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Background   U6  promoters have been used for single guide RNA (sgRNA) transcription in the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) genome editing system. However, no available  U6  promoters have been identified in  Aspergillus niger,  which is an important industrial platform for organic acid and protein production. Two CRISPR/Cas9 systems established in  A. niger  have recourse to the RNA polymerase II promoter or in vitro transcription for sgRNA synthesis, but these approaches generally increase cloning efforts and genetic manipulation. The validation of functional RNA polymerase II promoters is therefore an urgent need for  A. niger .    Results  Here, we developed a novel CRISPR/Cas9 system in  A. niger  for sgRNA expression, based on one endogenous  U6  promoter and two heterologous  U6  promoters. The three tested  U6  promoters enabled sgRNA transcription and the disruption of the polyketide synthase  albA  gene in  A. niger . Furthermore, this system enabled highly efficient gene insertion at the targeted genome loci in  A. niger  using donor DNAs with homologous arms as short as 40-bp.    Conclusions  This study demonstrated that both heterologous and endogenous  U6  promoters were functional for sgRNA expression in  A. niger . Based on this result, a novel and simple CRISPR/Cas9 toolbox was established in  A. niger,  that will benefit future gene functional analysis and genome editing.    Electronic supplementary material  The online version of this article (10.1186/s40694-018-0047-4) contains supplementary material, which is available to authorized users.

Heterologous and endogenous U6 snRNA promoters enable CRISPR/Cas9 mediated genome editing in Aspergillus niger