Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea
Abstract
© 2015 Muraguchi et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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 regulationmore »
- Authors:
-
- Akita Prefectural University, Akita (Japan)
- Tokyo Univ. of Agriculture and Technology, Tokyo (Japan)
- Tokyo Univ. of Agriculture and Technology, Tokyo (Japan). Dept.of Applied Biological Science
- Meijo Univ., Nagoya, Aichi (Japan)
- Okayama Univ., Okayama (Japan)
- Iwate Biotechnology Research Center, Kitakami, Iwate (Japan)
- DOE Joint Genome Inst., Walnut Creek, CA (United States)
- Univ. of North Carolina, Chapel Hill, NC (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (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. 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., and Pukkila, Patricia J. Wed .
"Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea". United States. https://doi.org/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 = {© 2015 Muraguchi et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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 = {Wed Oct 28 00:00:00 EDT 2015},
month = {Wed Oct 28 00:00:00 EDT 2015}
}
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- Krizsán, Krisztina; Almási, Éva; Merényi, Zsolt
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 15
Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea
journal, September 2018
- Lau, Amy Yuet Ting; Cheng, Xuanjin; Cheng, Chi Keung
- PLOS ONE, Vol. 13, Issue 9
The transcriptional regulator c2h2 accelerates mushroom formation in Agaricus bisporus
journal, May 2016
- Pelkmans, Jordi F.; Vos, Aurin M.; Scholtmeijer, Karin
- Applied Microbiology and Biotechnology, Vol. 100, Issue 16
Biosynthesis of lagopodins in mushroom involves a complex network of oxidation reactions
journal, January 2019
- Masuya, Takahiro; Tsunematsu, Yuta; Hirayama, Yuichiro
- Organic & Biomolecular Chemistry, Vol. 17, Issue 2
Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes
journal, June 2018
- Song, Ha-Yeon; Kim, Dae-Hyuk; Kim, Jung-Mi
- Scientific Reports, Vol. 8, Issue 1
Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes
journal, March 2019
- Tayyrov, Annageldi; Stanley, Claire E.; Azevedo, Sophie
- BMC Genomics, Vol. 20, Issue 1
Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression
journal, May 2017
- Donaldson, Michael E.; Ostrowski, Lauren A.; Goulet, Kristi M.
- BMC Genomics, Vol. 18, Issue 1
De novo transcriptome sequencing of Flammulina velutipes uncover candidate genes associated with cold-induced fruiting
journal, June 2018
- Wu, Tuheng; Ye, Zhiwei; Guo, Liqiong
- Journal of Basic Microbiology, Vol. 58, Issue 8
Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression
journal, May 2017
- Donaldson, Michael E.; Ostrowski, Lauren A.; Goulet, Kristi M.
- BMC Genomics, Vol. 18, Issue 1
Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
journal, June 2018
- Borgognone, Alessandra; Castanera, Raúl; Morselli, Marco
- DNA Research, Vol. 25, Issue 5
Modified recipe to inhibit fruiting body formation for living fungal biomaterial manufacture
journal, May 2019
- Chang, Jinhui; Chan, Po Lam; Xie, Yichun
- PLOS ONE, Vol. 14, Issue 5
Complex multicellularity in fungi: evolutionary convergence, single origin, or both?: Complex multicellularity in Fungi
journal, April 2018
- Nagy, László G.; Kovács, Gábor M.; Krizsán, Krisztina
- Biological Reviews, Vol. 93, Issue 4
Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species
journal, June 2019
- Wen, Jiawei; Zhang, Zhibin; Gong, Lei
- Genes, Vol. 10, Issue 6
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
text, January 2018
- Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas
- ETH Zurich
Transposon-associated epigenetic silencing during Pleurotus ostreatus life cycle
journal, June 2018
- Borgognone, Alessandra; Castanera, Raúl; Morselli, Marco
- DNA Research, Vol. 25, Issue 5
Modified recipe to inhibit fruiting body formation for living fungal biomaterial manufacture
journal, May 2019
- Chang, Jinhui; Chan, Po Lam; Xie, Yichun
- PLOS ONE, Vol. 14, Issue 5
Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species
journal, June 2019
- Wen, Jiawei; Zhang, Zhibin; Gong, Lei
- Genes, Vol. 10, Issue 6
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
journal, October 2018
- Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas
- The ISME Journal, Vol. 13, Issue 3
Identification of up-regulated transcripts during Pleurotus ostreatus primordium stage and characterization of PoALDH1
journal, September 2018
- Qi, Yuancheng; Sun, Xiankai; Zhang, Mengke
- Journal of Basic Microbiology, Vol. 58, Issue 12
Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea
posted_content, May 2018
- Lau, Amy Yuet Ting; Cheng, Xuanjin; Cheng, Chi Keung
- bioRxiv
Genome editing in the mushroom-forming basidiomycete Coprinopsis cinerea, optimized by a high-throughput transformation system
journal, April 2017
- Sugano, Shigeo S.; Suzuki, Hiroko; Shimokita, Eisuke
- Scientific Reports, Vol. 7, Issue 1
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
journal, October 2018
- Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas
- The ISME Journal, Vol. 13, Issue 3
The transcriptional landscape of basidiosporogenesis in mature Pisolithus microcarpus basidiocarp
journal, February 2017
- de Freitas Pereira, Maíra; Narvaes da Rocha Campos, André; Anastacio, Thalita Cardoso
- BMC Genomics, Vol. 18, Issue 1