Major characteristics of DGE libraries.

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

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

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

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

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

Effects of the formation of heterokaryon on gene expression.

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

Genetic Diversity and Population Structure of Rice Pathogen <i>Ustilaginoidea</i><i> virens</i> in China

<div><p>Rice false smut caused by the fungal pathogen <i>Ustilaginoidea</i><i>virens</i> is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two <i>U</i><i>. virens</i> isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of <i>U</i><i>. virens</i> in China. A total of 56 multilocus sequence types (haplotypes) were identified out of 162 representative isolates from 15 provinces covering five major rice-growing areas in China. However, the phylogeny, based on sequences at individual SNP-rich regions, strongly conflicted with each other and there were significant genetic differences between different geographical populations. Gene flow between the different geographical populations and genetic differentiation within each geographical population were also detected. In addition, genetic recombination and genetic isolation resulting from geographic separation was also found.</p> </div

SNP sites comparison between the genome sequences of two <i>U. virens</i> isolates.

<p>The SNP numbers per 10 kb DNA were compared using two genomes sequences and Biolign software version 4.0.6 (Hall 2001). Locations of the three SNP-rich markers are indicated by red lines.</p

Mantel test between genetics and horizontal distance.

<p>Horizontal geographical distances means distances based on longitudinal–latitudinal coordinates.</p

Population structure of <i>U. virens</i> inferred from 125 SNPs of 162 isolates using the program Structure (version 2.3.1), with different <i>K</i> values.

<p>An admixture model with correlated allele frequencies was used. Each isolate is represented by a single vertical line broken into <i>K</i> colored segments, with lengths proportional to each of the <i>K</i> inferred clusters.</p