The Cre/lox system: a practical tool to efficiently eliminate selectable markers in fungal endophytes

Interspecific hybridization is a common evolutionary process for the many epichloid fungi that consequently possess multiple gene copies accumulated from their parental strains. Serial gene manipulations in such strains are impeded by the limited availability of selectable resistance marker genes. Therefore, we developed a method for marker elimination suitable for a range of filamentous fungi that allows the reuse of the same marker for successive manipulations, and can also generate gene knockout mutants free of any foreign genes. For epichloae, the complete elimination of the marker gene from the genome would mitigate public concerns and regulatory hurdles to the use of such fungal strains in field experiments.