Gene deletion and genome perturbation

Fusarium verticillioides causes ear rot disease in maize and its contamination with fumonisins, mycotoxins toxic to humans and livestock. Lipids, and their oxidized forms, may drive the fate of this disease. In a previous study, we have explored the role of oxylipins in this interaction by deleting by standard transformation procedures a linoleate diol synthase-coding gene, lds1, in F. verticillioides. A profound phenotypic diversity in the mutants generated, has prompted us to investigate deeper the whole genome of two lds1-deleted strains. Surprisingly, bioinformatic analyses pinpoint significant differences in the genome sequences emerged between the wild type and the lds1-mutants further than those trivially attributable to the deletion of the lds1 locus such as single nucleotide polymorphisms, small deletion/insertion polymorphisms and structural variations. Difference among the three genomes were analyzed by using a high degree of filtering to decrease the bias due to sub-culturing practices and parasexual cycle operating in these fungi. The results suggest the possibility that the effect of a (theoretically) punctual transformation event might have caused an overall genomic instability, and that transformation practices, commonly used in the reverse genetic of fungi, may potentially be responsible of unexpected, stochastic and henceforth off-target rearrangements throughout the genome.