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Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8. doi: 10.1073/pnas.1400592111. Epub 2014 Jun 23.

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.

Author information

1
US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
2
US Department of Agriculture (USDA), Peoria, IL 61604;
3
Department of Biology, Clark University, Worcester, MA 01610;
4
University of Minnesota, St. Paul, MN 55108;
5
Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1163, Aix-Marseille Université, 13288 Marseille, France;
6
Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France;
7
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;
8
US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806;
9
DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824;
10
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354;
11
Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain; and.
12
USDA Forest Products Laboratory, Madison, WI 53726.
13
Department of Biology, Clark University, Worcester, MA 01610; IVGrigoriev@lbl.gov dhibbett@clarku.edu.
14
US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598; IVGrigoriev@lbl.gov dhibbett@clarku.edu.

Erratum in

  • Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14959.

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.

KEYWORDS:

bioenergy; lignocellulose; phylogenomics

PMID:
24958869
PMCID:
PMC4103376
DOI:
10.1073/pnas.1400592111
[Indexed for MEDLINE]
Free PMC Article

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