Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
Journal article, 2011
The 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 wholegenome 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
Gene Rearrangement
Gene Transfer
Gene Expression Profiling
Base Sequence
Evolution
Molecular
Genome
Horizontal
Computational Biology
Genetic Variation
Author
M. R. Andersen
Technical University of Denmark (DTU)
Margarita Salazar Pena
Technical University of Denmark (DTU)
Chalmers, Chemical and Biological Engineering
P. J. Schaap
Wageningen University and Research
P. J. I. Van De Vondervoort
DSM Biotechnology Centre
D. Culley
Pacific Northwest National Laboratory
J. Thykaer
Technical University of Denmark (DTU)
J. C. Frisvad
Technical University of Denmark (DTU)
K. F. Nielsen
Technical University of Denmark (DTU)
R. Albang
Biomax Informatics AG
K. Albermann
Biomax Informatics AG
R. M. Berka
Novozymes, Inc.
G. H. Braus
University of Göttingen
S. A. Braus-Stromeyer
University of Göttingen
L. M. Corrochano
University of Seville
Z. Dai
Pacific Northwest National Laboratory
P. W. M. Van Dijck
DSM Nutritional Products Ltd
G. Hofmann
Novozymes A/S
L. L. Lasure
Pacific Northwest National Laboratory
J. K. Magnuson
Pacific Northwest National Laboratory
H. Menke
DSM Biotechnology Centre
M. Meijer
CBS Fungal Biodiversity Center CBS - KNAW
S. L. Meijer
Technical University of Denmark (DTU)
J. B. Nielsen
Technical University of Denmark (DTU)
M. L. Nielsen
Technical University of Denmark (DTU)
A. J. J. Van Ooyen
DSM Biotechnology Centre
H. J. Pel
DSM Biotechnology Centre
L. Poulsen
Technical University of Denmark (DTU)
R. A. Samson
CBS Fungal Biodiversity Center CBS - KNAW
H. Stam
DSM Biotechnology Centre
A. Tsang
Concordia University
J. M. Van Den Brink
Chr. Hansen
A. Atkins
DOE Joint Genome Institute
A. Aerts
DOE Joint Genome Institute
H. Shapiro
DOE Joint Genome Institute
J. Pangilinan
DOE Joint Genome Institute
A. Salamov
DOE Joint Genome Institute
Y. Lou
DOE Joint Genome Institute
E. Lindquist
DOE Joint Genome Institute
S. Lucas
DOE Joint Genome Institute
J. Grimwood
Stanford University
I. V. Grigoriev
DOE Joint Genome Institute
C. P. Kubicek
Vienna University of Technology
D. Martinez
Los Alamos National Laboratory
University of New Mexico
N. N. M. E. Van Peij
DSM Biotechnology Centre
J. A. Roubos
DSM Biotechnology Centre
Jens B Nielsen
Chalmers, Chemical and Biological Engineering, Life Sciences
S. E. Baker
Pacific Northwest National Laboratory
Genome Research
1088-9051 (ISSN) 1549-5469 (eISSN)
Vol. 21 6 885-897Driving Forces
Sustainable development
Areas of Advance
Energy
Life Science Engineering (2010-2018)
Subject Categories
Genetics
DOI
10.1101/gr.112169.110