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

Genetic Variation

Base Sequence

Horizontal

Gene Transfer

Molecular

Gene Expression Profiling

Genome

Evolution

Computational Biology

Gene Rearrangement

Author

M. R. Andersen

Technical University of Denmark (DTU)

Margarita Salazar Pena

Technical University of Denmark (DTU)

Chalmers

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 Biotech, 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, System Biology

S. E. Baker

Pacific Northwest National Laboratory

Genome Research

1088-9051 (ISSN) 1549-5469 (eISSN)

Vol. 21 6 885-897

Driving Forces

Sustainable development

Areas of Advance

Energy

Life Science Engineering

Subject Categories

Genetics

DOI

10.1101/gr.112169.110

More information

Latest update

9/10/2018