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

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    Date
    2014
    Author
    Riley, Robert 
    Salamov, Asaf A. 
    Brown, Daren W. 
    Nagy, Laszlo G. 
    Floudas, Dimitrios 
    Held, Benjamin W. 
    Levasseur, Anthony 
    Lombard, Vincent 
    Morin, Emmanuelle 
    Pisabarro de Lucas, Gerardo Upna Orcid
    Version
    Acceso abierto / Sarbide irekia
    Type
    Artículo / Artikulua
    Version
    Versión publicada / Argitaratu den bertsioa
    Impact
     
     
     
    10.1073/pnas.1400592111
     
     
     
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    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 dec ... [++]
    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. [--]
    Subject
    Lignocellulose, Phylogenomics, Bioenergy
     
    Publisher
    National Academy of Sciences
    Published in
    PNAS July 8, 2014 111 (27) 9923-9928
    Departament
    Universidad Pública de Navarra. Departamento de Producción Agraria / Nafarroako Unibertsitate Publikoa. Nekazaritza Ekoizpena Saila
     
    Publisher version
    https://doi.org/10.1073/pnas.1400592111
    URI
    https://hdl.handle.net/2454/31890
    Sponsorship
    The work conducted by the US Department of Energy (DOE) Joint Genome Institute is supported by the Office of Science of the DOE under Contract DE-AC02-05CH11231. J.D.W. and D.J. were supported by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science Biological and Environmental Research Contract DE-FC02-07ER64494).
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    • Artículos de revista DPA - NES Aldizkari artikuluak [129]
    • Artículos de revista - Aldizkari artikuluak [4205]
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