RESEARCH ARTICLE Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea

The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellu-lar development. Fruiting bodies of C. cinerea are typical mushrooms, which can be pro-duced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was per-formed 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 uncovere