Aspergillus niger genomics: a tale of two strains

Scott Baker1, Mikael Andersen2, Margarita Salazar2, Diego Martinez3, Igor Grigoriev4, Jane Grimwood5, Jens Nielsen2

Author address: 

1Pacific Northwest National Laboratory, Richland, WA, United States, 2Technical University of Denmark, Lyngby, Denmark, 3Joint Genome Institute/LANL, Los Alamos, NM, United States, 4Joint Genome Institute/PGF, Walnut Creek, CA, United States, 5Stanfo


Used as both an organic acid and protein production strain, Aspergillus niger is a scientifically and economically important filamentous ascomycete. High quality draft genomic sequences for two strains of Aspergillus niger have been released. Genomic sequence was generated by the US DOE Joint Genome Institute (JGI) for A. niger strain ATCC 1015, an organic acid producer. The approximate size of the A. niger strain ATCC 1015 genome is approximately 34.85Mb, approximately 0.9Mb more sequence compared to the currently released genome of A. niger strain CBS 513.88, a protein production strain. The A. niger strain ATCC 1015 genome is spread across 24 scaffolds, none of which contain gaps. One half of the telomeres were captured in the eight chromosome A. niger strain ATCC 1015 sequence. Aspergillus niger strains ATCC 1015 and CBS 513.88 were compared at both the genome and transcriptome levels. At the genomic level, there are major chromosomal rearrangements between the two strains, including a chromosomal translocation and two large inversions. Using the JGI gene models as the basis for comparison there are differences in codon usage. Furthermore, the level of single nucleotide polymorphisms is greater between A. niger strains CBS 513.88 and ATCC 1015 than between A. niger strains ATCC 9029 and ATCC 1015. At the level of the transcriptome comparing batch fermentations of A. niger strains ATCC 1015 and CBS 513.888, we observed significant differences amino acid biosynthetic pathways. In addition, while the level of glucoamylase gene expression was ~3-fold higher in A. niger strain CBS 513.88 compared to strain ATCC 1015, measured glucoamylase activity was ~6-fold higher. In summary, there are significant and intriguing differences at the genome and transcriptome level between the two A. niger strains.

abstract No: 


Full conference title: 

    • ECFG 9th (2008)