The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract No. All assembled and annotated files are available from the JGI database ( ).įunding: The #326 AmutBmut pab1-1 genome sequencing, assembly and annotation, and the RNA-seq analysis were provided through JGI's Community Sequencing Program 'Functional genomics in the model mushroom Coprinopsis cinerea”. Microarray data, GSE37943_RAW and GSE37942_RAW, were downloaded from GEO DataSets. The #326 Amut Bmut pab1-1 genomic DNA was sequenced, assembled and used to predict 14,245 gene models (NCBI Accession PRJNA258994). This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedĭata Availability: Reads were deposited to SRA under the following accessions: SRA051294, SRA051421, and SRA050788. Received: JAccepted: OctoPublished: October 28, 2015Ĭopyright: © 2015 Muraguchi et al. PLoS ONE 10(10):Įditor: Erika Kothe, Friedrich Schiller University, GERMANY (2015) Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.Ĭitation: Muraguchi H, Umezawa K, Niikura M, Yoshida M, Kozaki T, Ishii K, et al.

We discuss events deduced from GO analysis of DEGs. 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. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. 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. cinerea are typical mushrooms, which can be produced synchronously on defined media in the laboratory. The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development.

Primordia hyphal knots