Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

Authors: GARCIA, J. - University Of California, Davis; MORALES-CRUZ, A. - Department Of Energy Joint Genome; COCHETEL, NOE - University Of California, Davis; MINIO, A. - University Of California, Davis; FIGUEROA-BALDERAS, R. - University Of California, Davis; ROLSHAUSEN, P. - University Of California, Riverside; Baumgartner, Kendra; CANTU, DARIO - University Of California, Davis

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2023
Publication Date: 3/8/2024
Citation: Garcia, J., Morales-Cruz, A., Cochetel, N., Minio, A., Figueroa-Balderas, R., Rolshausen, P., Baumgartner, K., Cantu, D. 2024. Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens. Molecular Plant-Microbe Interactions. 37(2):127-142. https://doi.org/10.1094/MPMI-09-23-0129-R.

Interpretive Summary: Variability in the rate at which a pathogen colonizes its host (‘virulence’) has been reported among various species of fungal pathogens that cause grapevine trunk diseases. However, studying the genetic bases of such intraspecific variation has been hampered by a focus the genome of one isolate per species. This approach does not take into account the diversity in the genomes of multiple isolates within a species. Our study introduces nucleotide-level, reference-free pangenomes, which are constructed from analyses of multiple isolates per species. We expect these pangenomes to become a valuable study tool for examining variation in virulence and, further, species evolution. As model species, we used Eutypa lata, Neofusicoccum parvum and Phaeoacremonium minimum, causal agents of the grapevine trunk diseases Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. These pangenomes revealed distinct evolutionary patterns within and between species. Indeed, we identified variation in virulence-related genes, but also in the non-coding regions, such as diverse Transposable Elements in the dispensable and private regions of the genome. Finally, our pangenomes serve as invaluable resources for future forward-genetic analyses, including panGWAS, with the goal of unveiling the genetic basis of specific pathogenic and virulence-related traits.

Technical Abstract: The permanent organs of grapevines (V. vinifera L.), like 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 Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced fifty isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examining 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, CAZymes were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthases genes in E. lata and P. minimum, glycosyltransferases in N. parvum). 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.