Author

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

1. Robert Rileya, 
2. Asaf A. Salamova, 
3. Daren W. Brownb, 
4. Laszlo G. Nagyc, 
5. Dimitrios Floudasc, 
6. Benjamin W. Heldd, 
7. Anthony Levasseure, 
8. Vincent Lombardf, 
9. Emmanuelle Moring, 
10. Robert Otillara, 
11. Erika A. Lindquista, 
12. Hui Suna, 
13. Kurt M. LaButtia, 
14. Jeremy Schmutza,h, 
15. Dina Jabbouri, 
16. Hong Luoi, 
17. Scott E. Bakerj, 
18. Antonio G. Pisabarrok, 
19. Jonathan D. Waltoni, 
20. Robert A. Blanchetted, 
21. Bernard Henrissatf, 
22. Francis Marting, 
23. Dan Cullenl, 
24. David S. Hibbettc,1, and 
25. Igor V. Grigorieva,1

Author Affiliations

1. Edited* by Thomas N. Taylor, University of Kansas, Lawrence, KS, and approved May 16, 2014 (received for review January 12, 2014)

• A correction has been published

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Significance

Wood decay fungi have historically been characterized as either white rot, which degrade all components of plant cell walls, including lignin, or brown rot, which leave lignin largely intact. Genomic analyses have shown that white-rot species possess multiple lignin-degrading peroxidases (PODs) and expanded suites of enzymes attacking crystalline cellulose. To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. Moreover, they appear to degrade lignin, based on decay analyses on wood wafers. Our results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms.

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. argillaceacan 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.

• lignocellulose
 
• phylogenomics
 
• bioenergy

Footnotes

• 1To whom correspondence may be addressed. E-mail: IVGrigoriev@lbl.gov or dhibbett@clarku.edu.

• Author contributions: R.R., S.E.B., A.G.P., J.D.W., R.A.B., B.H., F.M., D.C., D.S.H., and I.V.G. designed research; R.R., D.W.B., L.G.N., D.F., B.W.H., A.L., E.M., and R.A.B. performed research; A.G.P., J.D.W., B.H., and D.S.H. contributed new reagents/analytic tools; R.R., A.A.S., D.W.B., L.G.N., D.F., A.L., V.L., E.M., R.O., E.A.L., H.S., K.M.L., J.S., D.J., and H.L. analyzed data; and R.R., D.W.B., J.D.W., R.A.B., B.H., D.C., D.S.H., and I.V.G. wrote the paper.
• The authors declare no conflict of interest.
• *This Direct Submission article had a prearranged editor.
• Data deposition: The sequences reported in this paper have been deposited in the GenBank database [AYEP00000000(Botryobasidium botryosum), AYUM00000000 (Galerina marginata), AYUL00000000 (Jaapia argillacea), and AYUK00000000 (Pleurotus ostreatus)].
• This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1400592111/-/DCSupplemental.

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