Journal article
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark1
CBS-KNAW Fungal Biodiversity Centre2
Concordia University3
Chr. Hansen AS4
United States Department of Energy5
Stanford University6
Vienna University of Technology7
Los Alamos National Laboratory8
Department of Systems Biology, Technical University of Denmark9
Wageningen University & Research10
DSM Food Specialties11
Pacific Northwest National Laboratory12
Biomax Informatics13
Novozymes A/S14
University of Göttingen15
University of Seville16
...and 6 moreThe filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration.
We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88.
Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb).
High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain.
Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.
Language: | English |
---|---|
Publisher: | Cold Spring Harbor Laboratory Press |
Year: | 2011 |
Pages: | 885-897 |
ISSN: | 10889051 and 15495469 |
Types: | Journal article |
DOI: | 10.1101/gr.112169.110 |
ORCIDs: | Andersen, Mikael Rørdam , Frisvad, Jens Christian , Nielsen, Kristian Fog and Nielsen, Jakob Blæsbjerg |
Aspergillus niger Base Sequence Computational Biology Evolution, Molecular Gene Expression Profiling Gene Rearrangement Gene Transfer, Horizontal Genetic Variation Genome, Fungal Genomics Molecular Sequence Data Phylogeny Polymorphism, Single Nucleotide Sequence Analysis, DNA Species Specificity Synteny