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

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 develo...

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Published in:	PloS one 2015-10, Vol.10 (10), p.e0141586-e0141586
Main Authors:	Muraguchi, Hajime, Umezawa, Kiwamu, Niikura, Mai, Yoshida, Makoto, Kozaki, Toshinori, Ishii, Kazuo, Sakai, Kiyota, Shimizu, Motoyuki, Nakahori, Kiyoshi, Sakamoto, Yuichi, Choi, Cindy, Ngan, Chew Yee, Lindquist, Eika, Lipzen, Anna, Tritt, Andrew, Haridas, Sajeet, Barry, Kerrie, Grigoriev, Igor V, Pukkila, Patricia J
Format:	Article
Language:	eng
Subjects:	Antisense RNA BASIC BIOLOGICAL SCIENCES Basidiocarps Basidiomycota Basidiomycota - genetics Biotechnology Cell division Complementary DNA Computational Biology - methods Coprinopsis cinerea DNA microarrays Energy Fruit bodies Fruiting Bodies, Fungal - genetics Fruits Fungi Gene expression Gene Expression Profiling Gene Expression Regulation, Fungal Gene sequencing Genes Genetic aspects Genetic research Genetic transcription Genomes Genomics Growth Hyphae Methods Models, Biological Mushrooms Mutation Next-generation sequencing Pheromones Proteomics Reproducibility of Results Ribonucleic acid RNA RNA sequencing RNA, Antisense RNA, Fungal Schizophyllum commune Science Sequence Analysis, RNA Transcription (Genetics) Transcription factors Transcription Factors - genetics Transcriptome Ustilago maydis
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Summary:	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.
ISSN:	1932-6203 1932-6203