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

PLoS One. 2015 Oct 28;10(10):e0141586. doi: 10.1371/journal.pone.0141586. eCollection 2015.


The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Basidiomycota / genetics*
  • Computational Biology / methods
  • Fruiting Bodies, Fungal / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal
  • Hyphae
  • Models, Biological
  • RNA, Antisense
  • RNA, Fungal*
  • Reproducibility of Results
  • Sequence Analysis, RNA*
  • Transcription Factors / genetics
  • Transcriptome


  • RNA, Antisense
  • RNA, Fungal
  • Transcription Factors

Associated data

  • SRA/SRA050788
  • SRA/SRA051294
  • SRA/SRA051421

Grants and funding

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”. 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. DE-AC02-05CH11231. This work was supported in part (preparation of total RNA, and sending the samples from Japna to USA) by a fund from the Ministry of Agriculture, Forestry and Fisheries of Japan (23053).