Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.
Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. About 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.
Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged, Hungary lnagy@brc.hu.
László G
LG
Nagy
US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA.
Robert
R
Riley
Biology Department, Clark University, Worcester, MA.
Philip J
PJ
Bergmann
Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged, Hungary.
Krisztina
K
Krizsán
Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Université Henri Poincaré, Interactions Arbres/Micro-organismes, 02854 Champenoux, France.
Francis M
FM
Martin
US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA.
Igor V
IV
Grigoriev
US Department of Agriculture (USDA) Forest Products Laboratory, Madison, WI.
Dan
D
Cullen
Biology Department, Clark University, Worcester, MA.
David S
DS
Hibbett
D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D005658:Fungi / Q000235:genetics* / Q000378:metabolism; D056726:Genetic Association Studies; D016681:Genome, Fungal; D008031:Lignin / Q000378:metabolism; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D014934:Wood / Q000378:metabolism / Q000382:microbiology*
D005656:Fungal Proteins; D008031:Lignin
bioinformatics; comparative genomics; fungal enzymes; protein of unknown function; wood-decay