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 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.
Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, 010-0195, Japan.
Hajime
H
Muraguchi
Department of Environmental and Natural Resource Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
Kiwamu
K
Umezawa
Department of Environmental and Natural Resource Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
Mai
M
Niikura
Department of Environmental and Natural Resource Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
Makoto
M
Yoshida
Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
Toshinori
T
Kozaki
Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
Kazuo
K
Ishii
Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan.
Kiyota
K
Sakai
Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, Nagoya, Aichi, 468-0073, Japan.
Motoyuki
M
Shimizu
Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
Kiyoshi
K
Nakahori
Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
Yuichi
Y
Sakamoto
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Cindy
C
Choi
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Chew Yee
CY
Ngan
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Eika
E
Lindquist
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Anna
A
Lipzen
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Andrew
A
Tritt
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Sajeet
S
Haridas
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Kerrie
K
Barry
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, United States of America.
Igor V
IV
Grigoriev
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-3280, United States of America.
Patricia J
PJ
Pukkila
D001487:Basidiomycota / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D048690:Fruiting Bodies, Fungal / Q000235:genetics*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D025301:Hyphae; D008954:Models, Biological; D016372:RNA, Antisense; D012331:RNA, Fungal; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
D016372:RNA, Antisense; D012331:RNA, Fungal; D014157:Transcription Factors