Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens

• Published in: Molecular plant-microbe interactions Vol. 37; no. 2; pp. 127 - 142
• Main Authors: Garcia, Jadran F, Morales-Cruz, Abraham, Cochetel, Noé, Minio, Andrea, Figueroa-Balderas, Rosa, Rolshausen, Philippe E, Baumgartner, Kendra, Cantu, Dario
• Format: Journal Article
• Language: English
• Published: United States American Phytopathological Society 01.02.2024; The American Phytopathological Society
• Subjects: Body organs; Botryosphaeria; Carbohydrates; cell wall-degrading enzymes; Cell walls; comparative genomics; Damage; Dieback; Enzymes; Eutypa lata; fungal pangenomes; Fungi; Gene clusters; genome evolution; Genomes; Genomics; Grapevines; Metabolites; Neofusicoccum parvum; Nucleotides; Pathogens; Phaeoacremonium minimum; Polyketide synthase; Positive selection; secondary metabolism; Secondary metabolites; Signs and symptoms; Virulence; Virulence factors; Viticulture; Vitis vinifera; genome evolution; fungal pangenomes; secondary metabolism; cell wall-degrading enzymes; comparative genomics
• ISSN: 0894-0282; 1943-7706
• DOI: 10.1094/MPMI-09-23-0129-R

The permanent organs of grapevines ( L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on , , and , causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of and . The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in and , glycosyltransferases in ). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.