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Title: Comparative genome analysis of Basidiomycete fungi

Abstract

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may bemore » inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.« less

Authors:
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Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1241232
Report Number(s):
LBNL-7022E
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Conference
Resource Relation:
Conference: APS-MSA Joint Meeting, Austin, Texas, 08/10/14 - 08/14/14
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Riley, Robert, Salamov, Asaf, Henrissat, Bernard, Nagy, Laszlo, Brown, Daren, Held, Benjamin, Baker, Scott, Blanchette, Robert, Boussau, Bastien, Doty, Sharon L., Fagnan, Kirsten, Floudas, Dimitris, Levasseur, Anthony, Manning, Gerard, Martin, Francis, Morin, Emmanuelle, Otillar, Robert, Pisabarro, Antonio, Walton, Jonathan, Wolfe, Ken, Hibbett, David, and Grigoriev, Igor. Comparative genome analysis of Basidiomycete fungi. United States: N. p., 2013. Web.
Riley, Robert, Salamov, Asaf, Henrissat, Bernard, Nagy, Laszlo, Brown, Daren, Held, Benjamin, Baker, Scott, Blanchette, Robert, Boussau, Bastien, Doty, Sharon L., Fagnan, Kirsten, Floudas, Dimitris, Levasseur, Anthony, Manning, Gerard, Martin, Francis, Morin, Emmanuelle, Otillar, Robert, Pisabarro, Antonio, Walton, Jonathan, Wolfe, Ken, Hibbett, David, & Grigoriev, Igor. Comparative genome analysis of Basidiomycete fungi. United States.
Riley, Robert, Salamov, Asaf, Henrissat, Bernard, Nagy, Laszlo, Brown, Daren, Held, Benjamin, Baker, Scott, Blanchette, Robert, Boussau, Bastien, Doty, Sharon L., Fagnan, Kirsten, Floudas, Dimitris, Levasseur, Anthony, Manning, Gerard, Martin, Francis, Morin, Emmanuelle, Otillar, Robert, Pisabarro, Antonio, Walton, Jonathan, Wolfe, Ken, Hibbett, David, and Grigoriev, Igor. 2013. "Comparative genome analysis of Basidiomycete fungi". United States. https://www.osti.gov/servlets/purl/1241232.
@article{osti_1241232,
title = {Comparative genome analysis of Basidiomycete fungi},
author = {Riley, Robert and Salamov, Asaf and Henrissat, Bernard and Nagy, Laszlo and Brown, Daren and Held, Benjamin and Baker, Scott and Blanchette, Robert and Boussau, Bastien and Doty, Sharon L. and Fagnan, Kirsten and Floudas, Dimitris and Levasseur, Anthony and Manning, Gerard and Martin, Francis and Morin, Emmanuelle and Otillar, Robert and Pisabarro, Antonio and Walton, Jonathan and Wolfe, Ken and Hibbett, David and Grigoriev, Igor},
abstractNote = {Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.},
doi = {},
url = {https://www.osti.gov/biblio/1241232}, journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Aug 07 00:00:00 EDT 2013},
month = {Wed Aug 07 00:00:00 EDT 2013}
}

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