Nonhomologous end-joining deficiency allows large chromosomal deletions to be produced by replacement-type recombination in Aspergillus oryzae.

Gene targeting is a technique of introducing a genetic trait at a predetermined site within a genome; it is also used to eliminate undesirable chromosomal regions from the relevant genome. Thus far, replacement-type recombination between two homologous regions separated by a large nonhomologous sequence has been hardly achieved probably due to the low frequency of homologous recombination in filamentous fungi. In this study, we report the successful and highly efficient deletion by replacement-type recombination of up to 470-kb regions of chromosome 8 and 200-kb region in chromosome 3, which includes a homologue of aflatoxin gene cluster, by nonhomologous end-joining deficient strains of Aspergillus oryzae. Our study results indicate that the deficiency of nonhomologous end-joining increases the distance of nonhomologous regions in replacement-type recombination, i.e., the possible deletion range in generation of large chromosomal deletion by one cycle of replacement-type recombination is increased in nonhomologous end-joining deficient strains.