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Background  For  Aspergillus niger , a broad set of auxotrophic and dominant resistance markers is available. However, only few offer targeted modification of a gene of interest into or at a genomic locus of choice, which hampers functional genomics studies. We thus aimed to extend the available set by generating a histidine auxotrophic strain with a characterized  hisB  locus for targeted gene integration and deletion in  A. niger .    Results  A histidine-auxotrophic strain was established via disruption of the  A. niger hisB  gene by using the counterselectable  pyrG  marker. After curing, a  hisB    -    , pyrG    -   strain was obtained, which served as recipient strain for further studies. We show here that both  hisB  orthologs from  A. nidulans  and  A. niger  can be used to reestablish histidine prototrophy in this recipient strain. Whereas the  hisB  gene from  A. nidulans  was suitable for efficient gene targeting at different loci in  A. niger , the  hisB  gene from  A. niger  allowed efficient integration of a Tet-on driven luciferase reporter construct at the endogenous non-functional  hisB  locus. Subsequent analysis of the luciferase activity revealed that the  hisB  locus is tight under non-inducing conditions and allows even higher luciferase expression levels compared to the  pyrG  integration locus.    Conclusion  Taken together, we provide here an alternative selection marker for  A. niger ,  hisB , which allows efficient homologous integration rates as well as high expression levels which compare favorably to the well-established  pyrG  selection marker.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-017-0960-3) contains supplementary material, which is available to authorized users.

HisB as novel selection marker for gene targeting approaches in Aspergillus niger