title: Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.
abstract: Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
authors: Robert
authors: R
authors: Riley
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
authors: Asaf A
authors: AA
authors: Salamov
authors: US Department of Agriculture (USDA), Peoria, IL 61604;
authors: Daren W
authors: DW
authors: Brown
authors: Department of Biology, Clark University, Worcester, MA 01610;
authors: Laszlo G
authors: LG
authors: Nagy
authors: Department of Biology, Clark University, Worcester, MA 01610;
authors: Dimitrios
authors: D
authors: Floudas
authors: University of Minnesota, St. Paul, MN 55108;
authors: Benjamin W
authors: BW
authors: Held
authors: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1163, Aix-Marseille Université, 13288 Marseille, France;
authors: Anthony
authors: A
authors: Levasseur
authors: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France;
authors: Vincent
authors: V
authors: Lombard
authors: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes, 54280 Champenoux, France;
authors: Emmanuelle
authors: E
authors: Morin
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
authors: Robert
authors: R
authors: Otillar
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
authors: Erika A
authors: EA
authors: Lindquist
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
authors: Hui
authors: H
authors: Sun
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
authors: Kurt M
authors: KM
authors: LaButti
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806;
authors: Jeremy
authors: J
authors: Schmutz
authors: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824;
authors: Dina
authors: D
authors: Jabbour
authors: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824;
authors: Hong
authors: H
authors: Luo
authors: Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354;
authors: Scott E
authors: SE
authors: Baker
authors: Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain; and.
authors: Antonio G
authors: AG
authors: Pisabarro
authors: DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824;
authors: Jonathan D
authors: JD
authors: Walton
authors: University of Minnesota, St. Paul, MN 55108;
authors: Robert A
authors: RA
authors: Blanchette
authors: Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France;
authors: Bernard
authors: B
authors: Henrissat
authors: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes, 54280 Champenoux, France;
authors: Francis
authors: F
authors: Martin
authors: USDA Forest Products Laboratory, Madison, WI 53726.
authors: Dan
authors: D
authors: Cullen
authors: Department of Biology, Clark University, Worcester, MA 01610; IVGrigoriev@lbl.gov dhibbett@clarku.edu.
authors: David S
authors: DS
authors: Hibbett
authors: US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598; IVGrigoriev@lbl.gov dhibbett@clarku.edu.
authors: Igor V
authors: IV
authors: Grigoriev
mesh_terms: D001487:Basidiomycota / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D016681:Genome, Fungal; D008031:Lignin / Q000378:metabolism; D008969:Molecular Sequence Data; D010802:Phylogeny; D014934:Wood
chemical_list: C036909:lignocellulose; D008031:Lignin
keywords: bioenergy; lignocellulose; phylogenomics