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.