</i> show a very similar pattern as in (G). Scaffolds in this figure are not drawn to scale.</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>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