Notes, outline and divergence times of Basidiomycota

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Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.

Diego Martínez, Luis Larrondo, Nik Putnam … (2004)

White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These fungi use extracellular oxidative enzymes that are also able to transform related aromatic compounds found in explosive contaminants, pesticides and toxic waste. We have sequenced the 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using a whole genome shotgun approach. The P. chrysosporium genome reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay. Analysis of the genome data will enhance our understanding of lignocellulose degradation, a pivotal process in the global carbon cycle, and provide a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching. This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens.

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

Robert Riley, Asaf Salamov, Daren W. Brown … (2014)

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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Assembly history dictates ecosystem functioning: evidence from wood decomposer communities.

Tadashi Fukami, Ian Dickie, J. Paula Wilkie … (2010)

Community assembly history is increasingly recognized as a fundamental determinant of community structure. However, little is known as to how assembly history may affect ecosystem functioning via its effect on community structure. Using wood-decaying fungi as a model system, we provide experimental evidence that large differences in ecosystem functioning can be caused by small differences in species immigration history during community assembly. Direct manipulation of early immigration history resulted in three-fold differences in fungal species richness and composition and, as a consequence, differences of the same magnitude in the rate of decomposition and carbon release from wood. These effects - which were attributable to the history-dependent outcome of competitive and facilitative interactions - were significant across a range of nitrogen availabilities observed in natural forests. Our results highlight the importance of considering assembly history in explaining ecosystem functioning.

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Title: Fungal Diversity

Abbreviated Title: Fungal Diversity

Publisher: Springer Science and Business Media LLC

ISSN (Print): 1560-2745

ISSN (Electronic): 1878-9129

Publication date (Electronic): November 27 2019

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DOI: 10.1007/s13225-019-00435-4

SO-VID: ab69bcf7-0116-4d06-9a6e-abbebb47490f

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https://creativecommons.org/licenses/by/4.0

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Self URI (article page): http://link.springer.com/10.1007/s13225-019-00435-4

Self URI (pdf): http://link.springer.com/content/pdf/10.1007/s13225-019-00435-4.pdf

Notes, outline and divergence times of Basidiomycota

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Most cited references 2,308

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78.

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

Assembly history dictates ecosystem functioning: evidence from wood decomposer communities.

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