Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger.

Aspergillus niger / genetics Base Sequence Chromosome Mapping Genes, Mating Type, Fungal Genomics
ATCC 16888 Centromere Mating-type locus Mitochondrial DNA NRRL 326 Sexual development

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
21 Sep 2021
Historique:
received: 18 02 2021
accepted: 03 09 2021
entrez: 22 9 2021
pubmed: 23 9 2021
medline: 24 9 2021
Statut: epublish

Résumé

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. 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. The 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. This 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.

Sections du résumé

BACKGROUND BACKGROUND
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. 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.
RESULTS RESULTS
The 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.
CONCLUSIONS CONCLUSIONS
This 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.

Identifiants

DOI: 10.1186/s12864-021-07990-8 PMID: 34548025 PMC: PMC8454179
pubmed: 34548025
doi: 10.1186/s12864-021-07990-8
pii: 10.1186/s12864-021-07990-8
pmc: PMC8454179
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

679

Informations de copyright

© 2021. The Author(s).

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Auteurs

Valeria Ellena (V)

Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse, 18, Vienna, Austria.
Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße 1a BH, 1060, Vienna, Austria.

Sjoerd J Seekles (SJ)

TiFN, P.O. Box 557, 6700, AN, Wageningen, The Netherlands.
Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.

Gabriel A Vignolle (GA)

Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße 1a BH, 1060, Vienna, Austria.

Arthur F J Ram (AFJ)

TiFN, P.O. Box 557, 6700, AN, Wageningen, The Netherlands.
Leiden University, Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333, BE, Leiden, The Netherlands.

Matthias G Steiger (MG)

Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse, 18, Vienna, Austria. matthias.steiger@tuwien.ac.at.
Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Straße 1a BH, 1060, Vienna, Austria. matthias.steiger@tuwien.ac.at.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Champignons › Deuteromycota › Aspergillus › Aspergillus niger › Genome sequencing of the neotype strain CBS...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › Genome sequencing of the neotype strain CBS...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Cartographie chromosomique › Genome sequencing of the neotype strain CBS...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome fongique › Gènes fongiques › Gènes fongiques du type conjugant › Genome sequencing of the neotype strain CBS...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Genome sequencing of the neotype strain CBS...