Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi

Authors: GARCIA, JADRAN - University Of California, Davis; FIGUEROA-BALDERAS, ROSA - University Of California, Davis; COMONT, G - Inrae; DELMAS, C - Inrae; Baumgartner, Kendra; CANTU, DARIO - University Of California, Davis

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2024
Publication Date: 8/14/2024
Citation: Garcia, J.F., Figueroa-Balderas, R., Comont, G., Delmas, C., Baumgartner, K., Cantu, D. 2024. Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkae189.
DOI: https://doi.org/10.1093/g3journal/jkae189

Interpretive Summary: Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease Esca. We sequenced the genomes of four such species, including Europenean species Fomitiporia mediterranea, and North American species Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. In comparing these four genomes, we identified gene families potentially involved with the fungal ability to attack the plant (i.e., virulence factors). Also, we identified gene families associated with degradation of woody tissues, namely lignocellulosic substrates. The four genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2, which are typical of white-rot fungi. These findings verify previous characterization of Fomitiporia mediterranea, Fomitiporia polymorpha as white-rot fungi and suggest that Inonotus vitis, and Tropicoporus texanus are also white-rot fungi. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in Esca symptoms and host resistance.

Technical Abstract: Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease Esca. We present the genomes of four species associated with Esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing. The genomic and functional comparisons identified potential virulence factors, suggesting their roles in disease development. Similar to other white-rot fungi known for their ability to degrade lignocellulosic substrates, these four genomes encoded a variety of lignin peroxidases and carbohydrate-active enzymes (CAZymes) such as CBM1, AA9, and AA2. The analysis of gene family expansion and contraction revealed dynamic evolutionary patterns, particularly in genes related to secondary metabolite production, plant cell wall decomposition, and xenobiotic degradation. The availability of these genomes will serve as a reference for further studies of diversity and evolution of virulence factors and their roles in Esca symptoms and host resistance.