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

Abstract

We report that 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.

Authors:
 [1];  [2];  [2];  [2];  [3];  [3];  [4];  [4];  [5];  [6];  [7];  [7];  [7];  [7];  [7];  [7];  [7];  [7];  [8]
  1. Akita Prefectural University, Akita (Japan)
  2. Tokyo Univ. of Agriculture and Technology, Tokyo (Japan)
  3. Tokyo Univ. of Agriculture and Technology, Tokyo (Japan). Dept.of Applied Biological Science
  4. Meijo Univ., Nagoya, Aichi (Japan)
  5. Okayama Univ., Okayama (Japan)
  6. Iwate Biotechnology Research Center, Kitakami, Iwate (Japan)
  7. DOE Joint Genome Inst., Walnut Creek, CA (United States)
  8. Univ. of North Carolina, Chapel Hill, NC (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1256954
Alternate Identifier(s):
OSTI ID: 1378611
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 10; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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., and Pukkila, Patricia J. Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea. United States: N. p., 2015. Web. doi: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. United States. doi: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., and Pukkila, Patricia J. Wed . "Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea". United States. doi:10.1371/journal.pone.0141586. https://www.osti.gov/servlets/purl/1256954.
@article{osti_1256954,
title = {Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea},
author = {Muraguchi, Hajime and Umezawa, Kiwamu and Niikura, Mai and Yoshida, Makoto and Kozaki, Toshinori and Ishii, Kazuo and Sakai, Kiyota and Shimizu, Motoyuki and Nakahori, Kiyoshi and Sakamoto, Yuichi and Choi, Cindy and Ngan, Chew Yee and Lindquist, Eika and Lipzen, Anna and Tritt, Andrew and Haridas, Sajeet and Barry, Kerrie and Grigoriev, Igor V. and Pukkila, Patricia J.},
abstractNote = {We report that 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.},
doi = {10.1371/journal.pone.0141586},
journal = {PLoS ONE},
number = 10,
volume = 10,
place = {United States},
year = {2015},
month = {10}
}

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    Works referencing / citing this record:

    Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
    journal, October 2018


    Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
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