Aspergillus niger NRRL3

Aspergillus niger is extensively used for the industrial production of organic acids and extracellular enzymes. Two strains of A. niger have been sequenced previously: strain CBS 513.88, an industrial enzymes producer [1]; and strain ATCC 1015, the wild-type parent of the citric acid-producing strain ATCC 11414 [2]. In research laboratories, however, NRRL3 (ATCC 9029, CBS 120.49) and its descendants are the most widely used A. niger strains. Cees J. Bos of the University of Wageningen obtained CBS 120.49 from the Fungal Biodiversity Centre and renamed it N400 (FGSC A1143). A densely sporulating strain with short conidiophores, N402 (cspA1), was isolated following two rounds of low-dosed UV mutagenesis of about 75% survival each (personal communication, Fons Debets of the University of Wageningen). Strain N402 (ATCC 64974, FGSC A733) was used by Bos and his colleagues as a starting strain for genetic studies. Low doses of UV irradiation were used to generate morphological and nutritional mutants. These initial efforts have mapped over 80 markers to eight linkage groups [3, 4]. The Fungal Genetics Stock Center ( maintains over 300 genetically marked strains derived from N402. The FGSC strains were constructed by Bos and co-workers and by Etta Käfer of Simon Fraser University. Among these strains, N593 (ATCC 64973, FGSC EK31), which carries a mutation in the orotidine-5'-phosphate-decarboxylase (pyrG) gene, is often used for studies that involve genetic transformation. This is because pyrG can be used as a bidirectional dominant marker, either presence or absence of the marker can be selected [5].

The NRRL3 genome has been assembled to eight telomere-to-telomere chromosomes, with seven gaps corresponding to seven of the eight centromeres. Importantly, the gene models have been curated manually based on evidence from: de novo assembled transcripts, strand-specific RNA-seq coverage, distribution and orientation of predicted introns, peptide sequences determined by mass spectrometry, H3K4me3 ChIP-seq peaks, protein domains, and similarity to orthologues. This manually curated genome should provide a valuable reference for genetic manipulations and genome-wide studies of A. niger.

Financial support for this work came from Genome Canada and Génome Québec.



1.        Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K et al: Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature biotechnology 2007, 25(2):221-231. ( publication )

2.        Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K et al: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome research 2011, 21(6):885-897. ( publication )

3.        Bos CJ, Debets AJ, Swart K, Huybers A, Kobus G, Slakhorst SM: Genetic analysis and the construction of master strains for assignment of genes to six linkage groups in Aspergillus niger. Current genetics 1988, 14(5):437-443. ( PubMed )

4.        Debets F, Swart K, Hoekstra RF, Bos CJ: Genetic maps of eight linkage groups of Aspergillus niger based on mitotic mapping. Current genetics 1993, 23(1):47-53. ( PubMed )

5.        Goosen T, Bloemheuvel G, Christoph G, de Bie DA, Henk WJ, van den B, Klaas S: Transformation of Aspergillus niger using the homologous orotidine-5"-phosphate-decarboxylase gene Current genetics 1987, 11:499-503. ( PubMed )