Population genomics of the grapevine pathogen Eutypa lata reveals evidence for population expansion and intraspecific differences in secondary metabolite gene clusters

Abstract

Eutypa dieback of grapevine is an important disease caused by the generalist Ascomycete fungus Eutypa lata. Despite the relevance of this species to the global wine industry, its genomic diversity remains unknown, with only a single publicly available genome assembly. Whole-genome sequencing and comparative genomics was performed on forty Australian E. lata isolates to understand the genome evolution, adaptation, population size and structure of these isolates. Phylogenetic and linkage disequilibrium decay analyses provided evidence of extensive gene flow through sexual recombination between isolates obtained from different geographic locations and hosts. Investigation of the genetic diversity of these isolates suggested rapid population expansion, likely as a consequence of the recent growth of the Australian wine industry. Genomic regions affected by selective sweeps were shown to be enriched for genes associated with secondary metabolite clusters and included genes encoding proteins with a role in nutrient acquisition, degradation of host cell wall and metal and drug resistance, suggesting recent adaptation to both abiotic factors and potentially host genotypes. Genome synteny analysis using long-read genome assemblies showed significant intraspecific genomic plasticity with extensive chromosomal rearrangements impacting the secondary metabolite production potential of this species. Finally, k-mer based GWAS analysis identified a potential locus associated with mycelia recovery in canes of Vitis vinifera that will require further investigations.

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

“…In this study, we assembled and annotated the genomes of fifty isolates of the three critical pathogens associated with Eutypa dieback, Botryosphaeria dieback and Esca. The average assembly size, completeness and gene predictions of the species are consistent with previously published genomes (3, 5, 6, 20, 60). Prior to the construction of the three pangenomes, we validated the completeness of the fifty assemblies by structural and gene-content comparisons with chromosome-scale assemblies based on long-read sequencing, including a new one for E. lata assembled as part of this study.…”

“…The first notable difference observed was that E. lata possesses the largest number of nodes in its pangenome graph. This could be indicative of a more complex genomic structure, encompassing various genomic variants, as suggested by previous research (17, 20, 66). While the utilization of more isolates in building E. lata ’s pangenome might contribute to this observation (67), the similarity in node complexity between P. minimum and N. parvum —each with approximately four million nodes—supports that the number of genomes used is not the sole factor for greater node complexity.…”

“…Indels also impact complete genes responsible for the biosynthesis of polyketides, a diverse group of biologically active compounds found in fungi, such as mycotoxins, antifungal, and antibiotic products. Comparable findings were reported in E. lata , where structural variants and chromosomal rearrangements were linked to alterations in secondary-metabolite production (20).…”

“…The broad variability in virulence observed among isolates is likely due to differences in virulence-factor content, properties, and expression during infection (5, 20). For instance, in the case of P. minimum , genomes of different isolates exhibit approximately 1 Mbp of structural differences, resulting in the presence/absence polymorphisms of multiple adjacent genes, particularly associated with biosynthetic clusters related to secondary metabolism (5).…”

Phytotoxic Metabolites Produced by Fungi Involved in Grapevine Trunk Diseases: Progress, Challenges, and Opportunities

“…In 2015, Morales-Cruz and co-authors highlighted a great expansion of families of genes involved in the biosynthesis of toxins, including polyketide synthesis (t1PKS) [ 72 ]. More recently, the first whole-genome sequencing and comparative genomics study on 40 E. lata isolates from Australia was reported [ 73 ].…”