Comparison of secretomes of <i>R. irregularis</i> and other 43 fungi.

<p>Percentage of predicted proteome representing putative effectors, using stringent (lacking transmembrane domains; yellow bars) or relaxed criteria (including proteins with predicted single transmembrane domain that overlapped with the signal peptide; blue bars).</p

Genome sequence of single <i>R. irregularis</i> DAOM197198w nuclei.

<p>(<b>A</b>) Sytox Green stained spore containing numerous nuclei. (<b>B</b>) Single Sytox-stained nucleus trapped with a micropipette. (<b>C</b>) Level of homology between four individual nuclei (N6, N31, N33 and N36) and 2 mycelium DNA samples (DNA1 and DNA2). Presented are the 10 largest contigs of the reference genome (representing ∼1,278 kb). The occurrence of SNPs (marked in blue) and INDELs (marked in red), and gene distributions, in the different assemblies are indicated.</p

Characteristics of the seven genome assemblies from <i>R. irregularis</i> DAOM197198w.

<p>N50: the length for which the contigs (scaffolds) of that length or longer contains at least half of the total lengths of the contigs (scaffolds).</p

ML tree derived from the concatenation of 35 widespread, single-copy genes.

<p>The amino acid alignment was trimmed as explained in the <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004078#s3" target="_blank">Materials and methods</a> section to remove non-informative positions, resulting in 26,604 positions. The tree was estimated using the rtREV evolutionary model implemented in RAxML. Bootstrap analysis was performed based on 100 replicates, and the three nodes with support below 100 are indicated. Scale bar indicates average number of amino acid substitutions per site.</p

Top 100 ranked protein tribes containing putative effector candidates.

<p>Clusters were determined using hierarchical clustering of the top 100 ranked tribes containing putative effector candidates. A. Rank associated with each tribe based on their content of effector features. B. Score for number of members containing a nuclear localization signals (NLS). C. Score for number of members classified as repeat containing (RCPs). D. Score reflecting number of members classified as small and cysteine rich (SCRs). E. Score for number of members not annotated by searches against swissprot. F. Average protein sequence length for tribe members (ranging from 55 to 856 amino acids). Stars indicate tribes that contain members with similarity to the characterised effector SP7.</p