Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea

Hajime Muraguchi, Kiwamu Umezawa, Mai Niikura, Makoto Yoshida, Toshinori Kozaki, Kazuo Ishii, Kiyota Sakai, Motoyuki Shimizu, Kiyoshi Nakahori, Yuichi Sakamoto, Cindy Choi, Chew Yee Ngan, Eika Lindquist, Anna Lipzen, Andrew Tritt, Sajeet Haridas, Kerrie Barry, Igor V. Grigoriev, Patricia J. Pukkila

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article numbere0141586
JournalPLoS One
Volume10
Issue number10
DOIs
Publication statusPublished - Oct 28 2015

Fingerprint

Coprinopsis cinerea
fruiting bodies
Genes
RNA
genes
High-Throughput Nucleotide Sequencing
Basidiomycota
Agaricales
Mycelium
Microarrays
Fungi
Gene Library
Transcriptome
transcriptome
cDNA libraries
mushrooms
mycelium
fruiting
Transcription Factors
transcription factors

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Muraguchi, H., Umezawa, K., Niikura, M., Yoshida, M., Kozaki, T., Ishii, K., ... Pukkila, P. J. (2015). Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea. PLoS One, 10(10), [e0141586]. https://doi.org/10.1371/journal.pone.0141586

Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea. / 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.

In: PLoS One, Vol. 10, No. 10, e0141586, 28.10.2015.

Research output: Contribution to journalArticle

Muraguchi, H, Umezawa, K, Niikura, M, Yoshida, M, Kozaki, T, Ishii, K, Sakai, K, Shimizu, M, Nakahori, K, Sakamoto, Y, Choi, C, Ngan, CY, Lindquist, E, Lipzen, A, Tritt, A, Haridas, S, Barry, K, Grigoriev, IV & Pukkila, PJ 2015, 'Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea', PLoS One, vol. 10, no. 10, e0141586. https://doi.org/10.1371/journal.pone.0141586
Muraguchi H, Umezawa K, Niikura M, Yoshida M, Kozaki T, Ishii K et al. Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea. PLoS One. 2015 Oct 28;10(10). e0141586. https://doi.org/10.1371/journal.pone.0141586
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. / Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea. In: PLoS One. 2015 ; Vol. 10, No. 10.
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