Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long-reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that C. parasitica genome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high quality assembled genomes, and question the role of structural variations on the invasive success of this fungal pathogen species.