Abstract
BackgroundAspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus genomes to be sequenced in 2007, due to its economic importance and its role as model organism to study fungal fermentation. Nowadays, the genome sequences of more than 20 A. niger strains are available. These, however, do not include the neotype strain CBS 554.65.ResultsThe genome of CBS 554.65 was sequenced with PacBio. A high-quality nuclear genome sequence consisting of 17 contigs with a N50 value of 4.07 Mbp was obtained. The assembly covered all the 8 centromeric regions of the chromosomes. In addition, a complete circular mitochondrial DNA assembly was obtained. Bioinformatic analyses revealed the presence of a MAT1-2-1 gene in this genome, contrary to the most commonly used A. niger strains, such as ATCC 1015 and CBS 513.88, which contain a MAT1-1-1 gene. A nucleotide alignment showed a different orientation of the MAT1–1 locus of ATCC 1015 compared to the MAT1–2 locus of CBS 554.65, relative to conserved genes flanking the MAT locus. Within 24 newly sequenced isolates of A. niger half of them had a MAT1–1 locus and the other half a MAT1–2 locus. The genomic organization of the MAT1–2 locus in CBS 554.65 is similar to other Aspergillus species. In contrast, the region comprising the MAT1–1 locus is flipped in all sequenced strains of A. niger.ConclusionsThis study, besides providing a high-quality genome sequence of an important A. niger strain, suggests the occurrence of genetic flipping or switching events at the MAT1–1 locus of A. niger. These results provide new insights in the mating system of A. niger and could contribute to the investigation and potential discovery of sexuality in this species long thought to be asexual.
Highlights
Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes
The A. niger strain CBS 554.65 has not yet been sequenced it is the official neotype strain of this species [6]. This strain was isolated from a tannic-gallic acid fermentation in Connecticut (USA) and it is listed as thetype strain by international strain collections, such as the Westerdijk Institute (CBS 554.65), the American Type Culture Collection (ATCC 16888) and the ARS Culture Collection (NRRL 326)
Genetic comparison of MAT loci in different aspergilli and additional A. niger strains This study revealed a particular configuration for the MAT1–1 locus of strain ATCC 1015
Summary
Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. In 2007, the genome sequence of the enzyme-producing strain CBS 513.88 was published [4], followed by the sequencing of the citric acidproducing strain ATCC 1015 in 2011 [5]. The A. niger strain CBS 554.65 has not yet been sequenced it is the official neotype strain of this species [6]. This strain was isolated from a tannic-gallic acid fermentation in Connecticut (USA) and it is listed as the (neo-)type strain by international strain collections, such as the Westerdijk Institute (CBS 554.65), the American Type Culture Collection (ATCC 16888) and the ARS Culture Collection (NRRL 326). In 2016 the presence of a MAT1–2 locus in the genome of CBS 554.65 was mentioned in a study [12], making this strain an interesting candidate for investigating sexuality in A. niger
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