Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay
Hayat Hage, Shingo Miyauchi, Máté Virágh, Élodie Drula, Byoungnam Min, Delphine Chaduli, David Navarro, Anne Favel, Manon Norest, Laurence Lesage‐Meessen, Balázs Bálint, Zsolt Merényi, Laura I. de Eugenio, Emmanuelle Morin, Ángel T. Martı́nez, Petr Baldrián, Martina Štursová, Marı́a Jesús Martı́nez, Čeněk Novotný, Jon Magnuson, Joey Spatafora, Sundy Maurice, Jasmyn Pangilinan, Willian Andreopoulos, Kurt LaButti, Hope Hundley, Hyunsoo Na, Alan Kuo, Kerrie Barry, Anna Lipzen, Bernard Henrissat, Robert Riley, Steven Ahrendt, László G. Nagy, Igor V. Grigoriev, Francis Martin, Marie‐Noëlle Rosso
Abstract
Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.