Genomic Structural Variants of Sclerotinia sclerotiorum Lib de Bary Isolates Contrasting for Disease Aggressiveness

Structural variants (SV) are defined as genomic variations as small as 50 base pairs or as large as whole chromosomes. SVs can alter gene expression, influence virulence factors, and contribute to the pathogen’s ability to overcome host defenses. Traditional methods for Sclerotinia sclerotiorum Lib. de Bary (S. sclerotiorum) genomic variant analysis have been hindered by the inability of short-read sequencing technologies to capture the full extent of genomic variance, especially large structural variants. This study aimed to generate high-quality genome assemblies, identify and characterize SVs, and compare their distribution across seven S. sclerotiorum disease aggressiveness contrasting isolates using Oxford Nanopore long-read sequencing. A total of 2,830 unique SVs ranging from 50 bp to 10 Kb were identified across the seven isolates. Of these, 446 SVs (15.8%) were high-impact variants affecting 367 genes. High-impact SVs were predominantly deletions and insertions and varied among isolates. Of the 446 high-impact SVs, 28.9% (n=129) were present in a single isolate while 15.5% (n=69) were present in all seven isolates. Jaccard similarity analysis based on presence/absence of high-impact SVs clustered the seven isolates into three major clusters. The first cluster included isolates with higher disease aggressiveness compared to the second and third clusters. Characterization of structural variants provides a foundation for investigating the evolutionary processes and adaptation of S. sclerotiorum but require additional validation and sampling. The SVs reported in this study provide a valuable resource for future studies to understand the role of SVs in aggressiveness of the economically devastating pathogen S. sclerotiorum.