Additional file 3: Figure S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Snapshot of synteny dot plot between C. olivacea and C. puteana. (TIFF 582 kb

L'Auto-vélo : automobilisme, cyclisme, athlétisme, yachting, aérostation, escrime, hippisme / dir. Henri Desgranges

27 juin 19371937/06/27 (A38,N13339)

Additional file 2: Table S1. of Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales

Comparison of TE content estimation from REPET and Repeatexplorer. (XLSX 9 kb

Distribution of unique proteins experimentally identified in secretomes of four Ascomycete fungi.

<p>(A) Proteins unique to each fungus based on amino acid sequence (as determined by JGI protein ID). (B) Proteins unique to each fungus based on predicted function (evaluated manually). Proteins identified via LC-MS/MS over a 21-day study. Total number of unique proteins identified for each fungus is indicated in center of circles. Abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157844#pone.0157844.g001" target="_blank">Fig 1</a>.</p

Distribution of proteins identified in secretomes of four Ascomycete fungi among broad functional groups.

<p>(A) Experimentally observed secretome. Proteins identified via LC-MS/MS over a 21-day study. (B) Portion of experimental secretome predicted to be secreted based on genome analysis (see text for further explanation). (C) Full predicted secretome based on genomes only. Total number of proteins identified for each fungus is indicated in center of circles. Abbreviations from CAZy database: AA = auxiliary activities; CBM = carbohydrate-binding module; CE = carbohydrate esterase; GH = glycoside hydrolase; GT = glucosyltransferase; PL = polysaccharide lyase.</p

Genome-based evaluation of unique proteins experimentally identified in secretomes of four Ascomycete fungi.

<p>Genome-based evaluation of unique proteins experimentally identified in secretomes of four Ascomycete fungi.</p

Distribution of proteins experimentally identified in secretomes of four Ascomycete fungi among protein families.

<p>Glycoside hydrolase families (both top and bottom panels). Solid bars: Portion of experimental secretome predicted to be secreted based on genome analysis. Shaded bars: Portion not predicted to be secreted. Proteins identified via LC-MS/MS over a 21-day study and classified according to the CAZy database. Abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157844#pone.0157844.g001" target="_blank">Fig 1</a>.</p

Summary of identified CAZymes in secretomes of four Ascomycete fungi.

<p>Summary of identified CAZymes in secretomes of four Ascomycete fungi.</p

Venn diagram showing number of unique and shared proteins experimentally identified in Ascomycete fungi secretomes.

<p>Proteins identified via LC-MS/MS over a 21-day study. Total number of proteins identified for each fungus is indicated outside of diagram. Diagram generated with Venny 2.0 [<i>Oliveros</i>, <i>J</i>.<i>C</i>. <i>(2007–2015) Venny</i>. <i>An interactive tool for comparing lists with Venn’s diagrams. <a href="http://bioinfogp.cnb.csic.es/tools/venny/index.html" target="_blank">http://bioinfogp.cnb.csic.es/tools/venny/index.html</a></i>].</p

Strand-Specific RNA-Seq Analyses of Fruiting Body Development in <i>Coprinopsis cinerea</i>

<div><p>The basidiomycete fungus <i>Coprinopsis cinerea</i> is an important model system for multicellular development. Fruiting bodies of <i>C</i>. <i>cinerea</i> are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.</p></div