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

Riley, Robert; Salamov, Asaf A.; Brown, Daren W.; Nagy, Laszlo G.; Floudas, Dimitrios; Held, Benjamin W.; Levasseur, Anthony; Lombard, Vincent; Morin, Emmanuelle; Otillar, Robert; Lindquist, Erika A.; Sun, Hui; LaButti, Kurt M.; Schmutz, Jeremy; Jabbour, Dina; Luo, Hong; Baker, Scott E.; Pisabarro, Antonio G.; Walton, Jonathan D.; Blanchette, Robert A.; Henrissat, Bernard; Martin, Francis; Cullen, Dan; Hibbett, David S.; Grigoriev, Igor V.

doi:10.1073/pnas.1400592111

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

Journal Article · Mon Jun 23 00:00:00 EDT 2014 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1400592111· OSTI ID:1469149

Riley, Robert ^[1]; Salamov, Asaf A. ^[1]; Brown, Daren W. ^[2]; Nagy, Laszlo G. ^[3]; Floudas, Dimitrios ^[3]; Held, Benjamin W. ^[4]; Levasseur, Anthony ^[5]; Lombard, Vincent ^[6]; Morin, Emmanuelle ^[7]; Otillar, Robert ^[1]; Lindquist, Erika A. ^[1]; Sun, Hui ^[1]; LaButti, Kurt M. ^[1]; Schmutz, Jeremy ^[8]; Jabbour, Dina ^[9]; Luo, Hong ^[9]; Baker, Scott E. ^[10]; Pisabarro, Antonio G. ^[11]; Walton, Jonathan D. ^[9]; Blanchette, Robert A. ^[4] more »

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
US Dept. of Agriculture (USDA)., Peoria, IL (United States)
Clark Univ., Worcester, MA (United States). Dept. of Biology
Univ. of Minnesota, St. Paul, MN (United States)
Aix-Marseille Univ., Marseille (France). Inst. National de la Recherche Agronomique
Aix-Marseille Univ., Marseille (France). Centre National de la Recherche Scientifique
Inst. National de la Recherche Agronomique (INRA), Champenoux (France). Inst. National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. of Biotechnology, Huntsville, AL (United States)
Michigan State Univ., East Lansing, MI (United States). DOE Great Lakes Bioenergy Research Center
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Univ. Pública de Navarra, Pamplona (Spain). Dept. de Producción Agraria
Inst. National de la Recherche Agronomique (INRA), Champenoux (France). Inst. National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes
USDA Forest Products Lab., Madison, WI (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; FC02-07ER64494; AC05-76RL01830

OSTI ID:: 1469149

Alternate ID(s):: OSTI ID: 1556894

Report Number(s):: LBNL-178088; PNNL-SA-103485; ir:178088

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, Issue 27; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 468 works

Citation information provided by
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