Double clustering of the carbohydrate-cleaving families of 8 basidiomycete genomes.

<p><b>Top tree:</b> S. com. for <i>Schizophyllum commune</i>; V. vol. for <i>Volvariella volvacea</i>; P. chr. for <i>Phanerochaete chrysosporium</i>; C. cin. for <i>Coprinopsis cinerea</i>; P. pla. for <i>Postia placenta</i>; L. bio. for <i>Laccaria bicolor</i>; C. neo. for <i>Cryptococcus neoformans</i>; U. may. for <i>Ustilago maydis</i>. <b>Left tree:</b> the enzyme families are represented by their class (GH for glycoside hydrolase; PL for polysaccharide lyase; CE for carbohydrate esterase) and family number according to the carbohydrate-active enzyme database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Cantarel1" target="_blank">[23]</a>. <b>Right side:</b> known substrate of CAZy families. Abundance of the different enzymes within a family is represented by a colour scale from 0 (black) to >20 (red) occurrences per species.</p

Major characteristics of DGE libraries.

<p>Major characteristics of DGE libraries.</p

Gene expression in three strains of <i>V. volvacea</i>.

<p>(<b>a</b>) Venn diagrams showing genes expressed in the three strains. (<b>b</b>) The histogram shows the percentage of genes that are differentially expressed in the three strains of <i>V. volvacea</i>.</p

Comparison of the number of CAZymes in <i>V. volvacea</i> genome with those in other fungi genomes [3].

<p>Enzymes: GH for glycoside hydrolase, GT for glycosyltransferase, PL for polysaccharide lyases, and CE for carbohydrate esterases. Species abbreviations and genome references: V. vol. for <i>Volvariella volvacea</i> (current paper), S. com. for <i>Schizophyllum commune</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Ohm1" target="_blank">[3]</a>, P. chr. for <i>Phanerochaete chrysosporium</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Martinez2" target="_blank">[30]</a>, P. pla. for <i>Postia placenta</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Martinez3" target="_blank">[31]</a>, C. cin. for <i>Coprinopsis cinerea</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Stajich1" target="_blank">[14]</a>, L. bio. for <i>Laccaria bicolor</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Martin1" target="_blank">[32]</a>, C. neo. for <i>Cryptococcus neoformans</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Loftus1" target="_blank">[33]</a>; U. may. for <i>Ustilago maydis</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Kmper1" target="_blank">[34]</a>, S.cer. for <i>Saccharomyces cerevisiae</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Goffeau1" target="_blank">[35]</a>, N.cra. for <i>Neurospora crassa</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Galagan1" target="_blank">[36]</a>, T. mel. for <i>Tuber melanosporum</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Martin2" target="_blank">[37]</a>, A.nig. for <i>Aspergillus niger</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Pel1" target="_blank">[38]</a>, P.ind. for <i>Piriformospora indica</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Zuccaro1" target="_blank">[39]</a>, P. chr. for <i>Penicillium chrysogenum</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-vandenBerg1" target="_blank">[40]</a>, and T.ree. for <i>Trichoderma reesei</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058780#pone.0058780-Martinez1" target="_blank">[2]</a>.</p

The colonial characteristics of <i>V. volvacea</i> stains PYd15(a, b), H1521(c, d) and PYd21(e, f).

<p>(a,c,e). strains were growth on PDA plates and images were captured after 4 d of growth. (b,d,f). strains were growth on a straw-based medium and images were captured after 15 d of cultivation.</p

Effects of the formation of heterokaryon on gene expression.

a<p>TMP: Tags per million.</p

COG and KEGG based functional annotation of differentially expressed genes.

<p>Clear changes in regulation of biological functions are shown. The most important changes are: almost exclusive up-regulation of DNA replication and cell cycle related processes from BU to EG, down-regulation of those processes from EG to EL, and up-regulation of transport related processes from EL to MA (even though more genes are down- than up-regulated during transition from EL to MA).</p

Predicted regulatory factors of <i>V. volvacea</i> that are up-regulated in stipe tissue from EG to EL.

<p>Predicted regulatory factors of <i>V. volvacea</i> that are up-regulated in stipe tissue from EG to EL.</p

Changes in gene expression between succeeding stages; transitions T1, T2 and T3.

<p>Differentially expressed genes (DEGs) are divided over three groups of absolute log2 fold changes in expression; 2 to 4 fold (orange), 4 to 8 fold (purple) or 8 or more fold (green). Genes with expression in only one of two compared stages (thus uniquely expressed in that particular comparison) predominantly show >8 fold changes and are additionally indicated between brackets within this group. Considerably more genes are up-regulated from BU to EG, whereas more genes are down-regulated from EG to EL. Numbers of up- and down-regulated genes from EL to MA are more balanced, although more genes are down- than up-regulated. In each transition, the largest number of DEGs is represented by the 2–4 fold group (orange). Relative high numbers of genes are completely turned off from EG to EL (135) and turned on from EL to MA (97).</p