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Title: Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae

Authors:
 [1];  [1];  [1];  [1]; ORCiD logo [2];  [1];  [3];  [4]; ORCiD logo [5];  [3];  [6];  [6];  [6];  [6];  [6]; ORCiD logo [6]; ORCiD logo [1]
  1. Synthetic and Systems Biology Unit Institute of Biochemistry Biological Research Center HAS Szeged 6726 Hungary
  2. Department of Plant Anatomy Institute of Biology Eötvös Loránd University Budapest 1117 Hungary, Plant Protection Institute Centre for Agricultural Research Hungarian Academy of Sciences Budapest 1022 Hungary
  3. Seqomics Ltd. Mórahalom Mórahalom 6782 Hungary
  4. Architecture et Fonction des Macromolécules Biologiques (AFMB) CNRS Université Aix‐Marseille 163 Avenue de Luminy 13288 Marseille France, INRAUSC 1408 AFMB 13288 Marseille France
  5. Architecture et Fonction des Macromolécules Biologiques (AFMB) CNRS Université Aix‐Marseille 163 Avenue de Luminy 13288 Marseille France, INRAUSC 1408 AFMB 13288 Marseille France, Department of Biological Sciences King Abdulaziz University Jeddah 21589 Saudi Arabia
  6. US Department of Energy Joint Genome Institute 2800 Mitchell Drive Walnut Creek CA 94598 USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1545936
Grant/Contract Number:  
DE‐AC02‐05CH11231
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Name: New Phytologist Journal Volume: 224 Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Almási, Éva, Sahu, Neha, Krizsán, Krisztina, Bálint, Balázs, Kovács, Gábor M., Kiss, Brigitta, Cseklye, Judit, Drula, Elodie, Henrissat, Bernard, Nagy, István, Chovatia, Mansi, Adam, Catherine, LaButti, Kurt, Lipzen, Anna, Riley, Robert, Grigoriev, Igor V., and Nagy, László G. Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae. United Kingdom: N. p., 2019. Web. doi:10.1111/nph.16032.
Almási, Éva, Sahu, Neha, Krizsán, Krisztina, Bálint, Balázs, Kovács, Gábor M., Kiss, Brigitta, Cseklye, Judit, Drula, Elodie, Henrissat, Bernard, Nagy, István, Chovatia, Mansi, Adam, Catherine, LaButti, Kurt, Lipzen, Anna, Riley, Robert, Grigoriev, Igor V., & Nagy, László G. Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae. United Kingdom. doi:10.1111/nph.16032.
Almási, Éva, Sahu, Neha, Krizsán, Krisztina, Bálint, Balázs, Kovács, Gábor M., Kiss, Brigitta, Cseklye, Judit, Drula, Elodie, Henrissat, Bernard, Nagy, István, Chovatia, Mansi, Adam, Catherine, LaButti, Kurt, Lipzen, Anna, Riley, Robert, Grigoriev, Igor V., and Nagy, László G. Wed . "Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae". United Kingdom. doi:10.1111/nph.16032.
@article{osti_1545936,
title = {Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae},
author = {Almási, Éva and Sahu, Neha and Krizsán, Krisztina and Bálint, Balázs and Kovács, Gábor M. and Kiss, Brigitta and Cseklye, Judit and Drula, Elodie and Henrissat, Bernard and Nagy, István and Chovatia, Mansi and Adam, Catherine and LaButti, Kurt and Lipzen, Anna and Riley, Robert and Grigoriev, Igor V. and Nagy, László G.},
abstractNote = {},
doi = {10.1111/nph.16032},
journal = {New Phytologist},
number = 2,
volume = 224,
place = {United Kingdom},
year = {2019},
month = {6}
}

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Works referenced in this record:

Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii
journal, March 2015


A DNA Damage Checkpoint Pathway Coordinates the Division of Dikaryotic Cells in the Ink Cap Mushroom Coprinopsis cinerea
journal, June 2013


Distribution and bioinformatic analysis of the cerato-platanin protein family in Dikarya
journal, November 2013

  • Chen, Hongxin; Kovalchuk, Andriy; Keriö, Susanna
  • Mycologia, Vol. 105, Issue 6
  • DOI: 10.3852/13-115

Transcription factor genes of Schizophyllum commune involved in regulation of mushroom formation: Regulation of mushroom formation
journal, August 2011


Fruiting body production in basidiomycetes
journal, August 2000


Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea
journal, October 2015


Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
journal, June 2010

  • Stajich, J. E.; Wilke, S. K.; Ahren, D.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 26
  • DOI: 10.1073/pnas.1003391107

Cerato-platanins: a fungal protein family with intriguing properties and application potential
journal, April 2014

  • Gaderer, Romana; Bonazza, Klaus; Seidl-Seiboth, Verena
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 11
  • DOI: 10.1007/s00253-014-5690-y

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria
journal, October 2017

  • Sipos, György; Prasanna, Arun N.; Walter, Mathias C.
  • Nature Ecology & Evolution, Vol. 1, Issue 12
  • DOI: 10.1038/s41559-017-0347-8

New Phytologist ? an evolving host for mycorrhizal research
journal, April 2007


Fungal Galectins, Sequence and Specificity of Two Isolectins from Coprinus cinereus
journal, January 1997

  • Cooper, Douglas N. W.; Boulianne, Robert P.; Charlton, Stacy
  • Journal of Biological Chemistry, Vol. 272, Issue 3
  • DOI: 10.1074/jbc.272.3.1514

A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom Disease of cacao
journal, January 2008

  • Mondego, Jorge MC; Carazzolle, Marcelo F.; Costa, Gustavo GL
  • BMC Genomics, Vol. 9, Issue 1
  • DOI: 10.1186/1471-2164-9-548

How do Agaricomycetes shape their fruiting bodies? 1. Morphological aspects of development
journal, June 2015


Glycosylphosphatidylinositol-anchored Fungal Polysaccharide in Aspergillus fumigatus
journal, October 2005

  • Costachel, Corina; Coddeville, Bernadette; Latgé, Jean-Paul
  • Journal of Biological Chemistry, Vol. 280, Issue 48
  • DOI: 10.1074/jbc.M510163200

Anatomical changes in Syzygium cumuini Linn. wood decayed by two white rot fungi Schizophyllum commune Fries. and Flavodon flavus (Klotzsch) Ryvarden
journal, June 2011


Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth
journal, March 2017


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
  • DOI: 10.1007/s00253-016-7574-9

Size-Correction and Principal Components for Interspecific Comparative Studies
journal, December 2009


Comparative transcriptomics in human and mouse
journal, May 2017

  • Breschi, Alessandra; Gingeras, Thomas R.; Guigó, Roderic
  • Nature Reviews Genetics, Vol. 18, Issue 7
  • DOI: 10.1038/nrg.2017.19

phytools: an R package for phylogenetic comparative biology (and other things): phytools: R package
journal, December 2011


An endo-β-1,6-glucanase involved in Lentinula edodes fruiting body autolysis
journal, April 2011


SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Comparative proteomic analysis of different developmental stages of the edible mushroom Termitomyces heimii
journal, January 2014

  • Rahmad, Norasfaliza; Al-Obaidi, Jameel R.; Rashid, Noraswati Mohd
  • Biological Research, Vol. 47, Issue 1
  • DOI: 10.1186/0717-6287-47-30

Lentinula edode s tlg1 Encodes a Thaumatin-Like Protein That Is Involved in Lentinan Degradation and Fruiting Body Senescence
journal, April 2006

  • Sakamoto, Yuichi; Watanabe, Hisayuki; Nagai, Masaru
  • Plant Physiology, Vol. 141, Issue 2
  • DOI: 10.1104/pp.106.076679

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea
journal, January 2013


Fruiting body development in Coprinus cinereus: regulated expression of two galectins secreted by a non-classical pathway
journal, August 2000


Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source
journal, January 2014


Variability of Wood Degrading Enzymes of Schizophyllum commune
journal, January 1980


Schizophyllum commune as a Ubiquitous Plant Parasite
journal, January 2010

  • Takemoto, Shuhei; Nakamura, Hitoshi; Imamura, Yuji
  • Japan Agricultural Research Quarterly: JARQ, Vol. 44, Issue 4
  • DOI: 10.6090/jarq.44.357

A Novel Expansin Protein from the White-Rot Fungus Schizophyllum commune
journal, March 2015

  • Tovar-Herrera, Omar Eduardo; Batista-García, Ramón Alberto; Sánchez-Carbente, María del Rayo
  • PLOS ONE, Vol. 10, Issue 3
  • DOI: 10.1371/journal.pone.0122296

Developmental Regulation of Fungal Cell Wall Formation
journal, September 1994


The Candida albicans KRE9 gene is required for cell wall  -1,6-glucan synthesis and is essential for growth on glucose
journal, August 1998

  • Lussier, M.; Sdicu, A. -M.; Shahinian, S.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 17
  • DOI: 10.1073/pnas.95.17.9825

Some fungi express β-1,3-glucanases similar to thaumatin-like proteins
journal, September 2000


WoLF PSORT: protein localization predictor
journal, May 2007

  • Horton, P.; Park, K. -J.; Obayashi, T.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm259

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche
journal, October 2012

  • Morin, E.; Kohler, A.; Baker, A. R.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 43
  • DOI: 10.1073/pnas.1206847109

Thaumatin gene confers resistance to fungal pathogens as well as tolerance to abiotic stresses in transgenic tobacco plants
journal, March 2007


Full-length transcriptome assembly from RNA-Seq data without a reference genome
journal, May 2011

  • Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran
  • Nature Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1038/nbt.1883

Feruloyl esterases from Schizophyllum commune to treat food industry side-streams
journal, November 2016


MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
journal, January 2013

  • Katoh, K.; Standley, D. M.
  • Molecular Biology and Evolution, Vol. 30, Issue 4
  • DOI: 10.1093/molbev/mst010

Hydrophobins Sc3 and Sc4 gene expression in mounds, fruiting bodies and vegetative hyphae of Schizophyllum commune
journal, March 2008

  • Banerjee, Goutami; Robertson, Deborah L.; Leonard, Thomas J.
  • Fungal Genetics and Biology, Vol. 45, Issue 3
  • DOI: 10.1016/j.fgb.2007.10.018

Regulation of genes involved in cell wall synthesis and structure during Ustilago maydis dimorphism
journal, February 2013


Hydrophobin Gene Expression Affects Hyphal Wall Composition in Schizophyllum commune
journal, November 2000

  • van Wetter, Marie-Anne; Wösten, Han A. B.; Sietsma, J. Hans
  • Fungal Genetics and Biology, Vol. 31, Issue 2
  • DOI: 10.1006/fgbi.2000.1231

Identification, Characterization, and Biosynthesis of a Novel N -Glycan Modification in the Fruiting Body of the Basidiomycete Coprinopsis cinerea
journal, January 2010

  • Buser, Reto; Lazar, Zbigniew; Käser, Sonja
  • Journal of Biological Chemistry, Vol. 285, Issue 14
  • DOI: 10.1074/jbc.M109.076075

The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
journal, July 2017


The exp1 gene essential for pileus expansion and autolysis of the inky cap mushroom Coprinopsis cinerea (Coprinus cinereus) encodes an HMG protein
journal, June 2008

  • Muraguchi, Hajime; Fujita, Takashi; Kishibe, Yuya
  • Fungal Genetics and Biology, Vol. 45, Issue 6
  • DOI: 10.1016/j.fgb.2007.11.004

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
journal, June 2012


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009


Schizophyllum commune has an extensive and functional alternative splicing repertoire
journal, September 2016

  • Gehrmann, Thies; Pelkmans, Jordi F.; Lugones, Luis G.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep33640

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen
journal, March 2012


Secretome Analysis from the Ectomycorrhizal Ascomycete Cenococcum geophilum
journal, February 2018

  • de Freitas Pereira, Maíra; Veneault-Fourrey, Claire; Vion, Patrice
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.00141

limma powers differential expression analyses for RNA-sequencing and microarray studies
journal, January 2015

  • Ritchie, Matthew E.; Phipson, Belinda; Wu, Di
  • Nucleic Acids Research, Vol. 43, Issue 7
  • DOI: 10.1093/nar/gkv007

Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes
journal, June 2018


Genome sequence of the model mushroom Schizophyllum commune
journal, July 2010

  • Ohm, Robin A.; de Jong, Jan F.; Lugones, Luis G.
  • Nature Biotechnology, Vol. 28, Issue 9
  • DOI: 10.1038/nbt.1643

The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013

  • Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1178

Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins
journal, November 2015

  • Pellegrin, Clement; Morin, Emmanuelle; Martin, Francis M.
  • Frontiers in Microbiology, Vol. 6
  • DOI: 10.3389/fmicb.2015.01278

How a fungus escapes the water to grow into the air
journal, January 1999


A role for small secreted proteins (SSPs) in a saprophytic fungal lifestyle: Ligninolytic enzyme regulation in Pleurotus ostreatus
journal, November 2017


An abundant hydrophobin (ABH1) forms hydrophobic rodlet layers in Agaricus bisporus fruiting bodies
journal, May 1996


Functional analysis of a pathogenesis-related thaumatin-like protein gene TaLr35PR5 from wheat induced by leaf rust fungus
journal, May 2018


The Coprinopsis cinerea Tup1 homologue Cag1 is required for gill formation during fruiting body morphogenesis
journal, November 2016

  • Masuda, Ryo; Iguchi, Naoki; Tukuta, Kooki
  • Biology Open, Vol. 5, Issue 12
  • DOI: 10.1242/bio.021246

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis
journal, March 2017

  • Sakamoto, Yuichi; Nakade, Keiko; Sato, Shiho
  • Applied and Environmental Microbiology, Vol. 83, Issue 10
  • DOI: 10.1128/AEM.02990-16

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen
journal, January 2001

  • Krogh, Anders; Larsson, Björn; von Heijne, Gunnar
  • Journal of Molecular Biology, Vol. 305, Issue 3
  • DOI: 10.1006/jmbi.2000.4315

Comparative transcriptomics of the model mushroom Coprinopsis cinerea reveals tissue-specific armories and a conserved circuitry for sexual development
journal, January 2014

  • Plaza, David; Lin, Chia-Wei; van der Velden, Niels Sebastiaan
  • BMC Genomics, Vol. 15, Issue 1
  • DOI: 10.1186/1471-2164-15-492

Le.MAPK and its interacting partner, Le.DRMIP, in fruiting body development in Lentinula edodes
journal, May 2007


Hydrophobins—Unique Fungal Proteins
journal, May 2012


Endo-β-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family
journal, September 2011

  • Sakamoto, Yuichi; Nakade, Keiko; Konno, Naotake
  • Applied and Environmental Microbiology, Vol. 77, Issue 23
  • DOI: 10.1128/AEM.05581-11

All in the Family: the BTB/POZ, KRAB, and SCAN Domains
journal, June 2001


Purification and Characterization of a Novel Exo-β-1,3-1,6-glucanase from the Fruiting Body of the Edible Mushroom Enoki ( Flammulina velutipes )
journal, December 2008

  • Fukuda, Kenji; Hiraga, Michika; Asakuma, Sadaki
  • Bioscience, Biotechnology, and Biochemistry, Vol. 72, Issue 12
  • DOI: 10.1271/bbb.80213

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion
journal, February 2009

  • Martinez, Diego; Challacombe, Jean; Morgenstern, Ingo
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 6
  • DOI: 10.1073/pnas.0809575106

Mushroom Lectins: Specificity, Structure and Bioactivity Relevant to Human Disease
journal, April 2015

  • Hassan, Mohamed; Rouf, Razina; Tiralongo, Evelin
  • International Journal of Molecular Sciences, Vol. 16, Issue 12
  • DOI: 10.3390/ijms16047802

Targeted mutation of the SC3 hydrophobin gene of Schizophyllum commune affects formation of aerial hyphae
journal, July 1996


Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi
journal, March 2019

  • Krizsán, Krisztina; Almási, Éva; Merényi, Zsolt
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 15
  • DOI: 10.1073/pnas.1817822116

Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities
journal, December 2015

  • Nagy, László G.; Riley, Robert; Tritt, Andrew
  • Molecular Biology and Evolution, Vol. 33, Issue 4
  • DOI: 10.1093/molbev/msv337

The yeast KRE9 gene encodes an O glycoprotein involved in cell surface beta-glucan assembly.
journal, October 1993


MycoCosm portal: gearing up for 1000 fungal genomes
journal, December 2013

  • Grigoriev, Igor V.; Nikitin, Roman; Haridas, Sajeet
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1183

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
journal, June 2014

  • Riley, Robert; Salamov, Asaf A.; Brown, Daren W.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 27
  • DOI: 10.1073/pnas.1400592111

How to build a fungal fruit body: from uniform cells to specialized tissue
journal, May 2007


Novel Coprinopsis cinerea Polyesterase That Hydrolyzes Cutin and Suberin
journal, February 2009

  • Kontkanen, H.; Westerholm-Parvinen, A.; Saloheimo, M.
  • Applied and Environmental Microbiology, Vol. 75, Issue 7
  • DOI: 10.1128/AEM.02103-08